现代小麦高臭氧敏感性与野生及栽培亲本的遗传相关性研究 比斯沃斯，许宏，李永庚，刘美珍.，陈艳红，孙家柱，蒋高明* *通讯作者 中国科学院植物研究所植被与环境变化国家重点实验室, 北京香山南辛村20号，100093。 实验植物学报，2008，59:951-963.（IF=5.345, SCI 引用79） 现代小麦（Triticum aestivum L.）是对臭氧（O3）最敏感的作物之一，但人们对其O3敏感性的遗传背景知之甚少。探讨不同品种小麦对O3浓度升高的响应，是选育O3抗性品种的基础工作。将冬小麦野生种和栽培种（包括A、B和D基因组的供体）暴露于100ppb O3或活性炭过滤空气中21d，通过可见O3伤害症状、气体交换、叶绿素荧光、相对生长速率和生物量积累来评估不同年度小麦对O3升高的响应。臭氧显著降低了净光合速率（-37%）和瞬时蒸腾速率（-42%），但增加了气孔导度（+11%）和胞间CO2浓度（+11%）。高O3降低了基础荧光（-8%）、最大荧光（-26%）、可变荧光（-31%）和最大光化学效率（-7%）。臭氧降低了相对生长速率和异速生长系数，最终降低了总生物量累积（-54%），但根（-77%）比茎（-44%）降低程度更大。冬小麦在高O3对光合作用和生长的影响上表现出明显的种间变异。原始栽培小麦对O3的相对耐受性最高，现代小麦次之，野生小麦最低。在现代小麦基因组供体中，节节麦（DD）对O3最敏感，其次是单粒小麦（AA）和硬粒小麦（Triticum turgidumssp）。硬粒小麦（AABB）似乎是最耐O3的。结果表明，现代小麦对O3的敏感性较高是由于节节麦（DD）对O3的敏感性增加所致，而不是来自硬粒小麦（Triticum turgidumssp）形成过程中的硬粒基因（AABB）。 Assessing the genetic relatedness of higher ozone sensitivity of modern wheat to its wild and cultivated progenitors/relatives Biswas D.K., Xu H, Li Y.G., Liu M.Z., Chen Y.H., Sun J.Z. Jiang G.M* *correspondence author State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The ChineseAcademy of Sciences, 20 Nanxincun, 100093 Beijing, PR China Journal of Experimental Botany, 2008, 59 : 951-963.（IF=5.345, SCI citation 79） Abstract Modern wheat (Triticum aestivumL.) is one of the most ozone (O3)-sensitive crops. However, little is known about its genetic background of O3sensitivity, which is fundamental for breeding O3-resistant cultivars. Wild and cultivated species of winter wheat including donors of the A, B and D genomes of T. aestivumwere exposed to 100 ppb O3or charcoal-filtered air in open top chambers for 21 d. Responses to O3were assessed by visible O3injury, gas exchange, chlorophyll fluorescence, relative growth rate, and biomass accumulation. Ozone significantly decreased light-saturated net photosynthetic rate (-37%) and instantaneous transpiration efficiency (-42%), but increased stomatal conductance (+11%) and intercellular CO2concentration (+11%). Elevated O3depressed ground fluorescence (-8%), maximum fluorescence (-26%), variable fluorescence (-31%), and maximum photochemical efficiency (-7%). Ozone also decreased relative growth rate and the allometric coefficient, which finally reduced total biomass accumulation (-54%), but to a greater extent in roots (-77%) than in the shoot (-44%). Winter wheat exhibited significant interspecies variation in the impacts of elevated O3on photosynthesis and growth. Primitive cultivated wheat demonstrated the highest relative O3tolerance followed by modern wheat and wild wheat showed the lowest. Among the genome donors of modern wheat, Aegilops tauschii(DD) behaved as the most O3-sensitive followed by T. monococcum(AA) and Triticum turgidumssp. durum(AABB) appeared to be the most O3-tolerant. It was concluded that the higher O3sensitivity of modern wheat was attributed to the increased O3sensitivity of Aegilops tauschii (DD), but not to Triticum turgidumssp.durum(AABB) during speciation.
臭氧对不同年代推广的冬小麦光合作用和生长的影响 毕斯沃斯 许宏 李永庚 马宝林 蒋高明* *通讯作者 中国科学院植物学研究所植被与环境变化国家重点实验室，中国北京香山南辛村20号，100093 实验植物学报 , 2013, 64(6): 1485-1496. （影响因子：5.345） 【摘要】 二氧化碳升高对植物光合的有益影响，将受到其它全球变化所带来的负面影响所抵消，不同O3敏感性植物对于臭氧（O3）的响应，尤其在高CO2环境下的调节还知之甚少。本文研究了老品种小麦（北京6号，耐臭氧型）和现代品种（中麦9号，O3敏感型）暴露于CO2（714ppm）和O3（72ppb，7h d-1）中，在开顶室同化箱( OTC)中培养21d后的光合生理与生长变化。通过观察叶片症状、测定气体交换和叶绿素a荧光、体内生化特性和生长来评估植株对不同处理的反应。结果表明，与老品种相比，现代品种对CO2浓度升高表现为较高的能量捕获和电子传输速率。与老品种相比，现代品种由于更高的O3吸收和更大的光系统II效率（成熟叶）和叶肉细胞活性（幼叶）损失，而导致更大的生长减少。在高CO2和O3条件下，尽管高CO2保护了两个品种免受O3危害，但现代品种比老品种表现出更高的O3吸收和更大的O3光抑制，从而导致高CO2诱导的生长刺激相对损失。该研究结果表明，在CO2和O3浓度升高前提下，由于较高的能量捕获和电子传输速率，现代品种CO2诱导的生长刺激可能会受到其较高的O3吸收和更大的光抑制而影响。 Modification of photosynthesis and growth responses to elevated CO2 by ozone in two cultivars of winter wheat with different years of release D.K. Biswas, H. Xu, Y.G. Li, B.L. Ma, G.M. Jiang* State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of Sciences, 20 Nanxincun, 100093 Beijing, PR China. Journal of Experimental Botany , 2013, 64(6): 1485-1496. （IF=5.345） Abstract: The beneficial effects of elevated CO2 on plants are expected to be compromised by the negative effects posed by other global changes. However, little is known about ozone (O3)-induced modulation of elevated CO2 response in plants with differential sensitivity to O3. An old (Triticum aestivumcv. Beijing 6, O3 tolerant) and a modern (T. aestivumcv. Zhongmai 9, O3 sensitive) winter wheat cultivar were exposed to elevated CO2 (714 ppm) and/or O3 (72 ppb, for 7h d(-1)) in open-topped chambers for 21 d. Plant responses to treatments were assessed by visible leaf symptoms, simultaneous measurements of gas exchange and chlorophyll a fluorescence, in vivo biochemical properties, and growth. It was found that elevated CO2 resulted in higher growth stimulation in the modern cultivar attributed to a higher energy capture and electron transport rate compared with the old cultivar. Exposure to O3 caused a greater growth reduction in the modern cultivar due to higher O3 uptake and a greater loss of photosystem II efficiency (mature leaf) and mesophyll cell activity (young leaf) than in the old cultivar. Elevated CO2 completely protected both cultivars against the deleterious effects of O3 under elevated CO2 and O3. The modern cultivar showed a greater relative loss of elevated CO2-induced growth stimulation due to higher O3 uptake and greater O3-induced photoinhibition than the old cultivar at elevated CO2 and O3. Our findings suggest that the elevated CO2-induced growth stimulation in the modern cultivar attributed to higher energy capture and electron transport rate can be compromised by its higher O3 uptake and greater O3-induced photoinhibition under elevated CO2 and O3 exposure.
不同耕作与施肥方式对有机玉米田杂草群落和作物产量的影响 博文静 , 郭立月 , 李静 , 韦继光 , 李彩虹 , 李勇 , 蒋高明 * (*通讯作者 ) 中国科学院植物植物研究所植被与环境变化国家重点实验室 山东农业大学农学院 植物学报 , 2012, 47(6): 637-644. 【摘要】 农田杂草是农业生态系统的重要组成部分。有机农田杂草控制是农业生产的一大难题 ,通过施肥方式改变杂草的竞争格局有望成为杂草控制的新途径。以暖温带有机玉米田为研究对象,设置了5种不同处理,即不施肥对照处理(CK)、施用牛粪处理(CM)、施用蚯蚓处理过的牛粪处理(EM)、免耕秸秆不覆盖处理(NT)和免耕秸秆覆盖处理(NS),研究不同耕作和施肥方式对田间杂草密度、生物量、生物多样性及作物产量的影响。结果表明,在有机玉米农田内共发现杂草17种,CK杂草总密度最高,但杂草总生物量和生物多样性指数较低。EM杂草总生物量和牛筋草(Eleusine indica)生物量最高,分别比CK增加了192.6%和224.8%(P0.01),物种丰富度和生物多样性指数较低,优势集中度指数较高。NS杂草总密度、总生物量和生物多样性与NT相比显著降低。此外,EM玉米(Zea mays)产量比CK高40.2%(P0.01),比CM高19.6%(P0.01)。施用蚯蚓处理过的牛粪不仅提高了玉米产量,而且可以促进优势种杂草的生长,提高杂草群落的优势集中度。 关键词 ： 生物多样性；生物量；优势种；施肥；杂草 Effects of different tillage and fertilization methods on weed community and crop yield in an organic corn field Bo Wenjing , Guo Liyue , Li Xiao , Wei Jiguang , Li Caihong , Li Yong , Jiang Gaoming* (*Correspondence author) State Key Laboratory of vegetation and environmental change, Institute of Botany, Chinese Academy of Sciences, No. 20, Nanxin cun , Xiangshan, Beijing 100093 Agricultural College of Shandong Agricultural University Chinese Bulletin of Botany, 2 012, 47(6): 637-644 Weeds are an important part of agricultural ecosystem. Weed control in organic farmland is a big problem in agricultural production. It is expected to be a new way to change the competition pattern of weeds by applying fertilizer. Five different treatments, CK, cm, EM, NT and NS , were used to study the effects of different tillage and fertilization methods on weed density, biomass, biodiversity and crop yield. The results showed that 17 kinds of weeds were found in organic corn field, and CK had the highest weed density, but the total weed biomass and biodiversity index were low. The total biomass of EM weeds and the biomass of Eleusine indica were the highest, increased by 192.6% and 224.8% respectively compared with CK (P 0.01), the species richness and biodiversity index were lower, and the dominant concentration index was higher. The total density, biomass and biodiversity of NS weeds were significantly lower than NT. In addition, the yield of EM maize ( Zea mays ) was 40.2% higher than CK (P 0.01), 19.6% higher than CM (P 0.01). The application of cow manure treated by earthworm not only increased the yield of corn, but also promoted the growth of dominant species of weeds and the dominant concentration of weed community. Key words: biodiversity; biomass; dominant species; fertilization; weeds
播娘蒿竞争下臭氧污染对冬小麦产量和品质的影响 李彩虹 孟杰 郭立月 蒋高明* *通讯作者 中国科学院植物研究所植被与环境变化国家重点实验室，北京香山南辛村20号 100093 中国科学院大学资源与环境学院，北京玉泉路19号，100049 环境与实验植物学报， 2016, 129: 77–84（影响因子：5.345） 主要发现： 小麦净光合速率受到高浓度O3和播娘蒿竞争的双重抑制；脯氨酸积累可增强对O3的耐受性；O3和播娘蒿竞争降低了冬小麦生物量和产量；O3改变了籽粒中粗蛋白和矿质元素含量；播娘蒿竞争加剧了O3对小麦生长抑制作用。 摘要： 由于人为活动影响大气中的臭氧（O3）浓度而不断增加，严重影响了冬小麦（Triticum aestivum）生长发育和籽粒品质。播娘蒿（Descurainia sophia）是麦田最为棘手的一年生双子叶杂草之一。作为一个强有力的竞争对手，小麦播娘蒿的存在是影响小麦产量的主要因素。在播娘蒿竞争的条件下，很少有人研究臭氧对小麦生长和产量的影响。本文报道了不同密度播娘蒿竞争条件下，小麦对O3胁迫的生理生态响应。研究发现，高浓度O3降低了叶绿素浓度和叶面积。高浓度O3和播娘蒿都抑制了小麦的气体交换。此外，由于在转录水平上吡咯啉-5-羧酸合成酶的上调，小麦在O3升高下表现为脯氨酸累积，表明脯氨酸可能赋予O3污染引起的一定的氧化应激耐受性。高浓度O3对小麦地上生物量、产量和收获指数都有显著的不利影响，而播娘蒿的存在加剧了这些影响。高浓度O3使小麦籽粒粗蛋白含量显著增加，矿质元素含量降低。我们的研究结果表明，在今后的育种和栽培中，应考虑臭氧污染下播娘蒿竞争对冬小麦的影响。 关键词： 冬小麦；播娘蒿；臭氧；种间竞争；产量；品质 Effects of ozone pollution on yield and quality of winter wheat under flixweed competition CaihongLi, Jie Meng, Liyue Guo, Gaoming Jiang* State Key Laboratory of vegetation and environmental change, Institute of Botany, Chinese Academy of Sciences, No. 20, Nanxin village, Xiangshan, Beijing 100093 School of Resources and Environment, Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049 Environmental and Experimental Botany , 2016, 129: 77–84（IF=5.345） Highlights： Net photosynthesis of wheat was suppressed by both elevated O3and competition；The accumulation of proline may enhance O3tolerance；O3and flixweed competition decreased biomass and yield of winter wheat；O3changed crude protein and mineral element concentrations in grains；Flixweed competition aggravated the negative effects of O3in some extent. Abstract： The concentration of ozone (O3) is believed to continually increase due to anthrogenic activity, which might affect severely the growth and grain quality of winter wheat (Triticum aestivum). Flixweed (Descurainia sophia) is one of the most troublesome annual dicot weeds in wheat fields. As a vigourous competitor, the presence of flixweed in wheat field is a major factor to reduce wheat production. However, few studies have investigated the effects of ozone on wheat growth and yield under competition with flixweed. In the present study, physiological and ecological responses of wheat to O3stress with different density of flixweed competition were reported. Chlorophyll concentration and leaf area were reduced by elevated O3. Gas exchange of wheat was suppressed by both elevated O3and the presence of flixweed. Moreover, exposure of wheat to elevated O3induced accumulation of Proline due to the up-regulation ofpyrroline-5-carboxylate synthetaseat transcriptional level, suggesting that Proline may confer tolerance to oxidative stress induced by O3pollution. Finally, elevated O3had significant adverse impacts on wheat above-ground biomass, grain yield and harvest index, and these impacts were intensified by the presence of flixweed. Exposure of wheat to elevated O3led to a significant increase in crude protein concentration of grain, while decreases in mineral element concentrations of grain were observed. Our findings indicate that effects of ozone and flixweed competition on winter wheat should be considered for the future breeding and cultivation. Keywords: Winter wheat；Flixweed；Ozone；Species competition；Yield；Grain quality
牛粪堆肥与化肥配施对中国东部小麦 - 玉米轮作系统有机质、容重和蚯蚓活动的影响 土壤与耕作学研究 , 156 (2): 140–147. ( 影响因子： 4.675) 郭立月 ab1 吴光磊 a1 李勇 c 李彩虹 a 刘文静 d 孟杰 a 刘海涛 a 虞晓凡 ab 蒋高明 * a （ * 通讯作者） 中国科学院植物研究所植被与环境变化国家重点实验室、中国环境科学院 摘要 将牛粪堆肥（ CMC ）与化肥（ CF ）配施于我国东部小麦 - 玉米轮作田，对土壤理化性质、生物活性和土地生产力进行了评价。对表层土壤（ 0-20cm ）有机质、碳储量和固碳量、容重、含水量、全氮含量和蚯蚓种群等指标进行了分析。该研究（ 2009-2014 年）是在相同的氮、磷、钾总量（ 375.0 kg N ha-1 yr-1 、 92.4 kg P2O5 ha-1 yr-1 和 316.3 kg K2O ha-1 yr-1 ）的基础上进行的。六个处理设计为：（ 1 ）对照，不施肥；（ 2 ） NPK ， 100%CF ；（ 3 ） NPKM1 ， 25%CMC+ 75%CF ；（ 4 ） NPKM2 ， 50%CMC+50%CF ；（ 5 ） NPKM3 ， 75%CMC+25%CF ；（ 6 ） CM ， 100%CMC 。结果表明，表层土壤有机质、含水量、全氮和蚯蚓密度与 CMC 显著正相关（ P0.01 ），土壤容重与 CMC 显著负相关。与对照相比，小麦 - 玉米轮作系统的 NPK 、 NPKM1 、 NPKM2 、 NPKM3 和 CM 年平均产量显著提高（ P ≤ 0.05 ），其中 NPKM1 产量最高。单施 CF 不仅降低了蚯蚓的 SOM 、水分和全氮含量，而且对蚯蚓活动产生了负面影响，而 CMC 则减轻了这种负面影响。该发现可能有助于在环境友好前提下，增加粮食供应，改善土壤条件与有机肥堆肥的应用。 关键词： 牛粪堆肥、化肥、土壤有机质、土壤容重、土壤含水量、蚯蚓活性 Effects of cattle manure compost combined with chemical fertilizer on topsoil organic matter, bulk density and earthworm activity in a wheat-maize rotation system in Eastern China LiyueGuo ab1 GuangleiWu a1 YongLi c CaihongLi a WenjingLiu d Jie Meng a HaitaoLiu a XiaofanYu ab Gaoming Jiang a Soil tillage research , 156 (2): 140–147. (IF=4.675) Abstract Cattle manure compost (CMC) combined with chemical fertilizer (CF) was applied to a wheat–maize rotation field, in Eastern China, to assess soil physical and chemical properties, biological activity and land productivity. Indicators of organic matter, carbon storage and sequestration, bulk density, water content, total N content and earthworm population from topsoil (0–20cm) were quantified. This consecutive study (2009–2014) was carried out on the base of the same total N, P, K application rate (375.0kg Nha − 1yr − 1, 92.4kg P2O5ha − 1yr − 1and 316.3kg K2Oha − 1yr − 1) in each treatment that was fertilized. Six treatments were designed as: (1) CK, without any fertilizer; (2) NPK, 100% CF; (3) NPKM1, 25% CMC combined with 75% CF; (4) NPKM2, 50% CMC combined with 50% CF; (5) NPKM3, 75% CMC combined with 25% CF; and (6) CM, 100% CMC. The results demonstrated that organic matter, water content, total N content and earthworm density from topsoil were significantly and positively (P≤0.01) related to CMC input, with significantly negative correlation being observed between soil bulk density and CMC input. The average annual yield of the wheat–maize rotation system significantly increased (P≤0.05) in NPK, NPKM1, NPKM2, NPKM3, and CM compared with CK, with the highest yield being obtained from NPKM1. Applying merely CF not only led to the lower SOM, water content and total N content, but also resulted in negative effects on earthworm activity, while CMC alleviated such negative effects. Our finding may help to increase food supply by improving soil conditions with organic fertilizer compost application. Keywords: Cattle manure compost, Chemical fertilizer, Soil organic matter, Soil bulk density, Soil water content, Earthworm activity
2017年以来小麦基因克隆文章 抗病 1. Fhb1 Mutation of a histidine-rich calcium-binding-protein gene in wheat confers resistance to Fusarium head blight 2. Pm21 Pm21 from Haynaldia villosa Encodes a CC-NBS-LRR that Confers Powdery Mildew Resistance in Wheat 3. Pm60 The NB‐\LRR gene Pm60 confers powdery mildew resistance in wheat 4. Rph1 The Coiled-Coil NLR Rph1 , Confers Leaf Rust Resistance in Barley Cultivar Sudan 5. Sr21 Identification and characterization of wheat stem rust resistance gene Sr21 effective against the Ug99 race group at high temperature 6. Sr13 Identification and characterization of Sr13 , a tetraploid wheat gene that confers resistance to the Ug99 stem rust race group 7. Sr22 ， SrTm5 Mapping and characterization of wheat stem rust resistance genes SrTm5 and Sr60 from Triticum monococcum 8. Yr5/YrSP 和 Yr7 BED-domain-containing immune receptors confer diverse resistance spectra to yellow rust 9. Yr15 Cloning of the wheat Yr15 resistance gene sheds light on the plant tandem kinase-pseudokinase family 10. Stb6 Wheat receptor-kinase-like protein Stb6 controls gene-for-gene resistance to fungal pathogen Zymoseptoria tritici 11. Sr33 、 Sr45 、 Sr46 和 SrTA1662 Resistance gene cloning from a wild crop relative by sequence capture and association genetics 12. Lr22a rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly 雄性不育 13. Ms2 Wheat Ms2 encodes for an orphan protein that confers male sterility in grass species 14. Ms1 Molecular identification of the wheat male fertility gene Ms1 and its prospects for hybrid breeding 15. ms5 Wheat ms5 male-sterility is induced by recessive homoeologous A and D genome non-specific Lipid Transfer Proteins 生长发育 16. TaSPL8 Wheat TaSPL8 Modulates Leaf Angle Through Auxin and Brassinosteroid Signaling 17. TtBtr1 Wild emmer genome architecture and diversity elucidate wheat evolution and domestication 18. WAPO1 Identifcation of a candidate gene for a QTL for spikelet number per spike on wheat chromosome arm 7AL by high‑resolution genetic mapping 19. B1 locus/AWNS1/ALI-1 ALI-1 , candidate gene of B1 locus, is associated with awn length and grain weight in common wheat 20. SSt1 Shifting the limits in wheat research and breeding using a fully annotated reference genome 21. TB1 TEOSINTE BRANCHED1 Regulates Inflorescence Architecture and Development in Bread Wheat ( Triticum aestivum ) 22. Rht12 A wheat dominant dwarfing line with Rht12 , which reduces stem cell length and affects gibberellic acid synthesis, is a 5AL terminal deletion line 23. GNI1 Unleashing floret fertility in wheat through the mutation of a homeobox gene 24. Rht23 Rht23 (5Dq’) likely encodes a Q homeologue with pleiotropic effects on plant height and spike compactness 25. TmBr1 Cloning of a COBL gene determining brittleness in diploid wheat using a MapRseq approach 其它 26. TdHMA3-B1 Durum wheat genome highlights past domestication signatures and future improvement targets 如果一篇文章中克隆多个基因则把他们放到一起。 另外有个别基因可能被多个文章报道，这里只列出来一篇。 一些基因虽然不是传统意义上的图位克隆方法而来，但至少是有精确的定位结果支持。而那些同源克隆的基因不在此列表中，包括产量相关基因。
Nature Genetics发表文章解析现代小麦的起源 5月1号Nature Genetics发表了两篇小麦的文章。前几天我们还念叨着一篇文章即将在NG发表( 厉害了|小麦大规模外显子测序 )，没成想在五一假期的第一天就上线了，而且还是双黄蛋，其中一篇“ Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome ”，我们已邀请一作贺飞给我们介绍这篇文章。今天我们要说的的是另外一篇文章“ Tracing the ancestry of modern bread wheats ”。 简介 利用外显子组测序技术从全世界范围内选出的大约500个小麦品种进行基因分型，来探索10000年的杂交、选择、适应和植物育种如何塑造了现代面包小麦的基因组成。 在基因、染色体和亚基因组水平上观察到大量的遗传变异，并利用这些信息来破译现代小麦的可能起源、迁移以及自驯化以来选择的等位基因变异。 我们的数据支持先前的小麦进化模型（reconciled model of wheat evolution），并为未来的育种改良提供了新的途径。 背景 面包小麦具有三个密切相关的亚基因组(AABBDD)组成的异源六倍体基因组。 它被认为起源于两次多倍化事件: 第一次是野生四倍体小麦(Triticum urartu Tumanian ex Gandilyan，AA)与未发现的节节麦(Aegilops speltoides Tausch)谱系(BB)杂交形成的四倍体，距今约50万年; 第二次是原始四倍体杂种(AABB)与野生二倍体节节麦(DD)杂交形成的六倍体，约10,000 年。 考古植物学的证据表明，由此产生的六倍体小麦是在从以色列、约旦、黎巴嫩、叙利亚到土耳其东南部、伊拉克伊朗的西部一个地区新月沃土被驯化的。 因此，现代栽培的面包小麦是至少一万年来人类在驯化和栽培(改良和繁殖)过程中选择的产物。 今天，它们包括适应各种环境的高产品种，从尼日利亚、澳大利亚、印度和埃及的低湿度地区到南美洲等高湿度地区。 结果 为了探索目前可获得的小麦基因库中存在的遗传多样性的起源和模式，我们构建了一个由分布在全世界范围内的487个小麦材料组成的群体，包括野生二倍体和四倍体近亲、驯化的四倍体和六倍体地方品种、古老品种和现代优良品种。 将这些品系的外显子组捕获序列数据映射到中国春参考基因组序列，发现了620,158个高可信度遗传变异，分布在41,032个小麦基因上。 该变异数据集提供了小麦基因组多样性在不同尺度(基因、区域、染色体和基因组)的全面综述，并代表了丰富的遗传信息来源，可供学术界和农业研究界利用。 系统发育和主成分分析(PCAs)揭示了三个主要因素驱动文中所使用小麦品系的多样性分区(图2) : 春化要求(冬季 vs 春季) ，历史群体(i 至 IV，最古老到最新: 从古老的地方品种到现代精英品系)和地理起源(欧洲，亚洲，大洋洲，非洲和美洲)(图2a )。 在基于大小、代表性和统计支持度选择的11个主要树支中，单系保护的排列检验证实了这三个因子的强大作用( P 1 × 10^˗6^)。 然而，系统发育的深层结构主要围绕大陆差异，随后由于现代小麦育种实践中对产量的强烈选择导致生长习性性状(如春化要求)的近期变化。 国家和大陆同时叠加在系统发育群上表明，所观察到的遗传多样性主要是沿着东西轴构成的，与人类迁出新月沃土的既定路线相一致。 两条通往西欧的道路沿着一条内陆路线(经过安纳托利亚和巴尔干到中欧)和一条沿海路线(经过埃及到马格里布和伊比利亚半岛) ，辅之以东北和内亚山走廊的另外两条路线，随后在美国、大洋洲和非洲领土上又发生了殖民活动(图2b )。 接下来探讨了驯化(比较野生小麦和驯化小麦)和育种(比较历史面包小麦类群 i 和 IV)所产生的选择足迹。 为了检测驯化信号，我们计算了来自亚洲的野生二倍体(T.urartu，A.speltoides，A.tauschii)、野生四倍体(T.diccoides)和驯化的六倍体(T.aestivum)小麦的每个位点的核苷酸多样性。 野生小麦祖先和六倍体地方品种之间的对比表明，在小麦的驯化过程中，基因组多样性(ROD)的减少具有很大的异质性(补充图6)。 受到强烈影响的基因组区域(1221) ，显示至少丧失了五分之四的多样性 ，覆盖了9% 的小麦基因组(1.2 Gb)。 已知的驯化基因如脆性穗轴(Brt)、韧性颖片(Tg)、同源配对(Ph)和非自由脱粒性状(Q)位于受到选择的区域内(小于 5Mb)。 有趣的是，已知的驯化基因只占受选择基因组区域的一小部分，这表明进一步的驯化基因仍有待发现。 为了揭示在过去两个世纪中(自1830年以来)小麦改良育种者所选择的基因组区域，我们比较了欧洲研究小组在历史群体 II、 III 和 IV (即那些受到育种影响的群体)与群体 I (地方品种)的多样性减少统计数据(图3a)。 我们的结果与两轮主要的多样性减少是一致的，第一波在第 I和第 II 组之间(11.7% 的多样性减少) ，反映了早期的育种改良。第二波在第 III 和第 IV 组之间(13.3% 的多样性减少) ，反映了绿色革命期间的育种实践(即从1950年到1960年代后期开始的农业实践的更新)。 现代小麦品种与I类相比，核苷酸多样性平均损失21.8% ，染色体内和染色体之间变异很大(图3 b)。 与 D 亚基因组(中位数 多样性减少 为5.8%)相比，A亚基因组(中位数多样性减少为33.2%)和B亚基因组(中位数多样性减少为28.0%)似乎更强烈，这可能反映了它们对小麦改良的不同贡献(图3a)。 为了确定小麦育种者选择的遗传标记和区域，我们对所有样本进行了全基因组扫描，以考虑群体内部和群体之间的渐进群体结构，并在欧洲和亚洲样本中分别以较高的粒度(granularity)进行扫描。 我们确定了5,089个多态位点显示改善信号( P 0.0001)。 已知基因包括光周期敏感基因(Ppd)和春化基因(VRN)、矮化基因(Rht)、谷蛋白(Glu)和醇溶蛋白(Gli)基因、卷曲圆锥花序基因(FZP)、粒数基因(GNS)、蜡质基因(Wx)以及驱动植物构型的 都与这些改良信号密切相关(在5 Mb之内)。 大的基因组区域(10 Mb) ，在过去的两个世纪中(在历史的第I和第IV之间)选择似乎已经发生，并最终变得固定，特别是在染色体1A 和两个结构重新排列的染色体4A 和7B 上观察到(图3b)。 将欧洲和亚洲基因型的8,308和9,948个与改良足迹相关的多态位点扩展到超过2 Mb 的重叠窗口，定义了一个950 Mb (基因组的7%)和1.3 Gb (基因组的9%)的基因组空间，这两个地理区域分别具有选择标记。 有趣的是，在欧洲和亚洲种质之间，只有168 Mb的基因组区域的选择特征是相同的。 通过多环境全基因组关联研究(GWAS) ，检验了观察到的等位变异是否与抽穗期和株高这两个关键的生活史性状相关。 我们的调查了四个环境（法国、匈牙利、土耳其和英国）中的435个六倍体小麦基因型的开花期和株高。 我们分别鉴定了48个和40个与开花期和 株高变异显著相关的基因组位点，其中包括已知控制开花期的基因(Ppd，VRN，FDL，WPCL）和影响株高的Rht基因等。 目前的数据可以为从目前未知的位点中识别相关候选基因以进行功能验证提供了基础，例如在2A染色体上检测到的主要开花期关联的位点，其中 Cry (隐花色素)基因是一个推定的驱动因子。 值得注意的是，多样性、选择足迹和 GWAS 分析清楚地表明，只有一小部分同源基因座含有重合信号，这支持了现代六倍体面包小麦具有二倍体遗传行为的观点，正如前面从平行优势选择中得出的结论，选择同时发生在同源基因区域之间很罕见。 最后，利用一个基于网络的系统发育方法重建现代六倍体小麦的网状进化历史。 聚集共识网络(图4a)包括垂直(物种关系)和水平(网状)事件的信号在小麦-山羊草物种复合体。 小麦进化的综合模型(图4b)是深入分析网络的边缘和边缘权重(图4a)之后得出的综合结论得出的，并通过评价替代共识树拓扑等得到支持。 图4b中的模型通过野生二倍体AA和SS(接近BB)杂交产生野生四倍体AABB杂交后代，并与野生二倍体DD基因型杂交产生六倍体AADDBB)，大大改进了现代面包小麦的进化路径。 我们的分析证实，小麦B基因组来源于山羊草属(Aegilops)系，该系产生了小麦 s. speltoides (SS) ，而 tauschii 和 T.urartu 的祖先分别代表了D和A基因组系的起源。 T. araraticum (也被称作 T. araraticum Jakubz) 代表了 AAGG 四倍体祖先最接近的野生后代。 它似乎随后被驯化形成 T. timopheevii (Zhuk.) 同时也与 T. boeoticum 杂交，形成 T. zhukovskyi (Menabde Ericzjan)谱系(AAAAGG)。 该模型证实了野生二粒小麦是所有现代四倍体AABB和六倍体AABBDD基因型的现代A和B小麦亚基因组祖先的最近的后代。 我们的数据表明，在驯化和栽培的早期阶段，野生二粒小麦池 T. dicoccoides (Körn. ex Asch. and Graebner) Schweinf 产生了至少两个不同的栽培四倍体谱系， T. dicoccum Schrank ex Schübl. (domesticated emmer, also known as T. dicoccon Schrank) and T. durum Desf. (domesticated durum or hard or pasta wheat)。 最后，该模型支持了这样的假设，即普通小麦最有可能来源于 T. durum 和接近 A. tauschii 的 D 基因组之间的一个祖先杂交事件(图4b)。 随后，在六倍体小麦与四倍体小麦杂交中发现了 T. spelta ，至今仍有 T. dicoccum 渐渗的证据。 其他推定的网状事件 ，少于3个证据支持，需要进一步研究，并没有纳入我们的进化模型(图4b)。 网状进化场景在驯化期间和之后首先建立了一个基本的六倍体面包小麦基因库α(图4a, α community)。 这可能包括起源于新月沃土的原始小麦地方品种，并衍生了两个六倍体群落β和γ(图4a)，γ集群主要包括来自西欧的现代基因型，即1986年或更晚的品系主要由小麦品种和当前品种组成，β集群主要包括在东欧国家的一些材料，即冷战期间属于华沙条约组织的国家。 这两个现代群体（β和γ）在进化史上的明显分离可能反映了人类历史和由此产生的社会经济后果如何影响了现代小麦种质的遗传构成，β基因型今天仍在匈牙利和乌克兰种植，而γ基因型在欧洲联盟的许多地区仍占主导地位。 讨论 面包小麦的进化来源于其二倍体和四倍体的祖先，包括大规模和反复的杂交和基因流动事件， T. durum 是当今面包小麦种质资源最可能的祖先。 这种复杂的杂交和基因流动解释了在基因组尺度上观察到的多样性分配(D亚基因组贫乏) ，并支持这样的观点，即现代六倍体小麦在遗传上和表型上表现为类似二倍体的特征，只有一小部分同源基因位点同时具有驯化、选择等信号。 现代面包小麦起源于约10,000年前的新月沃土，今天在小麦基因库中观察到的变异是在人类迁徙、人为选择和后来的育种驯化过程中形成的。 重要的是，在气候变化加速期间，适应新环境的标志仍然是备受关注的研究课题，我们的选择性扫描分析和 GWAS 都强调了未来基因和 / 或等位基因发现的目标。 我们在这里报告的数据和种质收集，以及我们提供给更广泛的研究团体的数据和种质收集，代表了遗传多样性的丰富来源，可以应用于理解和改善多样性，从环境适应到抗病性和营养物质利用效率。
厉害了|小麦大规模外显子测序 今天给大家简单介绍一个将要在nature genetic 发表的小麦外显子测序的文章（小道消息）。 某天胖丫，查看NCBI上更新的SRA数据，发现新增了不少小麦方面的数据，其中就有今天我们要介绍的这个项目。 根据上图提供的网站信息（http://wheatgenomics.plantpath.ksu.edu/1000EC/） 点开进入网站，发现该项目竟然对多达1000份小麦材料进行了外显子测序。 而且文章即将在NG发表。 如果只是这些消息，当然不值得和大家分享。更具有吸引力的是，数据已经提前释放。 没有一丝犹豫，我们就将数据下载下来了。 随后，也将数据放到我们网站上了（http://202.194.139.32/jbrowse-1.12.3-release/?data=Chinese_Spring）。 材料信息 赶紧查阅感兴趣的的基因吧。 目前，网站上收集了众多材料的分型数据，目测有1600份了吧。有这些信息，就可以了解你感兴趣的区段或基因在群体中的基因型，结合手头的群体就可以做些有趣的分析了。 参考文献： He F., Pasam R., Shi F., Kant S., Keeble-Gagnere G., Kay P., Forrest K., Fritz A., Hucl P., Wiebe K., Knox R., Cuthbert R., Pozniak C., Akhunova A., Morrell P.L., Davies J., Webb S., Spangenberg G., Hayes B., Daetwyler H., Tibbits J., Hayden M., Akhunov E., Exome sequencing highlights the role of wild relative introgression in shaping the adaptive landscape of the wheat genome. Nature Genetics (in press) 此消息，在十几天前就在我的朋友圈公布了。欢迎扫描下方二维码围观我的朋友圈，了解小麦研究相关的最新进展。
在 http://apps.webofknowledge.com 搜索的，关键词是 TI=((miRNA OR microRNA OR small RNA) AND (wheat OR Triticum))。 未做进一步的筛选，仅供参考。 看看这些文献，如果有时间还可以看看这些文献里引用的文献，或者在ncbi里查看哪些文献引用了某篇文献。 1 Development of species specific putative miRNA and its target prediction tool in wheat (Triticum aestivum L.) SCIENTIFIC REPORTS DOI:10.1038/s41598-019-40333-y Date :MAR 7 2019 2019 Author : Jaiswal, Sarika; Iquebal, M. A.; Arora, Vasu; Sheoran, Sonia; Sharma, Pradeep; Angadi, U. B.; Dahiya, Vikas; Singh, Rajender; Tiwari, Ratan; Singh, G. P.; Rai, Anil; Kumar, Dinesh 2 PROFILING OF 21 NOVEL MICRORNA CLUSTERS AND THEIR TARGETS IN AN IMPORTANT GRAIN: WHEAT (TRITICUM AESTIVUM L.) PAKISTAN JOURNAL OF BOTANY DOI:10.30848/PJB2019-1(35) Date :Feb-19 2019 Author : Achakzai, Habibullah Khan; Barozai, Muhammad Younas Khan; Achakzai, Abdul Kabir Khan; Asghar, Muhammad; Din, Mohammad 3 Discovery and profiling of small RNAs from Puccinia triticina by deep sequencing and identification of their potential targets in wheat. Functional integrative genomics DOI:10.1007/s10142-018-00652-1 Date :2019-Jan-07 2019 Author : Dubey, Himanshu; Kiran, Kanti; Jaswal, Rajdeep; Jain, Priyanka; Kayastha, Arvind M; Bhardwaj, Subhash C; Mondal, Tapan Kumar; Sharma, Tilak Raj 4 TaMIR1119, a miRNA family member of wheat (Triticum aestivum), is essential in the regulation of plant drought tolerance JOURNAL OF INTEGRATIVE AGRICULTURE DOI:10.1016/S2095-3119(17)61879-3 Date :Nov-18 2018 Author : Shi Gui-qing; Fu Jing-ying; Rong Ling-jie; Zhang Pei-yue; Guo Cheng-jin; Xiao Kai 5 Wheat miRNA member TaMIR2275 involves plant nitrogen starvation adaptation via enhancement of the N acquisition-associated process ACTA PHYSIOLOGIAE PLANTARUM DOI:10.1007/s11738-018-2758-9 Date :Oct-18 2018 Author : Qiao, Qinghai; Wang, Xiaoying; Yang, Mengya; Zhao, Yingjia; Gu, Juntao; Xiao, Kai 6 Small RNA and degradome sequencing used to elucidate the basis of tolerance to salinity and alkalinity in wheat BMC PLANT BIOLOGY DOI:10.1186/s12870-018-1415-1 Date :SEP 15 2018 2018 Author : Han, Huanan; Wang, Qi; Wei, Lin; Liang, Yu; Dai, Jiulan; Xia, Guangmin; Liu, Shuwei 7 Uncovering key small RNAs associated with gametocidal action in wheat JOURNAL OF EXPERIMENTAL BOTANY DOI:10.1093/jxb/ery175 Date :SEP 14 2018 2018 Author : Wang, Dan; Ling, Lei; Zhang, Wenrui; Bai, Yan; Shu, Yongjun; Guo, Changhong 8 TaMIR1139: a wheat miRNA responsive to Pi-starvation, acts a critical mediator in modulating plant tolerance to Pi deprivation PLANT CELL REPORTS DOI:10.1007/s00299-018-2313-6 Date :Sep-18 2018 Author : Liu, Zhipeng; Wang, Xiaoying; Chen, Xi; Shi, Guiqing; Bai, Qianqian; Xiao, Kai 9 Wheat miRNA TaemiR408 Acts as an Essential Mediator in Plant Tolerance to Pi Deprivation and Salt Stress via Modulating Stress-Associated Physiological Processes FRONTIERS IN PLANT SCIENCE DOI:10.3389/fpls.2018.00499 Date :APR 18 2018 2018 Author : Bai, Qianqian; Wang, Xiaoying; Chen, Xi; Shi, Guiqing; Liu, Zhipeng; Guo, Chengjin; Xiao, Kai 10 Asymmetrical changes of gene expression, small RNAs and chromatin in two resynthesized wheat allotetraploids PLANT JOURNAL DOI:10.1111/tpj.13805 Date :Mar-18 2018 Author : Jiao, Wu; Yuan, Jingya; Jiang, Shan; Liu, Yanfeng; Wang, Lili; Liu, Mingming; Zheng, Dewei; Ye, Wenxue; Wang, Xiue; Chen, Z. Jeffrey 11 Identification of conserved miRNA molecules in einkorn wheat (Triticum monococcum subsp. monococcum) by using small RNA sequencing analysis TURKISH JOURNAL OF BIOLOGY DOI:10.3906/biy-1802-3 Date :2018 2018 Author : Unlu, Ercan Selcuk; Bataw, Sara; Aslan Sen, Didem; Sahin, Yunus; Zencirci, Nusret 12 Discovery of small RNAs in wheat: a survey Indian Journal of Plant Physiology DOI:10.1007/s40502-017-0338-4 Date :Dec-17 2017 Author : Pandey, Ritu; Bhardwaj, Ankur R.; Agarwal, Manu; Katiyar-Agarwal, Surekha 13 miR430: the novel heat-responsive microRNA identified from miRNome analysis in wheat (Triticum aestivum L.) Indian Journal of Plant Physiology DOI:10.1007/s40502-017-0341-9 Date :Dec-17 2017 Author : Kumar, Mahesh; Kumar, Ranjeet R.; Goswami, Suneha; Verma, Pooja; Rai, Raj D.; Chinnusamy, Viswanathan; Praveen, Shelly 14 Identification and molecular characterization of a trans-acting small interfering RNA producing locus regulating leaf rust responsive gene expression in wheat (Triticum aestivum L.) PLANTA DOI:10.1007/s00425-017-2744-2 Date :Nov-17 2017 Author : Dutta, Summi; Kumar, Dhananjay; Jha, Shailendra; Prabhu, Kumble Vinod; Kumar, Manish; Mukhopadhyay, Kunal 15 Novel Insights into miRNA Regulation of Storage Protein Biosynthesis during Wheat Caryopsis Development under Drought Stress FRONTIERS IN PLANT SCIENCE DOI:10.3389/fpls.2017.01707 Date :OCT 4 2017 2017 Author : Chen, Xin-yu; Yang, Yang; Ran, Li-ping; Dong, Zhao-di; Zhang, Er-jin; Yu, Xu-run; Xiong, Fei 16 Assembly and Annotation of Transcriptome Provided Evidence of miRNA Mobility between Wheat and Wheat Stem Sawfly FRONTIERS IN PLANT SCIENCE DOI:10.3389/fpls.2017.01653 Date :SEP 26 2017 2017 Author : Cagirici, Halise B.; Biyiklioglu, Sezgi; Budak, Hikmet 17 The contrasting microRNA content of a drought tolerant and a drought susceptible wheat cultivar JOURNAL OF PLANT PHYSIOLOGY DOI:10.1016/j.jplph.2017.05.012 Date :Sep-17 2017 Author : Bakhshi, Behnam; Fard, Ehsan Mohseni; Gharechahi, Javad; Safarzadeh, Mahdieh; Nikpay, Nava; Fotovat, Reza; Azimi, Mohammad Reza; Salekdeh, Ghasem Hosseini 18 Uncovering Male Fertility Transition Responsive miRNA in a Wheat Photo-Thermosensitive Genic Male Sterile Line by Deep Sequencing and Degradome Analysis FRONTIERS IN PLANT SCIENCE DOI:10.3389/fpls.2017.01370 Date :AUG 8 2017 2017 Author : Bai, Jian-Fang; Wang, Yu-Kun; Wang, Peng; Duan, Wen-Jing; Yuan, Shao-Hua; Sun, Hui; Yuan, Guo-Liang; Ma, Jing-Xiu; Wang, Na; Zhang, Feng-Ting; Zhang, Li-Ping; Zhao, Chang-Ping 19 Puccinia striiformis f. sp tritici microRNA-like RNA 1 (Pst-milR1), an important pathogenicity factor of Pst, impairs wheat resistance to Pst by suppressing the wheat pathogenesis-related 2 gene NEW PHYTOLOGIST DOI:10.1111/nph.14577 Date :Jul-17 2017 Author : Wang, Bing; Sun, Yanfei; Song, Na; Zhao, Mengxin; Liu, Rui; Feng, Hao; Wang, Xiaojie; Kang, Zhensheng 20 Identification and Characterization of miRNA Transcriptome in Asiatic Cotton (Gossypium arboreum) Using High Throughput Sequencing FRONTIERS IN PLANT SCIENCE DOI:10.3389/fpls.2017.00969 Date :JUN 15 2017 2017 Author : Farooq, Muhammad; Mansoor, Shahid; Guo, Hui; Amin, Imran; Chee, Peng W.; Azim, M. Kamran; Paterson, Andrew H. 21 Isolation of Early-Responsive MicroRNA From Diuraphis noxia (Hemiptera: Aphididae)-Resistant Wheat JOURNAL OF ECONOMIC ENTOMOLOGY DOI:10.1093/jee/tox103 Date :Jun-17 2017 Author : Nicolis, Vittorio F.; Greyling, Sonia-Mari; Venter, Eduard 22 Wheat miRNA ancestors: evident by transcriptome analysis of A, B, and D genome donors FUNCTIONAL INTEGRATIVE GENOMICS DOI:10.1007/s10142-016-0487-y Date :May-17 2017 Author : Alptekin, Burcu; Budak, Hikmet 23 Long noncoding miRNA gene represses wheat beta-diketone waxes PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA DOI:10.1073/pnas.1617483114 Date :APR 11 2017 2017 Author : Huang, Daiqing; Feurtado, J. Allan; Smith, Mark A.; Flatman, Leah K.; Koh, Chushin; Cutler, Adrian J. 24 Virus-Based MicroRNA Silencing and Overexpressing in Common Wheat (Triticum aestivum L.) FRONTIERS IN PLANT SCIENCE DOI:10.3389/fpls.2017.00500 Date :APR 10 2017 2017 Author : Jian, Chao; Han, Ran; Chi, Qing; Wang, Shijuan; Ma, Meng; Liu, Xiangli; Zhao, Huixian 25 Genotypic water-deficit stress responses in durum wheat: association between physiological traits, microRNA regulatory modules and yield components FUNCTIONAL PLANT BIOLOGY DOI:10.1071/FP16294 Date :2017 2017 Author : Liu, Haipei; Able, Amanda J.; Able, Jason A. 26 A novel comprehensive wheat miRNA database, including related bioinformatics software Current Plant Biology DOI:10.1016/j.cpb.2016.10.003 Date :Nov-16 2016 Author : Remita, Mohamed Amine; Lord, Etienne; Agharbaoui, Zahra; Leclercq, Mickael; Badawi, Mohamed A.; Sarhan, Fathey; Diallo, Abdoulaye Banire 27 Wheat microRNA Member TaMIR444a Is Nitrogen Deprivation-Responsive and Involves Plant Adaptation to the Nitrogen-Starvation Stress PLANT MOLECULAR BIOLOGY REPORTER DOI:10.1007/s11105-016-0973-3 Date :Oct-16 2016 Author : Gao, Si; Guo, Chengjin; Zhang, Yongsheng; Zhang, Feifei; Du, Xiaoming; Gu, Juntao; Xiao, Kai 28 Identification and Comparative Analysis of microRNA in Wheat (Triticum aestivum L.) Callus Derived from Mature and Immature Embryos during In vitro Culture FRONTIERS IN PLANT SCIENCE DOI:10.3359/fpls.2016.01302 Date :AUG 30 2016 2016 Author : Chu, Zongli; Chen, Junying; Xu, Haixia; Dong, Zhongdong; Chen, Feng; Cui, Dangqun 29 miRNA-based drought regulation in wheat FUNCTIONAL INTEGRATIVE GENOMICS DOI:10.1007/s10142-015-0452-1 Date :May-16 2016 Author : Akdogan, Guray; Tufekci, Ebru Derelli; Uranbey, Serkan; Unver, Turgay 30 Analysis of wheat microspore embryogenesis induction by transcriptome and small RNA sequencing using the highly responsive cultivar Svilena BMC PLANT BIOLOGY DOI:10.1186/s12870-016-0782-8 Date :APR 21 2016 2016 Author : Seifert, Felix; Boessow, Sandra; Kumlehn, Jochen; Gnad, Heike; Scholten, Stefan 31 Polycistronic artificial miRNA-mediated resistance to Wheat dwarf virus in barley is highly efficient at low temperature MOLECULAR PLANT PATHOLOGY DOI:10.1111/mpp.12291 Date :Apr-16 2016 Author : Kis, Andras; Tholt, Gergely; Ivanics, Milan; Varallyay, Eva; Jenes, Barnabas; Havelda, Zoltan 32 Characterization of Small RNAs Derived from tRNAs, rRNAs and snoRNAs and Their Response to Heat Stress in Wheat Seedlings PLOS ONE DOI:10.1371/journal.pone.0150933 Date :MAR 10 2016 2016 Author : Wang, Yu; Li, Hongxia; Sun, Qixia; Yao, Yingyin 33 Meta-analysis of potential miRNA in Triticum astivum reveals their genome biased association with different metabolisms EST based potential miRNA identification in Wheat 2016 INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND SYSTEMS BIOLOGY (BSB) DOI: Date :2016 2016 Author : Nigam, Deepti; Kadimi, Puneet Kumar; Kumar, Sanjeev; Mishra, Dwijesh Chandra; Pandey, Pankaj; Singh, Manoj Kumar; Rai, Anil; Sinha, Subodh Kumar 34 Nitrate Starvation Induced Changes in Root System Architecture, Carbon:Nitrogen Metabolism, and miRNA Expression in Nitrogen-Responsive Wheat Genotypes APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY DOI:10.1007/s12010-015-1815-8 Date :Nov-15 2015 Author : Sinha, Subodh Kumar; Rani, Manju; Bansal, Niketa; Gayatri; Venkatesh, K.; Mandal, P. K. 35 Small RNA and Degradome Sequencing Reveal Complex Roles of miRNAs and Their Targets in Developing Wheat Grains PLOS ONE DOI:10.1371/journal.pone.0139658 Date :OCT 1 2015 2015 Author : Li, Tian; Ma, Lin; Geng, Yuke; Hao, Chenyang; Chen, Xinhong; Zhang, Xueyong 36 Small RNAs from the wheat stripe rust fungus (Puccinia striiformis f.sp tritici) BMC GENOMICS DOI:10.1186/s12864-015-1895-4 Date :SEP 21 2015 2015 Author : Mueth, Nicholas A.; Ramachandran, Sowmya R.; Hulbert, Scot H. 37 Combined Small RNA and Degradome Sequencing Reveals Novel MiRNAs and Their Targets in the High-Yield Mutant Wheat Strain Yunong 3114 PLOS ONE DOI:10.1371/journal.pone.0137773 Date :SEP 15 2015 2015 Author : Chen, Feng; Zhang, Xiangfen; Zhang, Ning; Wang, Shasha; Yin, Guihong; Dong, Zhongdong; Cui, Dangqun 38 Genome-wide analysis of small RNAs in the wheat pathogenic fungus Zymoseptoria tritici FUNGAL BIOLOGY DOI:10.1016/j.funbio.2015.03.008 Date :Jul-15 2015 Author : Yang, Fen 39 Barley Stripe Mosaic Virus (BSMV) Induced MicroRNA Silencing in Common Wheat (Triticum aestivum L.) PLOS ONE DOI:10.1371/journal.pone.0126621 Date :MAY 8 2015 2015 Author : Jiao, Jian; Wang, Yichun; Selvaraj, Jonathan Nimal; Xing, Fuguo; Liu, Yang 40 Identification of Novel miRNAs and miRNA Expression Profiling in Wheat Hybrid Necrosis PLOS ONE DOI:10.1371/journal.pone.0117507 Date :FEB 23 2015 2015 Author : Zhou, Jianping; Cheng, Yan; Yin, Meiqi; Yang, Ennian; Gong, Wenping; Liu, Cheng; Zheng, Xuelian; Deng, Kejun; Ren, Zhenglong; Zhang, Yong 41 Microarray-based identification of conserved microRNA from wheat and their expression profiles response to Puccinia striiformis f. sp tritici CANADIAN JOURNAL OF PLANT PATHOLOGY DOI:10.1080/07060661.2014.999124 Date :JAN 2 2015 2015 Author : Feng, Hao; Sun, Yanfei; Wang, Bing; Wang, Xiaojie; Kang, Zhensheng 42 Identifying functions of effectors and small RNAs involved in wheat-rust interactions PHYTOPATHOLOGY DOI:unknown Date :Dec-17 2017 Author : Ramachandran, S. R.; Yin, C.; Mueth, N. A.; Tanaka, K.; Hulbert, S. H. 43 Small RNA-mediated gene regulation of pathogen and host during wheat stripe rust infection PHYTOPATHOLOGY DOI:unknown Date :Dec-17 2017 Author : Mueth, N. A.; Hulbert, S. H. 44 Identification of conserved microRNA molecules in einkorn wheat (Triticum monococcum spp. monococcum) by deep sequencing analysis FEBS JOURNAL DOI:unknown Date :Sep-16 2016 Author : Unlue, E. S.; Bataw, S.; Kaya, O.; Zencirci, N. 45 Resistance gene regulation by microRNA in Diuraphis noxia infested wheat SOUTH AFRICAN JOURNAL OF BOTANY DOI:10.1016/j.sajb.2016.02.187 Date :Mar-16 2016 Author : Venter, E.; Nicolis, V. F.
salmon软件于2017年发表在Nature Methods，论文题目是“ Salmon provides fast and bias-aware quantification of transcript expression ” 。不到两年的时间被引250多次。 根据文中的描述，salmon要优于kallisto和express软件。 今天我们结合小麦最新的IWGSCv1.1版本的基因集，介绍下其定量流程，与kallisto进行一个定量结果的比较，以及看一看基因拷贝数变化时TPM如何变化。 首选要对转录本进行index salmon index --keepDuplicates -t IWGSC_v1.1_HC_LC_20170706_transcripts.fasta -i IWGSC_v1.1_HC_LC 下载测试数据,该测试数据来自中国春的叶片。 axel -a -n 12 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR947/SRR947005/SRR947005_1.fastq.gz axel -a -n 12 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR947/SRR947005/SRR947005_2.fastq.gz 进行定量 salmon quant -i IWGSC_v1.1_HC_LC -l A -1 SRR947005_1.fastq.gz -2 SRR947005_2.fastq.gz -p 8 -o SRR947005_quant -i 指要使用的转录组index 这里是我们第一步生成的IWGSCv1.1版本的转录组index； -l 这里需要指定测序模式，这里-A是指自动判定。 -1 -2 分别要输入左端测序数据和右端测序数据 -p 则是要指定运行程序的cpu线程数 上述定量命令使用测序的原始reads进行的，这里还有另外一种基于比对的方式，即输入文件是BAM或SAM文件。 输出的结果文件如下所示，其中quant.sf里有每个基因的表达量。 salmon定量输出文件 kallisto定量过程 首先也是要对转录组进行index kallisto index -i IWGSC_v1.1_HC_LC_kallisto IWGSC_v1.1_HC_LC_20170706_transcripts.fasta 其次是定量过程。 kallisto quant -i IWGSC_v1.1_HC_LC_kallisto -t 10 -o SRR947005_kallisto SRR947005_1.fastq.gz SRR947005_2.fastq.gz 同样的结果文件如下图所示，其中abundance.tsv里有每个基因的表达量。 kallisto定量结果输出文件 salmon文章比较的内容，这里不再比较。下面我们做一个比较初步的分析。 首先看TPM大于0, 0.5, 1, 10的基因数目。注意两者转录本的总数是一致的。 TPM 0 0.5 1 10 Salmon 109998 58690 43160 7172 kallisto 116087 60805 44721 7443 kallisto-Salmon 6089 2115 1561 271 从基因数量上来看，kallisto有更多的基因有TPM值，而且相同转录本获得的TPM值，kallisto获得的往往要大于salmon获得的。但这也不是绝对的，如下图。以转录本TraesCS3B02G080100.1为例，这里使用salmon获得的TPM值是338.82，而使用kallisto获得的是168.69。那么针对这一个基因，哪个更准确一点呢？ image-20180902220909122 而查阅信息可知，主要是两者的 effecting length 不同导致，而count数量很相似。 Name Length EffectiveLength TPM(salmon) NumReads target_id length eff_length est_counts tpm(kallisto) TraesCS3B02G080100.1 171 35.605 338.816942 531.769 TraesCS3B02G080100.1 171 78.4896 532.115 168.686 This is the computed effective length of the target transcript. It takes into account all factors being modeled that will effect the probability of sampling fragments from this transcript, including the fragment length distribution and sequence-specific and gc-fragment bias (if they are being modeled). 而kallisto里的定义为： “Effective length” is a scaling of transcript length by the fragment length distribution 具体的可参见“https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/”。 查过一些资料，越看越糊涂。不过，如果使用同一软件处理所有的数据应该是没有问题的。 因为IWGSC官方也有这个数据集的count和TPM值，我去查可一下，竟然和我的不一样。 transcript COUNT \0 COUNT TPM TraesCS3B02G080100.1 294.42 96.0559 而我这边给的count是532.115，tpm是168.686。事情变得复杂起来。我细想了原因，可能有两方面的原因。其一，我们使用的软件版本不同，其二我们使用的数据SRR947005，他们可能经过一些预处理。而我直接下下来使用，没有经过预处理。 关于软件版本，他们用的是0.42.3，而我用的是kallisto 0.44.0 。所以，接下来我们就要排除软件版本的差异。 To calculate the read counts and TPMs we used Kallisto version 0.42.3 . The index was built with the default values and K=31. Kallisto was run with the default parameters. All the fastq files from a single sample are run together. The reference used was RefSeqv1.1, including the High and Low quality genes (IWGSC_v1.1_ALL_20170706_transcripts.fasta) 结果有点让我接受不了。即如果我使用0.42.3版本，得到的count和TPM就和IWGSC上下载的一样了。但显然与我0.44.0的版本不一致。所以中间出现了什么变故？ kallisto target_id length eff_length est_counts tpm(kallisto) 0.44.0 TraesCS3B02G080100.1 171 78.4896 532.115 168.686 0.42.3 TraesCS3B02G080100.1 171 79.8953 294.42 96.0563 有什么变故我们不得而知，但显然让我有点接受不了，我的结果里有多少这样任性的基因？做出来的差异基因有多少又是可信的？下面是作者的回答。软件作者建议使用最新版本。 image-20180903155107203 作者都这样说了，加上最新版本的count也与salmon一致，所以，这让本打算使用850 RNA-seq 样本做些分析的我有点迟疑。 第二部分，探究基因拷贝数对定量结果的影响 尽管最近science上转录组那篇文章也有相似的讨论，不过我还是想眼见为实。这个测试也非常简单，那就是人为增加某个基因的拷贝数，观察对这个基因本身的影响以及另外另个同源基因的影响。这里选取TraesCS3D02G074400.1 ，TraesCS3B02G080100.1 和TraesCS1D02G227700.1 。TraesCS3D02G074400.1是孤家寡人。而TraesCS3B02G080100.1则有多个同源基因，TraesCS3B02G080700.1， TraesCS3D02G067400.1, TraesCS3A02G067400.1, TraesCS3B02G080600.1, TraesCS3D02G067100.1, TraesCS7B02G443100.1, TraesCS3D02G067200.1, TraesCS3D02G219800.1, TraesCS3A02G233600.1 ；而TraesCS1D02G227700.1对应的有TraesCS1B02G240400.1，TraesCS1A02G226300.1,同时该基因还有可变剪切，TraesCS1D02G227700.2，TraesCS1B02G240400.2，TraesCS1A02G226300.2。 所以我们比较的重点就放在这几个基因上，看这几个基因的变化。 kallisto index -i IWGSC_v1 .1_HC_LC_kallisto_add IWGSC_v1 .1_HC_LC_add.fasta kallisto quant -i IWGSC_v1 .1_HC_LC_kallisto_add -t 10 -o SRR947005_kallisto_add SRR947005_1 .fastq.gz SRR947005_2 .fastq.gz 首先对这三个基因来说，其表达量减半。因为我们在序列上一字未改的复制了这3个序列。所以从结果看，复制的基因分享了一半的reads。 target_id length eff_length est_counts tpm(kallisto) add|TraesCS3B02G080100.1 171 79.2217 266.054 83.6109 TraesCS3B02G080100.1 171 79.2217 266.054 83.6109 add|TraesCS3D02G074400.1 752 561.072 4175.4 185.275 TraesCS3D02G074400.1 752 561.072 4175.4 185.275 add|TraesCS1D02G227700.1 1867 1675.73 284.687 4.22962 TraesCS1D02G227700.1 1867 1675.73 284.687 4.22962 同样的我们再比较多拷贝的情况。多拷贝的我们看这个基因TraesCS3B02G080100。复制之后，TraesCS3B02G080100的表达减半，其他拷贝几乎不变。 那么是否对可变剪切的转录本有影响呢？结果和上面一样，只是TraesCS1D02G227700.1自身TPM值减半。 既然拷贝数增加，只改变其自身的TPM值。那么同样的道理，如果减少一个拷贝数，其他拷贝数的TPM也不会发生显著变化。当然这里是有一个前提，那就是不同拷贝之间序列不是100%一致的。 刚才的复制我们一字未改，现在我们改变其中一个碱基，我们再观察结果如何。统一在这3个转录本序列的第80位改变一个碱基。理论上，改变之后这3个转录本的TPM值为0。 Kallisto的结果如下 target_id length eff_length est_counts tpm(kallisto) 1snp|TraesCS3D02G074400.1 752 561.072 0 0 1snp|TraesCS3B02G080100.1 171 79.2217 0 0 1snp|TraesCS1D02G227700.1 1867 1675.73 0.698188 0.010373 TraesCS1D02G227700.1 1867 1675.73 568.676 8.44886 TraesCS3B02G080100.1 171 79.2217 532.107 167.222 TraesCS3D02G074400.1 752 561.072 8350.8 370.551 如上表所示，实际情况也差不多如此，只有1snp|TraesCS1D02G227700.1有很小的TPM。 在改一个SNP的情况下，salmon表现似乎更好，修改的全部是0，而原来的TPM值也不变。 Name Length EffectiveLength TPM NumReads 1snp|TraesCS3D02G074400.1 752 550.209 0 0 1snp|TraesCS3B02G080100.1 171 35.447 0 0 1snp|TraesCS1D02G227700.1 1867 1665.119 0 0 TraesCS1D02G227700.1 1867 1665.119 7.729668 567.493 TraesCS3B02G080100.1 171 35.447 340.231283 531.757 TraesCS3D02G074400.1 752 550.209 343.102088 8323.484 所以总结来说，在同一个项目中，使用的软件版本要一致。至于哪一个salmon和kallisto哪个更好，我个人可能更偏向salmon，但kallisto毕竟是science使用的，所以做小麦的话，kallisto应该是公认的。kallisto算出来的差异基因数量要多于salmon。 但同时也要注意IWGSC注释的转录本的正确率。特别是对于低可信度的基因，基因结构不正确，做出来的TPM可能也不对。而且IWGSC注释的转录本其3’和5’的非翻译区有不少缺失。转录组里还可以组装出新的转录本或者新的可变剪切。 目前IWGSC给出的转录本是26万左右，而其中高可信的基因只有10万。我们进行差异表达分析时使用的是26个转录本，但只有那10万个高可信基因的功能注释较为可信。所以后续的功能富集分析，就要慎重。差异表达可以包括低可信的基因，但功能富集分析时可以不包括在里面，特别是不能用来充当总数，science上的那篇文章也正是这样做的。另外，功能富集分析时使用的背景基因应该是在某条件下表达的基因集，而不是总基因集。比如，总共有10个基因，其中只有5个基因表达，而这5个表达的基因里有2个差异表达，此时使用的总数是5而不是10。当然，如果差异基因里包括低可信的基因，那表达的总基因里也可以包括低可信度的基因。不过，我还是建议使用表达的高可信度的基因作为整体。 昨天我在推送里表达了在基因富集分析中背景基因如何选择的观点？我的观点是需要使用表达的基因，确切的说是使用表达的并且有功能注释的基因作为背景。比如，做GO分析，背景基因都得有GO注释信息，那些没有GO注释信息的显然不宜拿来当作背景。同样的拿来做GO分析的差异表达基因也得都GO注释信息，那些差异表达但没有GO注释信息的基因就不必包括在里边。为啥？道理很简单，我要做的是GO信息的富集分析，那些没有GO注释信息的基因即使放在里边也没毛用。 这是我的观点，也许不对。如果有大神跳出来吊打，我还是欢迎的。群里也有小伙伴发表自己的看法，看过之后很受启发。接下来，且听我细细道来。 这里所说的表达的基因，是指只要在分析所用样本中的一个里有表达（如TPM0.5就认为表达），比如在叶片和根里，只要基因在这两个组织中的任何一个里表达，我们就认为基因是表达的。即取的是不同样本间的并集。这里只是拿叶片和根说事，如果在文章里有人这样做，你可以将这篇文章扔到垃圾桶了。 同时我在google上也查了一些资料。在biostars（https://www.biostars.org/p/17628/）也有很多人在讨论。 基本的结论是，使用表达的基因作为背景是合适的，没有人明确反对这一做法不妥。 根据上面的回答，找到这篇文献“Multiple sources of bias confound functional enrichment analysis of global -omics data”。该文2015年发表在genome biology上。 文中的结论是： The generation of an estimated background ‘universe’ in RNA-seq data could be achieved by removing zero-count genes , but the nature of this ‘universe’ will still depend on many factors. This list should contain only factors (RNA or protein) that are both robustly ‘probed or sequenced’ (to avoid technology and detection bias) and ‘called’ as expressed (to avoid biological bias) in the experiment. After all, we do not want to carry out functional enrichment analysis of a specific tissue simply to be informed that we are studying that tissue! In conclusion, functional enrichment analysis must not be considered proof of biological plausibility or validity in the analysis of high-throughput -omics data. We strongly advocate for efforts to generate appropriate background expression ‘universes’. We also urge that background gene lists are provided for any functional enrichment analysis, and that a higher statistical threshold is used as a default, given the scale of the pre-existing biases, to avoid marginal (e.g., 1 × 10^−3^ or 1 × ^10−4^) enrichments being relied on to drive the interpretation of an experiment. 做差异基因功能富集分析的一定要看看本文。里边讨论了各种有可能导致最终结果不准确的情况。 一些在线进行GO富集分析的网站，如果不能自己背景序列，那就是耍流氓。 However, somewhat surprisingly, the Gene Ontology consortium website analysis tool does not allow for this option, making any analysis thoroughly unreliable. 实际上任何实验手段都不是完美的。我们现在做RNA-seq比较方便，RNA-seq并不是万能呢，蛋白水平就要比转录水平要好。还有组织毕竟是混杂，那单细胞结果又如何呢？代谢组呢？ 通过差异表达基因功能富集结果我们可以说参与了某些通路，或者在哪些通路上富集。但最好不要说与哪些通路无关，但可以说这些通路上的基因没有富集。
小麦抗白粉病基因定位研究进展 客观地讲，小麦白粉病远比赤霉病防控起来要容易的多。小麦对白粉病的抗性分为两种：水平抗性（即广谱抗性，或者成株抗性）和垂直抗性（粗略地讲，一个白粉病生理小种对应一个抗性基因），前者是数量性状基因控制着的，后者是由单显性基因控制的。我们对发表于2015年10月以前的关于小麦抗白粉病基因定位的文章进行了总结，共发现了至少102个主效抗白粉病基因或等位基因，这些基因中有54个基因被命名（ Pm1-Pm54 ），其中7个基因含有多个等位基因，即 Pm1 (Pm1a-1e), Pm2 (Pm2a-2c), Pm3 (Pm3a-3j), Pm4 (Pm4a-4d), Pm5 (Pm5a-5e), Pm8 (Pm8 and Pm17) 和 Pm24 (Pm24a-24b) ，分别位于7A、5D、1A、4A、7B、1R和1D。根据紧密连锁分子标记的物理定位信息，对上述102个抗病基因或等位基因进行物理定位分析，确定了57个基因或等位基因在小麦染色体上的大致物理位置，这一信息对于聚合不同抗病基因创制多基因聚合的小麦新种质具有重要参考价值。另外，对成株型抗病基因定位结果进行总结，共报道了140个抗白粉病QTL，分布于小麦21条染色体上，其中4个QTL已被证实且已在部分地区或单位广泛应用，即 Pm38/Lr34/Yr18/Sr57 （7DS）, Pm46/Lr67/Yr46/Sr55 （4DL）, Pm?/Lr27/Yr30/Sr2 （3BS）和 Pm39/Lr46/Yr29 （1BL），为兼抗性小麦新品种选育提供了理论依据。 以上是我们总结的小麦抗白粉病基因定位研究进展，全文详见如下链接： https: / /www.researchgate.net/profile/Jun_Guo53/publication/318814778_Molecular_and_physical_mapping_of_Pm_resistance_genes-A_review/links/598015240f7e9b8802ed2e53/ Molecular- and -physical-mapping-of-Pm-resistance-genes-A-review.pdf 目前已经定位了这么多的抗病基因或QTL，究竟有多少真正能够应用到育种工作中？Bernardo这样总结道“While scientists have certainly learned how to map QTL routinely in crops, the ability to utilize the favorable alleles in breeding is not fully developed.”无论是新基因挖掘还是新种质创新，农业科研工作都是为新品种培育服务。 image-20180711174139499 Fig. 2 img 上面命名的基因只到PM54，下面补上PM55,PM56,PM57,PM58,PM59,PM60。PM61是今天的第一条推送。 PM60以前我们推送过， 生命的机制是多样的-由Pm60克隆想到的 。 PM59, Characterization of Pm59, a novel powdery mildew resistance gene in Afghanistan wheat landrace PI 181356 (https://doi.org/10.1007/s00122-018-3067-9) image-20180711170241276 PM58, Identification of Pm58 from Aegilops tauschii (https://doi.org/10.1007/s00122-017-2874-8) image-20180711170550956 PM57,Homoeologous recombination-based transfer and molecular cytogenetic mapping of powdery mildew-resistant gene Pm57 from Aegilops searsii into wheat.（https://doi.org/10.1007/s00122-017-2855-y） image-20180711170713571 PM56, Introgression of powdery mildew resistance gene Pm56 on rye chromosome arm 6RS into wheat(https://www.frontiersin.org/articles/10.3389/fpls.2018.01040/abstract) image-20180711171341726 Powdery mildew, caused by the fungus Blumeria graminis f. sp. tritici, represents a yield constraint in many parts of the world. Here, the introduction of a resistance gene carried by the cereal rye cv. Qinling chromosome 6R was transferred into wheat in the form of spontaneous balanced translocation induced in plants doubly monosomic for chromosomes 6R and 6A. The translocation, along with other structural variants, was detected using in situ hybridization and genetic markers. The differential disease response of plants harboring various fragments of 6R indicated that a powdery mildew resistance gene(s) was present on both arms of rye chromosome 6R. Based on karyotying, the short arm gene, designated Pm56, was mapped to the subtelomere region of the arm. The Robertsonian translocation 6AL•6RS can be exploited by wheat breeders as a novel resistance resource. Pm55, a developmental-stage and tissue-specific powdery mildew resistance gene introgressed from Dasypyrum villosum into common wheat. image-20180711172037086 已经克隆的白粉病抗病基因有PM2, PM3b,PM8, PM21，PM60.如果有遗漏还请留言补充。 下面是3篇2017年的毕业论文，供参考，可以在知网上下载。 1 杨立军 武汉大学 博士 《小麦品种抗白粉病和条锈病性评价及其抗性QTL定位》 2 徐晓丹 中国农业大学 博士 《5份小麦农家品种的抗白粉病基因分析及定位》 3 赵鹏宇 西北农林科技大学 硕士《两个小麦新种质抗白粉病基因的遗传分析和染色体定位》 最后，最重要的是随手再送给大家一个链接（https://shigen.nig.ac.jp/wheat/komugi/genes/symbolClassList.jsp）。 应该有不少人知道，但是应该还有更多人不知道。 参考文献 Guo, J., Zhao, Z., Song, J., Liu, C., Zhai, S., Li, H., et al. 2017. Molecular and physical mapping of powdery mildew resistance genes and QTLs in wheat: A Review. Agricultural Science Technology: 18(6), 965-970. Bernardo, R. 2008. Molecular markers and selection for complex traits in plants: Learning from the last 20 years. Crop Sci. 48:1649-1664. \0 \0
作者：麦夕 自上次推送抗条锈基因的克隆后，见链接。不知做抗病的小伙伴对BED-NLR的整合结构还有印象没？小编当时说要好好介绍一下目前植物抗病基因方面的研究进展。闲话少说，先抛出几篇曾较新看到的文章：分别题为 Defended to the Nines: 25 Years of Resistance Gene Cloning Identifies Nine Mechanisms for R Protein Function 、 What Do We Know About NOD-Like Receptors in Plant Immunity? 、 Molecular genetics and evolution of disease resistance in cereals 和 Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions 。当然由于能力有限，可能还有其他较好的综述类文章，欢迎大家在留言区里推荐，我们一起共同学习。今天先讲一讲发表在 The Plant Cell 上的文章“ Defended to the Nines: 25 Years of Resistance Gene Cloning Identifies Nine Mechanisms for R Protein Function ”《不断完善的防卫：25年来抗病基因的克隆及其九种抗病机制的发现》。作者之一是国际国际著名分子植物病理学家、英国牛津大学教授Renier van der Hoorn。感兴趣的伙伴可以搜索一下他的文章，几乎每月都有进展，他们还有实验室主页 http://www.plantchemetics.org/index.php 。 自1992年第一个抗病基因-玉米的抗圆斑病（ Helminthosporium carbonum ）开始，截止2017年相继有314个抗病R基因被鉴定出来。见图1A。当然，这个数目是随时增长的。在这314个R基因中，有128个基因给出了可能的抗病机制。本文作者根据这些结果总结出当前存在九种抗病机制。见1B。说到抗病机制，就要提到经典的PTI（病原相关分子模式引起的免疫反应，基础防卫反应）和ETI（效应子激发的免疫反应）模型，这两种的主要区别是后者引发过敏性坏死反应（HR）。 图1A 但对于本文的分类，作者没有采取上面的依据，而是根据胞外和胞内两种对病原菌识别的机制划分，见图1B。因此，这九种抗病机制大体可分为：I）感知/响应和 II)丧失感病性。 对于感知/响应又可大致分为三种亚类型 ： Ia） 类受体蛋白/激酶 (receptor-like proteins/kinases, RLPs/RLKs); Ib） 类腺苷酸识别位点受体(Nod-likereceptors, NLRs); Ic） 执行基因 (Executor genes)。对于前两种，RLPs/RLKs可直接/间接识别PAMPs ( ① 和 ② ), NLRs又分为直接/间接识别（ ③ 和 ④ ）以及整合的功能域（ ⑤ integrated domains, IDs)。另外 ⑥ 通过识别转录激活蛋白 (transcription activator-like, TAL)能够引发下游防卫执行基因的表达。 对于丧失感病性也可大致分为三种亚类型 ： ⑦ 主动丧失感病性（active loss of susceptibility）即通过加强表达免疫相关基因或者特异性降解/减弱病原菌毒素的酶； ⑧ 被动丧失感病性 （passive loss of susceptibility）即“丢失 ”与病原菌互作的关键靶标基因； ⑨ 通过寄主的“重新编程”（Reprogramming）减缓病原菌的生长。可参见图2。 图1B 图2 当作者把这些R基因按对应的物种分类后，发现除了第 ⑥ 类型外，其他机制都不是某一物种独有的或者专门针对某一病原菌的，见图1C。这些类型的抗病机制在植物王国里具有普遍性。但毕竟目前克隆到的R基因仍较少，所体现的分布不能反应出其自然的频率。 图1C 接下来对这九种抗病机制分别举例说明： ① 细胞外直接感应 许多PAMPs都能够被RLPs和RLKs直接识别感应。这方面最经典的就是拟南芥类受体激酶RLK FLAGELLIN-SENSITIVE2 (FLS2)基因识别细菌的鞭毛蛋白flg22，flg22的肽链绑定FLS2后直接招来BRI1-ASSOCIATED RECEPTOR KINASE (BAK1)的结合，这三者的晶体结构表明，flg22在其中扮演着分子胶体的作用来促进FLS2和BAK1复合体的形成。随着研究的深入，人们发现许多其他微生物的PAMPs都会发生与鞭毛蛋白类似的直接识别现象，这种直接感应的策略很普遍，有的会引起完全的免疫反应，有的会引起部分抗病反应。 ② 细胞外间接感应 这方面主要是在西红柿抗叶霉病中发现的。Cf-2是一个类受体蛋白RLP并对黄枝孢霉菌有抗性，能够识别黄枝孢霉的效应子Avr2和线虫的效应子GrVap1，但对于它们的识别需要一个中间介体Rcr3，Rcr3是一个编码类木瓜酵素的半胱氨酸蛋白酶 papain-like Cys protease。作者认为Rcr3更像是一个诱饵来诱使Cf-2对Avr2/GrVap1的识别，但Rcr3本身不是效应子，它的同源基因广泛存在西红柿、马铃薯和胡椒中；而Cf-2只存在于西红柿中，说明它更可能是后期进化产生的。 ③ 细胞内直接识别效应子 直接识别效应子不仅发生在细胞表面，一些NLRs基因在细胞内也会直接与效应子作用，比如拟南芥的NLR RECOGNITION OF PERONOSPORA PARASITICA1 (RPP1)基因直接识别卵菌的效应子ARABIDOPSIS THALIANA RECOGNIZED1 (ATR1)；而在锈菌领域，必须要提到的就是亚麻锈的经典案例：亚麻锈无毒基因AvrL567能够直接被亚麻的抗病等位基因L5、L6和L7识别。这种方式最简单地解释了 “基因对基因”的互作，R和Avr蛋白直接结合并激发抗病反应。在亚麻锈最新的研究进展中，作者发现一个有趣的现象，NLRs受体在体内保持着结合ADP—ATP平衡状态，而一旦无毒蛋白侵入，就会打破这一平衡，且不同的等位基因由于其结合ATP能力的不同，导致最终产生的抗病反应程度也不同。关于这一块，小编抽时间好好讲讲。 ④ 细胞内间接识别—诱捕和卫兵模式 许多NLRs基因与效应子的作用是通过酶的修饰或者寄主上的其他元件来实现的。这些额外的寄主蛋白被称为诱捕或卫兵，即他们是效应子的靶标或者模仿效应子的靶标。以西红柿抗病基因Prf为例，它能够与多个类受体细胞质激酶家族基因receptor-like cytoplasmic kinase (RLCK) XII family member作用，包括Pto和Fen。当Prf与Pto作用后会引起病原菌无毒蛋白AvrPto和AvrPtoB结合到Pto上，Prf识别pto-AvrPto的复合体或识别结合AvrPto后构象发生改变的Pto，从而激发下游的抗病反应。当卫兵蛋白不存在时，Avr蛋白与靶蛋白结合下调防卫反应，导致感病。靶蛋白结构的变化可能的机制为：Avr诱导靶蛋白发生磷酸化或水解靶蛋白。 ⑤ NLR-IDs (integrated domains)NLR整合结构—受体上嵌入传感器 而这种抗病基因的整合结构近几年才人们提出，最早在拟南芥RRS1和水稻RGA5及Pik上发现。而在我们小麦里上期刚推出的抗条锈基因Yr5/YrSP和Yr7就是这种结构，对于整合的结构BED domain，它在抗条锈研究中是参与识别病原物的无毒基因的，至少在该区域碱基发生变化影响了抗病性。作者认为整合的这部分结构可以看做是一个类似传感器的作用，目前这块研究还比较少，今后可能会有更多的与此有关的基因被解析出来。 ⑥ 执行基因—转录激活效应子的启动诱饵 在黄单胞菌和宿主互作关系中，病原菌中有一种转录激活效应子(transcription activator-like effectors (TALEs)，这个效应子的作用类似启动子，当宿主中没有抗性基因的时候，TALEs可以启动宿主中一些可以增强感病的基因来促进病原菌的侵染。面对这种病原菌，宿主的对策是进化出一种执行基因（Executor Genes）（也算是R基因的一种）。首先，这种执行基因可以引发（initiate）植物的抗病反应，其次执行基因的启动子序列跟TALEs也有很强的结合力。综合这两个特性，执行基因就可以捕获TALEs，让TALEs不能够去启动那些增强感病的基因，而是启动执行基因，进而引发下游防卫执行基因的表达。 ⑦ 主动丧失感病性—阻断病原菌的主要策略 主动丧失感病性（active loss of susceptibility）通过过表达寄主免疫相关基因或特异性降解/减弱病原菌毒素的酶可阻滞病原菌的生活过程，从而实现抗病。这一类大多数具有广谱抗性，对多种不同的病原菌都有抗性，也有个别是专化抗性。大部分是组成型表达，个别也有特异性表达。如抗玉米圆斑病基因Hm1，编码基于NADPH的还原酶，能特异性参与降解圆斑病菌毒素。 ⑧ 被动丧失感病性—在寄主中丢失与病原菌互作的关键靶标基因 寄主中直接“丢失”与病原菌互作的关键性感病因子而获得隐性的抗性，这是一种常见的机制。在马铃薯中，绝大多数鉴定出来的隐性R基因都抗病毒，通过编码突变后的4E或4G家族的翻译起始因子使其无法与病毒的转录本帽子结构相互作用，从而获得对马铃薯病毒的抗病性。此外，水稻中约有三分之一的抗稻旁叶螨和白叶枯病的基因都是隐性遗传。 ⑨ 通过寄主的重新编程而被动的丧失感病性 寄主中通过突变细胞通路中的基因元件导致对多种病原菌呈现广谱抗性，这同样是一种常见的策略。这种类型的抗病跟第八种一样通常是隐性的。通常这一类型也叫成株期抗性Adult Plant Resistance (APR)，因为这种抗性往往在植物生长后期才会出现。这一类型最经典的就是大麦的 MLO 基因，显性 MLO 会抑制大麦的抗病性，而当 MLO 位点突变为non-functional的时候，也就是变为隐性的 mlo ，对抗病性的抑制丧失，从而使得 mlo 呈现抗性。类似的还有水稻中的抗稻瘟病基因 Pi21 ，其编码的HMA区域能够抑制植物的防卫反应，而一旦 HMA 区域功能丧失，其等位基因（隐性基因）就具有了广谱抗性。 对⑧和⑨丧失感病性的小结：首先，在这里，显性跟隐性基因可以简单的定义为有功能的蛋白（显性基因）和失去功能的蛋白（隐性基因）。在⑧的病毒例子中，由于病毒本身产生的蛋白非常有限，它必须利用宿主的蛋白来进行核酸复制，所以当宿主相应的蛋白是正常的有功能的时候，病毒顺利利用并造成病害；但是当宿主中的这个蛋白突变为无功能时（对宿主本身也有一定负面影响），病毒不能进行复制，所以植物在这时就是抗病的。而在⑨的例子中，在宿主中存在一种抑制抗病反应的蛋白（这些蛋白可能有其它重要作用），所以当这个蛋白是有功能的时候，病原菌可以顺利侵染造成病害，但当植物中的这个蛋白失去作用后，抗病机制顺利得到发挥，所以就表现为抗病。总之，⑧和⑨是典型的感病为显性，植物通过loss function（变成隐性）来达到抗病，但其中又有细微的差别。 另外，基于衰老策略的抗性(senescence-associated resistance)也广泛存在于小麦中，多抗位点（三锈+白粉）Lr34/Yr18/Pm38编码蛋白通过运输抗性相关的代谢物而影响病原菌的生长，达到抗病的目的；Yr36基因编码蛋白高温条件下可以结合条锈菌的脂质，使病原菌的构造发生改变而抗病，进一步研究表明，编码蛋白通过跨膜运输进入叶绿体，与类囊体抗坏血酸过氧化物酶结合使其磷酸化，干扰其分解过氧化氢过程，造成过氧化氢积累，从而加速细胞死亡，有效地限制了条锈菌在小麦叶片组织内增殖；类似的成株期抗病基因Lr67/Yr46，编码一个己糖转运子蛋白，通过产生杂二聚体来减少植物细胞自身对葡萄糖的吸收，从而抑制活体寄生菌的生长和繁殖。3个已克隆的小麦成株抗性基因，抗病机理都是与能量代谢和糖转运有关，这些基因表达，在抗病性加强的同时，也加速细胞衰老和死亡。 随着技术的不断进步，越来越多的抗病基因会被挖掘出来，可能新的抗病机制也会探究出来，我想这也就是作者为什么标题会用到 to the nines（不断接近完美）的原因吧。 \0 \0
乌拉尔图小麦里有3万个miRNA？ 我们上周发了关于A基因组的解读 Nature在线发表小麦二倍体祖先乌尔图基因组的研究论文 ，后面有位小伙伴留言对我们文中提到的31,269个miRNA表示怀疑，并建议我们复查原文是否我们写错了，是mRNA，而我们写成了miRNA。这一点在阅读原文的时候我们也注意到了，并且特意查看了材料与方法中所使用的方法，原文就是这么写的。那么31,269miRNA是怎么来的呢？ Moreover, we identified 31,269 microRNAs (miRNAs), 5,810 long non-coding RNAs (lncRNAs), 3,620 transfer RNAs (tRNAs), 80 ribosomal RNAs (rRNAs) and 2,519 small nuclear RNAs (snRNAs) throughout the genome (Extended Data Table 1d ). 文中提供的信息来看是通过Infernal来预测的，就是纯预测的，假阳性非常高，不然那些研究miRNA的专家可以找个地方哭去了。如果用过softberry预测基因想必对此不会陌生。如果按照一般的miRNA鉴定思路会怎么来呢？ 1 可以通过同源搜索，加上二级结构预测。即已知水稻，拟南芥等的miRNA序列，搜索小麦的同源序列，进而进行二级结构预测。这样能够找到一些非常保守的miRNA。小麦很早期的研究里会包括这样一个过程。 2 构建 small RNA文库，mapping至基因组或转录组，进而利用软件进行二级结构预测，选出符合条件的miRNA。关于miRNA的标准，我们前面曾介绍过 在大数据时代重新审视植物miRNA注释的标准 ，文中明确说到，如果一篇文章里鉴定到成百上千的新miRNA，那一定是有问题的。这里mapping的对象首要的选择是转录本序列，而不是基因组序列。之所以用基因组，是因为转录本是有限条件下获取的，不能代表所有真实存在的转录本。而使用基因组序列呢，也要注意一些不能mapping至基因组的小RNA也可能是因为位于可变剪切位点上。 研究单独的一个miRNA序列，还需要找到star sequence，前体序列以及初级转录本。甚至预测并验证其真正的靶基因，这才算是真正有功能的miRNA。这一点完全可以参照毛龙研究员14年发表在 plant cell上的文章“mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in Nascent Hexaploid Wheat”。 小麦的研究miRNA也有些难点，我们常说小麦有很多重复序列，实际上在前期确实也鉴定到一些和重复序列有关的miRNA，但这些miRNA到底是有哪些位点转录出来的，确定起来还是有一定的难度。 最后要提醒大家，在使用这些参考序列时，心里面一定要数，这些参考序列不是100%正确的，给你的基因也有可能会出错。拿中国春来说，现在是1.0版本，相信不久就会推出2.0版本来纠正1.0版本的错误。人类基因组也是随着技术的进步不断在完善。当我们碰到结果矛盾的时候，最好也考虑下这方面的问题。
小麦族多组学数据网站——序列获取 5/2 本期作者 Neal 眨眼五一假期已过，其实很大一部分做小麦的往往没有五一假期。今天我们想要说一说与microRNA的话题。前面我们谈过一些microRNA的话题，我整理了一下列在下面，感兴趣的可以去看看，也欢迎大家就small RNA方面的内容与我们交流。 今天要谈的这篇文章前几天刚刚在plant journal在线。文章的题目是“ Identification and characterisation of a previously unknown drought tolerance—associated microRNA in barley ”。作者系澳大利亚常春藤名校联盟“八大名校”之一的阿德莱德大学（The University of Adelaide ）。通讯作者是 Shi Bujun , 第一作者是 Zhou Hui 。文章的DOI是 10.1111/tpj.13938 ，输入DOI可在网站sci-hub.tw上下载。 本文是一个反向遗传的例子，不像图位克隆这样正向遗传的文章，一换扣一环，逻辑方面较简单，文章阅读起来也相对容易，貌似小麦里图位克隆也比较简单，文章所呈现出来的内容也是行云流水。实际上在小麦做图位克隆并不简单，图位克隆过程中很多的曲折实际上很少会在文章中有所呈现。而反向遗传学方面，也即基因功能和机制的方面研究，很大程度上需要转基因技术和基因编辑技术，这才是反向遗传学的硬通货。除此之外，一些必要的点缀也是需要的，毕竟红花还得绿叶配。从一个简单的idea到最终论文里呈现的完美故事，统领整个研究的是逻辑思维能力，这才是一篇论文研究的灵魂所在。反向遗传学对逻辑方面的能力要求要比正向遗传学高。今天我们就以这一篇文章为例谈一谈。 首先先从文章的干货开始谈起。过表达hvu-miRX的大麦植株耐旱性与对照相比得到提高，表型见下图，文中也对一些耐旱性的指标进行了评价，结果也是阳性的。可能只是先在线的原因，图片里的文字看不清楚。 现在我们知道miRNA是通过剪切靶基因的转录本而行使生物学功能的，在表达水平上往往成相反的趋势，也即当miRNA的表达量升高时，靶基因的表达量就降低，反之亦然。这里为了行文的方便，miRNA和靶基因之间的关系做了简单化处理。在这里hvu-miRX的靶基因之一是编码NAD(P)-binding domain的基因，该基因的表达水平在过表达hvu-miRX的大麦里与对照相比降低了，这符合我们的预期。但是该基因不受干旱诱导。文中没有对此作出解释，其实我们可以做这样一个假设，含有NAD(P)-binding domain的基因负调控大麦的抗旱性。大家认为这个假设对不对呢？同时文中回避了过表达hvu-miRX的大麦在干旱处理过后，该靶基因的表达水平。所以hvu-miRX是否真的通过这个靶基因来提高大麦对干旱的耐受性还没有一锤定音，也即不能排除其他未知的途径。大家可以进一步思考下，如果要验证这个假设需要安排哪些实验呢？其实我认为这才是文章的亮点所在，然而本文并没有更进一步。 说完了转基因，我们再谈一谈这个研究的来龙去脉。这就不得不提2011年的两篇研究，一篇是在组学水平上鉴定大麦的miRNA（ Discovery of barley miRNAs through deep sequencing of short reads ），另外一篇发现在过表达TaDREB3的大麦里有一个miRNA与对照相比上调表达（ Improvement of stress tolerance of wheat and barley by modulation of expression of DREB/CBF factors ），同时过表达TaDREB3的大麦对干旱的耐受性增加。这是为啥本篇为啥要研究miRX。我们前面提到也有过表达miRX的大麦，但文中作者没有提到是否DREB3的表达是否受miRX调控，也许因为DREB3并不是miRX的靶基因吧。这其实也是一种常见的研究思路，先广撒网，再从捞到的鱼里挑挑拣拣，选择一条上好的鱼苗子养大。我们以前常说生信就是指路的也是这样一个道理，数据越多，方向也就更坚定，脚下的路也就越平坦。 接下来是对miRX的研究，希望说明miRX确实是一个miRNA，并且也确实收到干旱的诱导。除了这些，本文还发现pri-miRX的正向上有8个ORF，其中最长的一个编码65个氨基酸。前面已经有研究表明pri-miRNA是可以编码一些小肽的，本文没有再进一步去验证。获得的15个cDNA（pri-miRX）克隆中，有2个存在单碱基变异，作者认为很可能是反转录过程中引起的错误。是不是反转录引起的错误，多重复几次反转录是不是就可以验证了？另外有没有可能是RNA编辑？ 这一部分在讨论里还提到pri-miRX的5'末端多了四个碱基GAAA。我们知道mRNA会在5'末端加帽，即加1个G，而这里却加了4个碱基？作者表示还需要更多的时间来研究GAAA可能的生物学作用。看到此处，我首先想到的有没有可能是接头序列？我查了下材料方法，本文使用的反转录试剂盒是GeneRacer，在附件一里看到其接头引物的3'末端就是GAAA，如下图。所以我不太清楚作者是否排除了加上的这四个碱基？有兴趣的小伙伴可以仔细研究下，看看这个GAAA是不是真的？ 接下来作者继续分析了这个miRX的启动子序列。这里先卖个关子，大家想一下为啥要花很多精力分析和研究启动子呢？ 作者在分析了一些启动子的基本元件后将启动子截成4段启动GUS，用来寻找核心启动子。通过数GUS的细胞数目的来衡量启动子效率的高低。由于我没做过这种实验和文中材料方法部分介绍也比较少，不了解这个实验的可靠性。有懂的小伙伴可以评价下。下图是结果的柱状图，因为文中没有交代该实验重复了几次，这个实验误差有点大，所以对文中所下的结论还是有点疑问的？ 这里要交代为啥要研究miRX的启动子。因为在转TaDREB3的材料里，miRX上调表达，考虑到DREB3是一个转录因子，所以就假设DREB3通过结合其启动子区基序来调控miRX的表达。但是仅从启动子序列上来来看，没有迹象表明受DREB3调控,后续的共表达实验也没有证明DREB3直接调控miRX。 下面说一说miRNA的靶基因。预测得到15个靶基因，降解组支持的有3个。然而文中并没有交代支持靶基因的降解组read是多少，也没有具体交代使用了哪个组织的降解组文库，以及原始的降解组数据是否已提交至公共数据库。 有降解组支持的3个靶基因，选择了那个编码NAD(P)-binding domain的基因进行了验证（The target gene encoding the NAD(P)-binding domain-containing protein was further verified using gene specific 5′ RACE）。这里列出了文中的原话。按照我的理解如果要验证miRNA的靶基因，一般使用的是3' PPM-RACE和5' RLM-RACE。而这里作者所讲的5′ RACE是不是5' RLM-RACE我就不太确定了。在材料方法和附件里也没有对这一实验的描述。下图中3个黑色箭头上方的数字表示一共验证了8个克隆，其中有6个克隆支持在经典的10-11位之间剪切靶基因，当然这是按照我的理解，至于是降解组的read还是克隆，得向作者确认。这个地方最好再放上测序的峰图。 然而，定量PCR结果表明NAD(P)-binding domain-containing 的基因的表达没有发生变化。 除了以上内容，本文还分析了miRX在大麦基因组的拷贝数和位置，以及miRX在植物里的保守性。 以上就是本文的全部内容。建议大家有时间的话读读原文，结合本次的解读，希望能够有自己的思考。本文的亮点有两条，第一证明miRX受DREB3调控，第二证明过表达miRX的大麦对干旱的耐受性是通过哪个靶基因起作用。然而，本文在这两方面得到的都是阴性结果。本文对大部分实验结果的描述和分析很到位，这点是我要学习地方，写文章的时候几句话就把结果交代完了，在往下就没东西写了。而对实验方法部分的描述却很不到位，一些关键信息缺失。
原创小程序-让你的引物设计又快又准！ 本期作者：Rui Wang 这次我们按照计划继续我们的生信菜鸟养成记（以往的推送文章请看文章末尾列表），今天已经来到了这个系列的第六集，我们也开始上一些code。这些code由Jorge实验室张军利博士开发，专治各种引物设计的疑难杂症，本人已亲测，非常好用，起码比PolyMarker又快又准！ 其实今天以下的主要内容也都来自军利兄在一次小麦基因克隆的workshop中教大家设计引物的课件，经军利兄允许，今天无私奉献给大家！想到当前无论是设计引物的软件还是自己编写的小程序均是以英文为主，所以今天的推送也就给大家原汁原味的用英文奉上。另外，对今天的推送中一些基本原理有什么问题请参见我们上次生信系列的推送： 小麦生信菜鸟归来(五)—系列总结以及特异性引物设计 。 Steps to design genome-specific primers 以下这六步其实就是特异性引物设计的核心，其实所有软件和方法都是根据这六步开发的。我们不仅要会用，更要知其所以然。 1. Blast the marker sequence against the pseudomolecule andfind all the homeologsand potentially paralogs: 90% similarity 2. Extract the sequences for all the homeologs and potentially paralogs 3. Multiple Sequence Alignment 4. Find all the variation sites among the homeologs and paralogs 5. Use variation sites or combination of variation sites that are unique to yourtargets to design primers 6. Blast all the primers against the pseudomolecule v1.0 with word length 7 to see whether they also hit other chromosomes Common practices of PCR primers · Length: 18 - 25 nt · Melting temperature: around 60 °C · GC clamp: G or C bases within the last five basesin the 3' end helps promote specific binding, but more than 3 G/C should beavoided · NO secondary structures · Avoid template secondary structure or othercomplex regions, such as retros · Amplicon length: KASP and dCAPS are short (300 bp), other markers usually 1 kb · Primer pair Tm difference 5 °C Primer Design Tips 以下中第二点不知有多少小伙伴知道，这个思路很巧妙，用过的都说好！ 1. Usethe unique variation site as the primer 3' end 7A CGAGCTTGATGACGAAGAAGGA T 7B CGAGCTTGATGACGAAGAAGGA C 2. Two variation sites in the first 4 nt from the 3' end: we canintroduce 1 mutation in the 3rd nt from 3' end (may need to use touchdown PCR) 7A CGAGCTTGATGACGAAGAAGGA T 7B CGAGCTTGATGACGAAGAAGGA C CGAGCTTGATGACGAAGAAG A A T Nucleotide substitution principle : A → C ； T → C ； G → A ； C → T Validate Primer Location Using Chinese Spring Nullitetrasomic (NT) Lines If we tested our primers target for 7A: N7AT7D (7D7B7D): Absent N7BT7D (7A7D7D): Present N7DT7B (7A7B7B): Present Are our primers 7A-specific? Common PCR-based genotyping methods for SNP markers 以下的三种标记种类大家可能熟悉CPAS和KASP，不知有多少小伙伴熟悉dCAPS, 这个和上面第二点所用到的思路是一样的。 1. CAPS (Cleaved Amplified Polymorphic Sequences) One SNP allele creates or removes a naturally occurring restriction site Codominant 2. dCAPS (Derived CAPS) For SNPs that donot create a natural restriction site Uses introduced mismatches in one PCR primer to create a restriction site forone allele Codominant 3. KASP (Kompetitive Allele Specific PCR) A homogenous,fluorescence-based genotyping variant of PCR Codominant 为了让大家熟悉这个dCAPs，以下是一个例子： IWB1998:CGAGCTTGATGACGAAGAAGGAGA CGGGCAGACCCACGACGT EcoRV: GAT'ATC 这里又有一个巧妙的思路： We can add some tails to make dCAPS primer longer to better separate after digestion： GAAGGTGACCAAGTTCATGCT CGAGCTTGATGACGAAGAAGGATA Primer design software · Primer3 ( http://primer3.ut.ee/ ) · Polymarker for KASP in wheat ( https://github.com/TGAC/biorubypolyploid tools ) · CAPS Designer ( https://solgenomics.net/tools/caps_designer/caps_input.pl ) · dCAPS Finder 2.0 ( http://biology4.wustl.edu/dcaps ) · indCAPS ( http://indcaps.kieber.cloudapps.unc.edu/ ) · GSP (Genome Specific Primers) ( https://probes.pw.usda.gov/GSP/ ) SNP Primer Design Pipeline 这个就是军利兄自己编写的Python小程序，以下也附上了在github上的源代码和相应说明文件。强烈推荐大家下载应用，说明文件也非常详细 ， 学起来也不难。 1. Apipeline to design KASP/CAPS/dCAPS primers for SNPs in wheat 2. A Python script which incorporates: · Muscle: Multiple sequence alignment program ( http://www.drive5.com/muscle/ ) · Primer3: program for designing PCR primers ( http://primer3.sourceforge.net/ ) · blast+: BLAST the wheat genome ( https://blast.ncbi.nlm.nih.gov/Blast.cgi ) 3. I have a github repository for this tool https://github.com/pinbo/SNP_Primer_Pipeline 下面是Pipeline的工作原理： 1.Blast each SNP sequence against the pseudomolecule and get hits that are · 90% similarity and · 90% of length of the best hit AND 50 bp 2.Get 500 bps on each side of the SNP for all the hits ( SNP is at 501 ) 3. Multiple Sequence Alignment of the homeolog sequences with MUSCLE 4. Find all the variation sites that can differ the target from other homeologs 5. Use these sites as forced 3' end in Primer3 and design homeolog specific primers 6. Blast all the primers against the pseudomolecule v1.0 with word length 7 to see whether it also hits other chromosomes · Criterion of matches: 2 mismatches in thefirst 4 bps from 3' 引申阅读：小麦生信系列文章 1. 第一篇是为序，介绍了一个常用的生信网站 Graingenes 小麦生信必备网站和数据库（一） 2. 接下来三篇主要介绍了小麦物理图谱的介绍和应用，其中对小麦基因组数据库的总结介绍是非常基础且重要的知识。另外，也介绍了一些比较基因组学的知识和应用，包括野生二粒小麦，山羊草，拟南芥，和水稻。 小麦生信菜鸟成长记(二)--高手请直接看第二部分 小麦基因组数据库介绍 小麦生信菜鸟(三)--常见问题 如何获取小麦中一个基因家族的所有成员 如何根据模式作物拟南芥和水稻的基因序列 寻找小麦里的直系同源基因 3. 接下来几篇小编打算介绍三个主题：基因表达，特异性引物设计，以及突变体库。 小麦生信菜鸟(四)—基因表达数据库 小麦生信菜鸟归来(五)—系列总结以及特异性引物设计 小麦生信菜鸟(六)—特异性引物设计 （今天推送） 小麦生信菜鸟 ( 七 )— 基因表达数据分析（待续） 小麦生信菜鸟 ( 八 )— 小麦突变体数据库介绍及应用（待续） 4. 其它相关推送： 野生二粒小麦基因组在science发布 野生二粒小麦基因组下载 Nature在线发表小麦D基因组供体——粗山羊草的基因组研究论文 又一篇节节麦基因组文章来袭--聊一聊你的关注点在哪？ 节节麦基因组数据使用和下载 吐血推荐：小麦或植物常用网站 欢迎关注 “ 小麦研究联盟 ”， 了解小麦新进展 投稿、转载、合作以及信息发布等请联系： wheatgenome
2018年第13周小麦文献推荐（4.1） 今天是4.1号，大家要小心呢。还有别忘了我们的线上摄影展（ 第一届“小麦研究联盟”线上摄影展 ），现在就可以发给我们了。 听说最近天气变化剧烈，特地查了下天气预报。下面播报下天气预报 。下周一，北方大部气温将抬升近期最高点，河北南部、山东西北部、河南北部、陕西关中等地，将再次向30℃以上发起冲击，局地或将有高温现身。省会级城市中，郑州、济南、银川、兰州有望创下今年气温新高，其中郑州、济南将超30℃。南方大部最高气温也多在25-30℃左右。不过，北方温暖的春意还不能完全站稳脚跟。下周前期，较强冷空气来袭，各地气温将迅速下降。明天，冷空气的先头部队就率先在新疆发动攻势，乌鲁木齐最高气温将从今天的26℃降到明天的8℃，随后还将逐步跌落至仅有6℃，寒冷如冬。4月3-6日，冷空气东移南下，逐渐影响全国大部，北方大部地区的气温将转为偏低，华北地区最高气温纷纷降到15℃左右，而东北则降至个位数，最低气温将再度跌破冰点。其中，降温最猛烈的河南、山东一带，累积降幅可达到20℃上下，例如济南、郑州最高气温将由2日的30℃出头降至10℃左右。我们的麦S特别提醒大家注意倒春寒（ 低温、高温对起身拔节期小麦的影响 ）。 说完了天气，我们开始说一说我们这一周的文献更新。 1 Genome-wide identification of wheat (Triticum aestivum) expansins and expansin expression analysis in cold-tolerant and cold-sensitive wheat cultivars. PMID:29596529 DOI:10.1371/journal.pone.0195138 2 Coupled ultradian growth and curvature oscillations during gravitropic movement in disturbed wheat coleoptiles PMID: 29596500 DOI: 10.1371/journal.pone.0194893 3 Quantitative trait loci associated with soft wheat quality in a cross of good by moderate quality parents. PMID: 29593939 PMCID: PMC5868479 DOI: 10.7717/peerj.4498 4 Genetic Diversity and Population Structure of F3:6 Nebraska Winter Wheat Genotypes Using Genotyping-By-Sequencing PMID: 29593779 PMCID: PMC5857551 DOI: 10.3389/fgene.2018.00076 5 The Role of Hydrogen Peroxide in Mediating the Mechanical Wounding-Induced Freezing Tolerance in Wheat PMID: 29593774 PMCID: PMC5861560 DOI: 10.3389/fpls.2018.00327 6 Zinc and Iron Concentration as Affected by Nitrogen Fertilization and Their Localization in WheatGrain. PMID: 29593765 PMCID: PMC5855893 DOI: 10.3389/fpls.2018.00307 7 Genetic Dissection of End-Use Quality Traits in Adapted Soft White Winter Wheat PMID: 29593752 PMCID: PMC5861628 DOI: 10.3389/fpls.2018.00271 8 Identification and Characterization of Wheat Yellow Striate Virus, a Novel Leafhopper-Transmitted Nucleorhabdovirus Infecting Wheat PMID: 29593700 PMCID: PMC5861215 DOI: 10.3389/fmicb.2018.00468 9 Genome-wide association mapping for resistance to leaf rust, stripe rust and tan spot in wheatreveals potential candidate genes PMID: 29589041 DOI: 10.1007/s00122-018-3086-6 10 Efficient anchoring of alien chromosome segments introgressed into bread wheat by new Leymus racemosus genome-based markers PMID: 29587653 DOI: 10.1186/s12863-018-0603-1 11 Expression of Pinellia pedatisecta Lectin Gene in Transgenic Wheat Enhances Resistance to Wheat Aphids PMID: 29587341 DOI: 10.3390/molecules23040748 12 Wheat starch with low retrogradation properties produced by modification of the GtfB enzyme 4,6-α-glucanotransferase from Streptococcus thermophilus PMID: 29582651 DOI: 10.1021/acs.jafc.8b00550 13 TaEDS1 genes positively regulate resistance to powdery mildew in wheat PMID: 29582247 DOI: 10.1007/s11103-018-0718-9 14 Identification of Wheat Inflorescence Development-Related Genes Using a Comparative Transcriptomics Approach PMID: 29581960 PMCID: PMC5822904 DOI: 10.1155/2018/6897032 15 Dynamic Evolution of α-Gliadin Prolamin Gene Family in Homeologous Genomes of Hexaploid Wheat PMID: 29581476 DOI: 10.1038/s41598-018-23570-5 16 Contrasting plant height can improve the control of rain-borne diseases in wheat cultivar mixture: modelling splash dispersal in 3-D canopies PMID: 29579151 DOI: 10.1093/aob/mcy024 17 Transgenic expression of plastidic glutamine synthetase increases nitrogen uptake and yield in wheat PMID: 29577547 DOI: 10.1111/pbi.12921 18 Wheat expansin gene TaEXPA2 is involved in conferring plant tolerance to Cd toxicity PMID: 29576078 DOI: 10.1016/j.plantsci.2018.02.022 19 Molecular Diversity and Landscape Genomics of the Crop Wild Relative Triticum urartu Across the Fertile Crescent PMID: 29573496 DOI: 10.1111/tpj.13888 20 Responses of seminal wheat seedling roots to soil water deficits PMID: 29567416 DOI: 10.1016/j.jplph.2018.03.002 最后，告诉大家一个小技巧，在PubMed数据库里按照如下格式搜索，可以搜索关键词wheat在2018年3月24日至2018年3月30日的文献更新。 ( (wheat ) AND 2018/03/24 15.00 :2018/03/30 15.00 ) 欢迎关注 “ 小麦研究联盟 ”， 了解小麦新进展
2018年第12周小麦文献推荐（3.24） 这一周文献很多，值得一读的文献也有几篇。 1 Genome editing of bread wheat using biolistic delivery of CRISPR/Cas9 in vitro transcripts or ribonucleoproteins In recent years, CRISPR/Cas9 has emerged as a powerful tool for improving crop traits. Conventional plant genome editing mainly relies on plasmid-carrying cassettes delivered by Agrobacterium or particle bombardment. Here, we describe DNA-free editing of bread wheat by delivering in vitro transcripts (IVTs) or ribonucleoprotein complexes (RNPs) of CRISPR/Cas9 by particle bombardment. This protocol serves as an extension of our previously published protocol on genome editing in bread wheat using CRISPR/Cas9 plasmids delivered by particle bombardment. The methods we describe not only eliminate random integration of CRISPR/Cas9 into genomic DNA, but also reduce off-target effects. In this protocol extension article, we present detailed protocols for preparation of IVTs and RNPs; validation by PCR/restriction enzyme (RE) and next-generation sequencing; delivery by biolistics; and recovery of mutants and identification of mutants by pooling methods and Sanger sequencing. To use these protocols, researchers should have basic skills and experience in molecular biology and biolistic transformation. By using these protocols, plants edited without the use of any foreign DNA can be generated and identified within 9–11 weeks. 2 Yield and grain weight responses to post-anthesis increases in maximum temperature under field grown wheat as modified by nitrogen supply High-temperatures reduce yield of wheat and with global warming episodes of heat waves (only few days of high maximum temperatures) during grain filling will become more frequent. It has been recently reported that the magnitude of the yield penalties imposed by high temperatures under field conditions may interact with nitrogen (N) availability both in barley and maize. We determined, under field conditions, the penalties imposed by post-anthesis high-temperatures waves (increased maximum –but not minimum– temperatures during part of the grain filling period) on wheat yield under contrasting soil N supply during two consecutive years. The high temperature treatment was imposed for 10 d starting 10 d after anthesis by placing over the crops transparent polyethylene film (125 μm) mounted on wood structures of 1.5 m height above the ground. This high-temperature and the unheated controls were imposed on 5 modern and well adapted cultivars under contrasting N availabilities (376, 268 and 68 KgN ha−1). Averaged across N conditions, high-temperature treatments reduced yield by c . 1.5 Mg ha−1 (a loss of c . 17%) even though the treatment was rather mild in terms of different average temperature during grain filling. The magnitude of the loss was consistently shaped by the N condition in which the treatment was imposed: yield penalty produced by high-temperature increased from less than 1 to 2.6 Mg ha−1 (which represents losses from 10 to 25%) in parallel with the increased N supply. The penalties were related to both yield components (grain number and average grain weight) which also were more severely penalised under high than under low N supply. As episodes of high-temperature waves will become more frequent in the future the tools used to establish the needs of N fertilisation should be revised as the rates maximising yield (or gross margin) might induce higher sensitivities to these episodes. Also simulation models used to upscale physiological responses to regional or even global domains might need to be revised to include the effect of heat waves (which would be larger per °C increase than what is estimated from experiments increasing temperature during the whole day and over longer periods) as well as the interaction with N supply. 3 Identification and characterization of phenolic compounds extracted from barley husks by LC-MS and antioxidant activity in vitro Phenolic compounds were extracted from Tunisian barley husks obtained through a pearling process, by using two different extraction solvents: acid treatment with sulfuric acid and alkaline delignification with sodium hydroxide. Their antioxidant properties in vitro were investigated using 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging test and butylated hydroxyanisole (BHA). Antioxidants composition was evaluated with LC-MS analysis. Findings suggest that the best yields of crude extracts with high level of phenolic compounds exhibiting strong antioxidant activities were found after pre-hydrolysis and delignification step of barley husks. The lowest average total phenolic content found was 763.665 mg/100 g, presenting an EC50 value of 0.93 g/L, four higher antioxidant levels than BHA (0.24 g/L). All extracted fractions showed high contents of p-coumaric acid (≥491.189 mg/100 g), trans-ferulic acid (≥501.475 mg/100 g) and syringic acid (≥192.228 mg/100 g). These results contribute to enhancing the value of barley husks as a good source of natural antioxidants, which serve as new functional food ingredients and dietary supplements. 4 Improving water use efficiency and grain yield of winter wheat by optimizing irrigations in the North China Plain Achieving the combination of high water use efficiency (WUE) and high yield is very important for the sustainable development of wheat production in the North China Plain (NCP). For this study, we investigated how to optimize timing of two irrigations to improve winter wheat grain yield and WUE under field conditions. No-irrigation after sowing (W0) as a control, and six irrigation treatments as follows: irrigation of 75 mm each at late tillering and booting (TB), at late tillering and anthesis (TA); at late tillering and medium milk (TM), at jointing and anthesis (JA), at jointing and medium milk (JM) and at booting and medium milk (BM). Experiments were conducted between the 2014–2016 growing seasons. In all the treatments, JA achieved the highest grain yield (9,267.6 kg ha−1) and WUE (20.2 kg ha−1 mm−1). Compared with TB, TA and TM, JA coordinated pre- and post-anthesis water use, reduced pre-anthesis and total evapotranspiration (ET), and increased post-anthesis water use amount and ratio; JA reduced biomass at anthesis, but optimized allocation of assimilation, increased spike partitioning index and maintained high fruiting efficiency, and thus obtained the highest grain number per m2(GN, 23.7 103 m−2). Meanwhile, JA optimized crop characteristics with appropriate leaf area index (LAI), delayed leaf senescence, extended grain filling duration by 1–3 days, then increased biomass post-anthesis and harvest index (HI). Compared with JM and BM, JA increased GN, biomass post-anthesis and grain yield as well. These results demonstrated that irrigation at jointing and anthesis could improve grain yield and WUE by increasing biomass post-anthesis, HI and GN. Therefore, we propose that under adequate soil moisture conditions before sowing, two irrigations at jointing and anthesis with 150 mm irrigation amount is the optimal limited irrigation practice for wheat production in NCP. 5 Integrated agronomic practices management improve yield and nitrogen balance in double cropping of winter wheat-summer maize 6 Tillage and residue management for long-term wheat-maize cropping in the North China Plain: I. Crop yield and integrated soil fertility index Conservation tillage has been gaining increasing recognition for its role in improving soil quality and maintaining agricultural sustainability. This is the first in a series of papers describing the impacts of reduced/no-tillage with and without residue based on the field experiment in the North China Plain. The experiment was established in 2006 on a sandy loam soil and involved a winter wheat-summer maize rotation system per year. The objective of this study was to investigate the impacts of different conservation tillage systems on crop yield and soil fertility that was quantified by a minimum data set and integrated index. Soil samples were collected since 2011, and the stocks of soil organic matter (SOM), total nitrogen (TN), alkali-hydrolyzale nitrogen (AN), total phosphorus (TP), available phosphorus (AP), total potassium (TK) and available potassium (AK) were measured for each year as well as soil aggregates were fractionated for 2016. Compared to continuous tillage, the reduced/no-tillage, regardless of residue, significantly increased the macroaggregate mass and soil nutrient stocks at the 0–10 cm depth, while further improvements in these soil attributes apart from TK were observed at the 0–10 and 10–20 cm depths for residue returning relative to residue removing. The accumulations of soil nutrients were closely related to soil macroaggregation. The path analysis revealed that TN was the most important soil attribute to directly determine wheat and maize yields while other soil attributes apart for TK primarily made indirect contributions to the yields. The first two factors extracted using 8 soil attributes through factor analysis were selected as the integrated indicators for the minimum data set, and their integrated score was calculated to quantify soil fertility. It was found that reduced/no-tillage did not improved soil fertility at the 0–20 cm depth. Consequently, an average 6.9% decrease in wheat yield across all years was observed under no-tillage while reduced tillage only increased the yield in the first two years in a periodic reduced tillage event. No significant difference was observed for the mean maize yield among the three tillage regimes averaged across all years and residue managements. Wheat and maize yields were significantly correlated with the integrated score for soil fertility, and thus significant increases in grain yields of wheat and maize were observed for residue returning. It can be concluded that grain yields of wheat and maize within a given residue management practice were not significantly higher for reduced/no-tillage than continuous tillage, regardless of the effects of tillage on aggregates and soil nutrients. 7 Wheat miR9678 Affects Seed Germination by Generating Phased siRNAs and Modulating Abscisic Acid/Gibberellin Signaling Seed germination is important for grain yield and quality and rapid, near-simultaneous germination helps in cultivation; however, cultivars that germinate too readily can undergo pre-harvest sprouting (PHS), which causes substantial losses in areas that tend to get rain around harvest time. Moreover, our knowledge of mechanisms regulating seed germination in wheat (Triticum aestivum) remains limited. In this study, we analyzed function of a wheat-specific microRNA 9678 (miR9678), which is specifically expressed in the scutellum of developing and germinating seeds. Overexpression of miR9678 delayed germination and improved resistance to PHS in wheat through reducing bioactive gibberellins (GAs) levels; miR9678 silencing enhanced germination rates. We provide evidence that miR9678 targets a long non-coding RNA(WSGAR)and triggers the generation of phased siRNA which play a role in the delay of seed germination. Finally, we found that abscisic acid (ABA) signaling proteins bind the promoter of miR9678 precursor and activate its expression, indicating that miR9678 affects germination by modulating the GA/ABA signaling. 8 Effect of sowing time and seeding rate on yield components and water use efficiency of winter wheat by regulating the growth redundancy and physiological traits of root and shoot 9 The activity of superoxide dismutases (SODs) at the early stages of wheat deetiolation Unbound tetrapyrroles, i . e . protochlorophyllide (Pchlide), chlorophyllide and chlorophylls, bring the risk of reactive oxygen species (ROS) being generated in the initial stages of angiosperm deetiolation due to inefficient usage of the excitation energy for photosynthetic photochemistry. We analyzed the activity of superoxide dismutases (SODs) in etiolated wheat ( Triticum aestivum ) leaves and at the beginning of their deetiolation. Mn-SOD and three isoforms of Cu/Zn-SODs were identified both in etiolated and greening leaves of T . aestivum . Two Cu/Zn-SODs, denoted as II and III, were found in plastids. The activity of plastidic Cu/Zn-SOD isoforms as well as that of Mn-SOD correlated with cell aging along a monocot leaf, being the highest at leaf tips. Moreover, a high Pchlide content at leaf tips was observed. No correlation between SOD activity and the accumulation of photoactive Pchlide, i . e . Pchlide bound into ternary Pchlide:Pchlide oxidoreductase:NADPH complexes was found. Cu/Zn-SOD I showed the highest activity at the leaf base. A flash of light induced photoreduction of the photoactive Pchlide to chlorophyllide as well as an increase in all the SODs activity which occurred in a minute time-scale. In the case of seedlings that were deetiolated under continuous light of moderate intensity (100 μmol photons m-2 s-1), only some fluctuations in plastidic Cu/Zn-SODs and Mn-SOD within the first four hours of greening were noticed. The activity of SODs is discussed with respect to the assembly of tetrapyrroles within pigment-protein complexes, monitored by fluorescence spectroscopy at 77 K. 10 Fungicide and cultivar management of leaf spot diseases of winter wheat in western Canada A complex of leaf spotting diseases are frequently observed on winter wheat in western Canada; however, there are few studies indicating varietal differences in reaction to these diseases or the benefit of fungicide application. To determine the benefit of varietal improvement, and multiple fungicide treatments and application timings, field experiments were conducted at six site-years in western Canada. Two cultivars varying in reaction to leaf spot diseases were used in combination with fungicide treatments. Disease severity ranged from trace to 64% of the combined flag and penultimate leaf area diseased, differed between cultivars, and was reduced from the check by some fungicide treatments. Yield improvement by fungicide treatment varied from 3.3 to 13.2% greater than the non-treated check. At two site-years, the split application of two half rates of fungicide resulted in the greatest yield; however, in both cases the yield benefit did not differ from a single application at the flag leaf growth stage. Cultivar selection and fungicide use under environments conducive to disease are beneficial components of an integrated leaf spot disease management program for winter wheat in western Canada. 11 First report of Fusarium pseudograminearum causing crown rot of wheat in Europe 12 Long-Term Irrigation Affects the Dynamics and Activity of the Wheat Rhizosphere Microbiome 13 Proteomic analysis of melatonin-mediated osmotic tolerance by improving energy metabolism and autophagy in wheat ( Triticum aestivum L.) Melatonin is known to play multiple roles in plant abiotic stress tolerance. However, its role in wheat has been rarely investigated. In this study, 25% polyethylene glycol 6000 (PEG 6000) was used to simulate osmotic stress, and wheat seeds and seedlings were treated with different concentrations of melatonin under PEG stress. Isobaric tag for relative and absolute quantification (iTRAQ)-based proteomic techniques were used to identify the differentially accumulated proteins from melatonin-treated and non-treated seedlings. Seeding priming with melatonin significantly increased the germination rate, coleoptile length, and primary root number of wheat under PEG stress, as well as the fresh weight, dry weight, and water content of wheat seedlings. Under PEG stress, melatonin significantly improved reactive oxygen species homeostasis, as revealed by lower H2O2 and O 2 · content; and the expression of antioxidant enzymes at the transcription and translation levels was increased. Melatonin maintained seedling growth by improving photosynthetic rates and instantaneous and intrinsic water use efficiencies, as well as carbon fixation and starch synthesis at the protein level. Melatonin treatment significantly affected the expression of glycolytic proteins, including fructose-1,6-bisphosphate aldolase, hexokinase, glyceraldehyde-3-phosphate dehydrogenase, and enolase, and remarkably increased the expression of the nicotinamide adenine dinucleotide transporter and nicotinamide adenine dinucleotide binding protein, thereby indirectly modulating electron transport in the respiratory chain. This indicated that melatonin improved energy production in PEG-stressed seedlings. Further, melatonin played a regulatory role in autophagy, protease expression, and ubiquitin-mediated protein degradation by significantly upregulating rab-related protein, fused signal recognition particle receptor, aspartyl protease, serine protease, ubiquitin-fold modifier 1, and ubiquitin at the mRNA or protein level. These findings suggested that melatonin might activate a metabolic cascade related to autophagy under PEG stress in wheat seedlings. 14 The wheat TabZIP2 transcription factor is activated by the nutrient starvation-responsive SnRK3/CIPK protein kinase Basic leucine zipper (bZIP) transcription factors (TFs) play key roles in the regulation of grain development and plant responses to abiotic stresses. We investigated the role and molecular mechanisms of function of the TabZIP2 gene isolated from drought-stressed wheat plants. Molecular characterisation of TabZIP2 and derived protein included analyses of gene expression and its target promoter, and the influence of interacting partners on the target promoter activation. Two interacting partners of TabZIP2, the 14-3-3 protein, TaWIN1 and the bZIP transcription factor TaABI5L, were identified in a Y2H screen. We established that under elevated ABA levels the activity of TabZIP2 was negatively regulated by the TaWIN1 protein and positively regulated by the SnRK3/CIPK protein kinase WPK4, reported previously to be responsive to nutrient starvation. The physical interaction between the TaWIN1 and the WPK4 was detected. We also compared the influence of homo- and hetero-dimerisation of TabZIP2 and TaABI5L on DNA binding. TabZIP2 gene functional analyses were performed using drought-inducible overexpression of TabZIP2 in transgenic wheat. Transgenic plants grown under moderate drought during flowering, were smaller than control plants, and had fewer spikes and seeds per plant. However, a single seed weight was increased compared to single seed weights of control plants in three of four evaluated transgenic lines. The observed phenotypes of transgenic plants and the regulation of TabZIP2 activity by nutrient starvation-responsive WPK4, suggest that the TabZIP2 could be the part of a signalling pathway, which controls the rearrangement of carbohydrate and nutrient flows in plant organs in response to drought. 15 Characterization of Pm59 , a novel powdery mildew resistance gene in Afghanistan wheat landrace PI 181356 Powdery mildew, caused by Blumeria graminis f. sp. tritici ( Bgt ), is an important foliar disease of wheat worldwide. In the Great Plains of the USA, Bgt isolates virulent to widely used powdery mildew resistance genes, such as Pm3a , were previously identified. The objectives of this study were to characterize the powdery mildew resistance gene in Afghanistan landrace PI 181356, which exhibited high resistance to Bgt isolates collected in southern Great Plains, and identify molecular markers for marker-assisted selection. An F2 population and F2:3 lines derived from a cross between PI 181356 and OK1059060-126135-3 were used in this study. Genetic analysis indicated that PI 181356 carries a single dominant gene, designated Pm59 , in the terminal region of the long arm of chromosome 7A. Pm59 was mapped to an interval between sequence tag site (STS) markers Xmag1759 and Xmag1714 with genetic distances of 0.4 cM distal to Xmag1759 and 5.7 cM proximal to Xmag1714. Physical mapping suggested that Pm59 is in the distal bin 7AL 0.99–1.00. Pm59 is a novel powdery mildew resistance gene, and confers resistance to Bgt isolates collected from the Great Plains and the state of Montana. Therefore, Pm59 can be used to breed powdery mildew-resistant cultivars in these regions. Xmag1759 is ideal for marker-assisted selection of Pm59 in wheat breeding. 16 Characterisation and mapping of adult plant stripe rust resistance in wheat accession Aus27284 Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is among the most important constraints to global wheat production. The identification and characterisation of new sources of host plant resistance enrich the gene pool and underpin deployment of resistance gene pyramids in new cultivars. Aus27284 exhibited resistance at the adult plant stage against predominant Pst pathotypes and was crossed with a susceptible genotype Avocet S. A recombinant inbred line (RIL) population comprising 121 lines was developed and tested in the field at three locations in 2016 and two in 2017 crop seasons. Monogenic segregation for adult plant stripe rust response was observed among the Aus27284/Avocet S RIL population and the underlying locus was temporarily designated YrAW11 . Bulked-segregant analysis using the Infinium iSelect 90K SNP wheat array placed YrAW11 in chromosome 3B. Kompetitive allele specific PCR (KASP) primers were designed for the linked SNPs and YrAW11 was flanked by KASP_65624 and KASP_53292 (3 cM) proximally and KASP_53113 (4.9 cM) distally. A partial linkage map of the genomic region carrying YrAW11 comprised nine KASP and two SSR markers. The physical position of KASP markers in the pseudomolecule of chromosome 3B placed YrAW11 in the long arm and the location of markers gwm108 and gwm376 in the deletion bin 3BL2-0.22 supported this conclusion. As no other stripe rust resistance locus has been reported in chromosome 3BL, YrAW11 was formally designated Yr80 . Marker KASP_ 53113 was polymorphic among 94% of 81 Australian wheat cultivars used for validation. 17 Systematic analysis of the lysine malonylome in common wheat In total, 342 lysine malonylated sites were identified in 233 proteins. Bioinformatics analysis showed that the frequency of arginine (R) in position + 1 was highest, and a modification motif, KmaR, was identified. The malonylated proteins were located in multiple subcellular compartments, especially in the cytosol (45%) and chloroplast (30%). The identified proteins were found to be involved in diverse pathways, such as carbon metabolism, the Calvin cycle, and the biosynthesis of amino acids, suggesting an important role for lysine malonylation in these processes. Protein interaction network analysis revealed eight highly interconnected clusters of malonylated proteins, and 137 malonylated proteins were mapped to the protein network database. Moreover, five proteins were simultaneously modified by lysine malonylation, acetylation and succinylation, suggesting that these three PTMs may coordinately regulate the function of many proteins in common wheat. 18 The Impact of Phosphorus Supply on Selenium Uptake During Hydroponics Experiment of Winter Wheat ( Triticum aestivum ) in China Selenium (Se) is a necessary trace element for humans and animals, and Se fertilization is an efficient way to increase Se concentration in the edible parts of crops, thus enhance the beneficiary effects of Se in human and animal health. Due to the similarity of physical and chemical properties between phosphate ( ) and selenite ( ), phosphorus (P) supply often significantly impacts the absorption of Se in plants, but little is known about how P supply influences the subcellular distribution and chemical forms of Se. In this study, the effects of P supply on subcellular distribution and chemical forms of Se in winter wheat were investigated in a hydroponic trial with medium Se level (0.1 mg Se L-1). P was applied with three concentrations (0.31, 3.1, and 31 mg P L-1) in the experiment. The results showed that increasing P supply significantly decreased the concentration and accumulation of Se in the roots, stems, and leaves of winter wheat. An increase in P supply significantly inhibited Se accumulation in the root cell wall, but enhanced Se distribution in the organelles and soluble fraction of root cells. These findings suggest that increased P supply inhibited the root-to-shoot transport of Se. An increase in P supply enhanced Se accumulation in the cell wall of plant stems (both apical and axillary stem) and cell organelles of plants leaves, but inhibited Se distribution in the soluble fraction of stems and leaves. This suggests that P supply enhances Se transportation across the cell membrane in shoots of winter wheat. In addition, increased P supply also altered the chemical forms of Se in tissues of winter wheat. These findings will help in understanding of the regulation grain Se accumulation and provide a practical way to enhance Se intake for humans inform Se-enriched grains. 19 Pm21 from Haynaldia villosa Encodes a CC-NBS-LRR that Confers Powdery Mildew Resistance in Wheat 20 Pm21 , encoding a typical CC-NBS-LRR protein, confers broad-spectrum resistance to wheat powdery mildew disease 21 Genetic relationship of diploid wheat ( Triticum spp.) species assessed by SSR markers Genetic diversity of 139 accessions of diploid Triticum species including Triticum urartu , Triticum boeoticum and Triticum monococcum was studied using 11 SSR (simple sequence repeats) markers. A total of 111 alleles with an average of 10 alleles per locus were detected. The polymorphism information content (PIC) of each SSR marker ranged from 0.30 to 0.90 with an average value of 0.62. Among the three Triticum species T. urartu had the highest number of total alleles (Na = 81), private alleles (Npa = 15) and showed higher genetic diversity (Hex = 0.58; PIC = 0.54). The genotypes from Turkey exhibited the highest genetic diversity (PIC = 0.6), while the least diversity was observed among 4 Georgian accessions (PIC = 0.11). Cluster analysis was able to distinguish 139 wheat accessions at the species level. The highest genetic similarity (GS) was noted between T. boeticum and T. monococcum (GS = 0.84), and the lowest between T. urartu and T. monococcum (GS = 0.46). The grouping pattern of the PCoA analysis corresponded with cluster analysis. No significant differences were found in clustering of T. urartu and T. monococcum accessions with respect to their geographic regions, while within T. boeoticum species, accessions from Iran were somewhat associated with their geographical origin and clustered as a close and separate group. The results from our study demonstrated that SSR markers were good enough for further genetic diversity analysis in einkorn wheat species. 22 A new player in race-specific resistance 23 Complex regulation of the TaMyc1 gene expression in wheat grain synthesizing anthocyanin pigments The wheat TaMyc1 gene encodes for transcriptional factor (TF) with bHLH domain. The gene is expressed in purple wheat grains and activates transcription of the anthocyanin biosynthesis structural genes. To reveal the features of TaMyc1 regulation in wheat pericarp transcription start sites (TSS) were identified by 5′ RACE mean and translation efficiency was predicted by in silico methods. Three alternative transcript variants of TaMyc1 differing by 5′ leader sequence only were identified in purple pericarp. The three transcripts are generated from distinct TATA boxes and thereby are differed by TSS. Two transcripts ( TaMyc1a, -b ) have identical initiation AUG codons that lead to the TaMYC1 regulatory protein with bHLH domain. However because of different stability of secondary structures predicted in 5′ leader the two transcripts might be translated with different efficiency. The third transcript is assumed to be not effectively translated. qRT-PCR and colonies counting were applied to assess contribution each of the transcripts to total TaMyc1 gene transcription level. TaMyc1c has the lowest contribution ( ca . 16%), whereas the others two transcripts contribute equally ( ca . 42%) to total TaMyc1 expression level. The role of the tree mRNA isoforms transcribed in one tissue is discussed. 24 Exploiting the Rht portfolio for hybrid wheat breeding Plant height is an important trait in wheat line breeding, but is of even greater importance in hybrid wheat breeding. Here, the height of the female and male parental lines must be controlled and adjusted relative to each other to maximize hybrid seed production. In addition, the height of the resulting hybrids must be fine-tuned to meet the specific requirements of the farmers in the target regions. Moreover, this must be achieved without adversely impacting traits relevant for hybrid seed production. In this study, we explored Reduced height ( Rht ) loci effective in elite wheat and exploited their utilization for hybrid wheat breeding. We performed association mapping in a panel of 1705 wheat hybrids and their 225 parental lines, which besides the Rht - B1 and Rht - D1 loci revealed Rht24 as a major QTL for plant height. Furthermore, we found that the Rht - 1 loci also reduce anther extrusion and thus cross-pollination ability, whereas Rht24 appeared to have no adverse effect on this trait. Our results suggest different haplotypes of the three Rht loci to be used in the female or male pool of a hybrid breeding program, but also show that in general, plant height is a quantitative trait controlled by numerous small-effect QTL. Consequently, marker-assisted selection for the major Rht loci must be complemented by phenotypic selection to achieve the desired height in the female and male parents as well as in the wheat hybrids. 25 Molecular Cytogenetic Characterization of New Wheat— Dasypyrum breviaristatum Introgression Lines for Improving Grain Quality of Wheat As an important relative of wheat ( Triticum aestivum L), Dasypyrum breviaristatum contains novel high molecular weight glutenin subunits (HMW-GSs) encoded by Glu-1Vb genes. We identified new wheat— D. breviaristatum chromosome introgression lines including chromosomes 1Vb and 1VbL.5VbL by fluorescence in situ hybridization (FISH) combined with molecular markers. We found that chromosome changes occurred in the wheat— D. breviaristatum introgression lines and particularly induced the deletion of 5BS terminal repeats and formation of a new type of 5B-7B reciprocal translocation. The results imply that the D. breviaristatum chromosome 1Vb may contain genes which induce chromosomal recombination in wheat background. Ten putative high molecular weight glutenin subunit (HMW-GS) genes from D. breviaristatum and wheat— D. breviaristatum introgression lines were isolated. The lengths of the HMW-GS genes in Dasypyrum were significantly shorter than typical HMW-GS of common wheat. A new y-type HMW-GS gene, named Glu-Vb1y , was characterized in wheat— D. breviaristatum 1Vb introgression lines. The new wheat— D. breviaristatum germplasm displayed reduced plant height, increased tillers and superior grain protein and gluten contents, improved gluten performance index. The results showed considerable potential for utilization of D. breviaristatum chromosome 1Vb segments in future wheat improvement. 26 Wheat ear counting in-field conditions: high throughput and low-cost approach using RGB images The results demonstrate high success rate (higher than 90%) between the algorithm counts and the manual (image-based) ear counts, and precision, with a low standard deviation (around 5%). The relationships between algorithm ear counts and grain yield was also significant and greater than the correlation with manual (field-based) ear counts. In this approach, results demonstrate that automatic ear counting performed on data captured around anthesis correlated better with grain yield than with images captured at later stages when the low performance of ear counting at late grain filling stages was associated with the loss of contrast between canopy and ears. 27 Dynamics of Floret Initiation/Death Determining Spike Fertility in Wheat as Affected by Ppd Genes under Field Conditions As wheat yield is linearly related to grain number, understanding the physiological determinants of the number of fertile florets based on floret development dynamics due to the role of the particular genes is relevant. The effects of photoperiod genes on dynamics of floret development are largely ignored. Field experiments were carried out to (i) characterize the dynamics of floret primordia initiation and degeneration and (ii) to determine which are the most critical traits of such dynamics in establishing genotypic differences in the number of fertile florets at anthesis in near isogenic lines (NILs) carrying photoperiod insensitive alleles. Results varied in magnitude between the two growing seasons, but in general introgression of Ppd-1a alleles reduced the number of fertile florets. The actual effect was affected not only by the genome and the doses but also by the source of the alleles. Differences in the number of fertile florets were mainly explained by differences in the floret generation/degeneration dynamics and in most cases associated with floret survival. Manipulating photoperiod insensitivity, unquestionably useful for changing flowering time, may reduce spike fertility but much less than proportionally to the change in duration of development, as the insensitivity alleles did increase the rate of floret development. 28 Rht18 Semi-Dwarfism in Wheat is Due to Increased Expression of GA 2-oxidaseA9 and Lower GA Content Semi-dwarfing genes have contributed to major yield increases in crop species by reducing height, improving lodging resistance, and partitioning more assimilates to grain growth. In wheat, the Rht18 semi-dwarfing gene was identified and deployed in durum wheat before it was transferred into bread wheat where it was shown to have agronomic potential. Rht18, a dominant and gibberellin (GA) responsive mutant, is genetically and functionally distinct from the widely used GA insensitive semi-dwarfing genes Rht-B1b and Rht-D1b. In this study, the Rht18 gene was identified by mutagenizing the semi-dwarf durum cultivar Icaro (Rht18) and generating mutants with a range of tall phenotypes. Isolating and sequencing chromosome 6A of these 'overgrowth' mutants showed that they contained independent mutations in the coding region of GA2oxA9, a gene predicted to encode a GA 2-oxidase that metabolises GA biosynthetic intermediates into inactive products, thereby lowering the amount of bioactive GA (GA1). Functional analysis of the GA2oxA9 protein demonstrated conversion of the intermediate GA12 to the inactive metabolite GA110. Analysis of transcript abundance and GA content showed that the expression of GA 2-oxA9 was higher, and the GA content lower, in Rht18 compared with its tall parent. These data indicate that the increased expression of GA2oxA9 in Rht18 results in a reduction of both bioactive GA content and plant height. This study describes a height reducing mechanism that can generate new genetic diversity for semi-dwarfism in wheat by combining increased expression with mutations of specific amino acid residues in the GA2oxA9 gene. 29 Photosynthetic and ascorbate-glutathione metabolism in the flag leaves as compared to spikes under drought stress of winter wheat (Triticum aestivum L.). Ascorbate-glutathione (ASA-GSH) cycle is a major pathway of H2O2 scavenging and an effective mechanism of detoxification in plants. The differences in photosynthesis, chlorophyll content (Chl), relative water content (RWC), antioxidants and antioxidative enzyme activities involved in ASA-GSH metabolism were measured between the flag leaves and spike bracts (glumes and lemmas) during grain filling under drought stress. The expression of APX1, GRC1, DHAR, MDHAR, GPX1, and GS3 in ASA-GSH cycle was also measured. Compared with the flag leaves, the spike bracts exhibited stable net photosynthetic rate (PN) and chlorophyll content (Chl), a lower accumulation of reactive oxygen species (ROS), and more enhanced percentages of antioxidant enzyme activities and key enzymes gene transcription levels involved in ASA-GSH metabolism during the grain-filling stage under drought conditions. This could be the reasonable explanation for the more stable photosynthetic capacity in spikes, and the glumes and lemmas senesced later than the flag leaves at the late grain-filling stage. Also, the function of ASA-GSH cycle could not be ignored in alleviating oxidative damage by scavenging more excess ROS in spikes under drought stress. 30 Proteomic analysis of melatonin-mediated osmotic tolerance by improving energy metabolism and autophagy in wheat (Triticum aestivum L.). Melatonin is known to play multiple roles in plant abiotic stress tolerance. However, its role in wheat has been rarely investigated. In this study, 25% polyethylene glycol 6000 (PEG 6000) was used to simulate osmotic stress, and wheat seeds and seedlings were treated with different concentrations of melatonin under PEG stress. Isobaric tag for relative and absolute quantification (iTRAQ)-based proteomic techniques were used to identify the differentially accumulated proteins from melatonin-treated and non-treated seedlings. Seeding priming with melatonin significantly increased the germination rate, coleoptile length, and primary root number of wheat under PEG stress, as well as the fresh weight, dry weight, and water content of wheat seedlings. Under PEG stress, melatonin significantly improved reactive oxygen species homeostasis, as revealed by lower H2O2 and O 2 · content; and the expression of antioxidant enzymes at the transcription and translation levels was increased. Melatonin maintained seedling growth by improving photosynthetic rates and instantaneous and intrinsic water use efficiencies, as well as carbon fixation and starch synthesis at the protein level. Melatonin treatment significantly affected the expression of glycolytic proteins, including fructose-1,6-bisphosphate aldolase, hexokinase, glyceraldehyde-3-phosphate dehydrogenase, and enolase, and remarkably increased the expression of the nicotinamide adenine dinucleotide transporter and nicotinamide adenine dinucleotide binding protein, thereby indirectly modulating electron transport in the respiratory chain. This indicated that melatonin improved energy production in PEG-stressed seedlings. Further, melatonin played a regulatory role in autophagy, protease expression, and ubiquitin-mediated protein degradation by significantly upregulating rab-related protein, fused signal recognition particle receptor, aspartyl protease, serine protease, ubiquitin-fold modifier 1, and ubiquitin at the mRNA or protein level. These findings suggested that melatonin might activate a metabolic cascade related to autophagy under PEG stress in wheat seedlings. 31 Analysis of the functions of TaGW2 homoeologs in wheat grain weight and protein content traits GW2 is emerging as a key genetic determinant of grain weight in cereal crops, and has three homoeologs (TaGW2-A1, -B1 and -D1) in hexaploid common wheat (Triticum aestivum L.). Here, by analyzing the gene editing mutants lacking one (B1 or D1), two (B1 and D1) or all three (A1, B1 and D1) homoeologs of TaGW2, several insights are gained into the functions of TaGW2-B1 and -D1 in common wheat grain traits. First, both TaGW2-B1 and -D1 affect thousand grain weight (TGW) through influencing grain width and length, but the effect conferred by TaGW2-B1 is stronger than that by TaGW2-D1. Second, there exists functional interaction between TaGW2 homoeologs because the TGW increase shown by a double mutant (lacking B1 and D1) was substantially larger than that by their single mutants. Third, both TaGW2-B1 and -D1 modulate cell number and length in the outer pericarp of developing grains, with TaGW2-B1 being more potent. Finally, TaGW2 homoeologs also affect grain protein content (GPC) as this parameter was generally increased in the mutants, especially in the lines lacking two or three homoeologs. Consistent with this finding, two wheat end-use quality related parameters, flour protein content and gluten strength, were considerably elevated in the mutants. Collectively, our data shed light on functional difference and additive interaction of TaGW2 homoeologs in the genetic control of grain weight and protein content traits in common wheat, which may accelerate further research on this important gene and its application in wheat improvement. This article is protected by copyright. All rights reserved. 32 Dynamics of Leaf and Spikelet Primordia Initiation in Wheat as Affected by Ppd-1a Alleles under Field Conditions Wheat adaptation is affected by Ppd genes, but the role of these alleles on the rates of leaf and spikelet initiation has not been properly analysed. Twelve near isogenic lines (NILs) combining Ppd-1a alleles from different donors introgressed in A, B and/or D genomes were tested under field conditions during two growing seasons together with the wild type, Paragon. Leaf initiation rate was unaffected by Ppd-1a alleles so final leaf number (FLN) was reduced in parallel with reductions in the duration of vegetative phase. Spikelet primordia initiation was accelerated and consequently the effect on spikelets per spike was less than proportional to the effect on the duration of spikelet initiation. The magnitude of these effects on spikelet-plastochron depended on the doses of Ppd-1 homoeoalleles and the specific insensitivity alleles carried. Double ridge was consistently later than floral initiation but the difference between them was not affected by Ppd-1a alleles. These findings open potential for selecting best combinations from the Ppd-1 homoeoallelic series for manipulating adaptation considering particular effects on spikelet number. 33 Molecular Mapping of Fusarium Head Blight Resistance in the Spring Wheat Line ND2710. ND2710 is a hard red spring wheat line with a very high level of resistance to Fusarium head blight (FHB). It was selected from the progeny of a cross between ND2603 (an advanced breeding line derived from the Sumai 3/Wheaton cross) and Grandin (a spring wheat cultivar). The FHB resistance of ND2710 is presumably derived from Sumai 3 since the other parents Grandin and Wheaton are very susceptible to FHB. To identify and map the quantitative trait loci (QTL) for FHB resistance in ND2710, we developed a mapping population consisting of 233 recombinant inbred lines (RILs) from the cross between ND2710 and the spring wheat cultivar 'Bobwhite'. These RILs along with their parents and checks were evaluated for reactions to FHB in three greenhouse experiments and one field experiment during 2013 to 2014. The population was also genotyped with the wheat 90K SNP iSelect assay, and a genetic linkage map was developed with 1373 non-co-segregating SNP markers, which were distributed on all 21 wheat chromosomes spanning 914.98 cM of genetic distance. Genetic analyses using both phenotypic and genotypic data identified one major QTL (Qfhb.ndwp-3B) on the short arm of chromosome 3B, explaining up to 20% of the phenotypic variation in all experiments, and three minor QTL (Qfhb.ndwp-6B, Qfhb.ndwp-2A, and Qfhb.ndwp-6A) on 6B, 2A, and 6A, respectively. The three minor QTL explained 5 to 12% phenotypic variation in at least two experiments, except for Qfhb.ndwp-2A, which was only detected in the field experiment. Qfhb.ndwp-3B and Qfhb.ndwp-6B were mapped to the genomic regions containing Fhb1 and Fhb2, respectively, confirming that they were originated from Sumai 3. The additive effect of the major and minor QTL may contribute to the high level of FHB resistance in ND2710. The SNP markers closely linked to the FHB resistance QTL will be useful for marker-assisted selection of FHB resistance in wheat breeding programs. 34 Characterization of an Integrated Active Glu-1Ay Allele in Common Wheat from Wild Emmer and Its Potential Role in Flour Improvement. Glu-1Ay , one of six genes encoding a high molecular weight glutenin subunit (HMW-GS), is frequently silenced in hexaploid common wheat. Here, an active allele of Glu-1Ay was integrated from wild emmer wheat ( Triticum turgidum ssp. dicoccoides ) accession D97 into the common wheat ( Triticum aestivum ) cultivar Chuannong 16 via the repeated self-fertilization of the pentaploid interspecific hybrid, culminating in the selection of a line TaAy7-40 shown to express the wild emmer Glu-1Ay allele. The open reading frame of this allele was a 1830 bp long sequence, demonstrated by its heterologous expression in Escherichia coli to encode a 608-residue polypeptide. Its nucleotide sequence was 99.2% identical to that of the sequence within the wild emmer parent. The TaAy7-40 introgression line containing the active Glu-1Ay allele showed higher protein content, higher sodium dodecyl sulfate (SDS) sedimentation value, higher content of wet gluten in the flour, higher grain weight, and bigger grain size than Chuannong 16. The end-use quality parameters of the TaAy7-40 were superior to those of the medium gluten common wheat cultivars Mianmai 37 and Neimai 9. Thus, the active Glu-1Ay allele might be of potential value in breeding programs designed to improve wheat flour quality. 35 Systematic analysis of the lysine malonylome in common wheat In total, 342 lysine malonylated sites were identified in 233 proteins. Bioinformatics analysis showed that the frequency of arginine (R) in position + 1 was highest, and a modification motif, KmaR, was identified. The malonylated proteins were located in multiple subcellular compartments, especially in the cytosol (45%) and chloroplast (30%). The identified proteins were found to be involved in diverse pathways, such as carbon metabolism, the Calvin cycle, and the biosynthesis of amino acids, suggesting an important role for lysine malonylation in these processes. Protein interaction network analysis revealed eight highly interconnected clusters of malonylated proteins, and 137 malonylated proteins were mapped to the protein network database. Moreover, five proteins were simultaneously modified by lysine malonylation, acetylation and succinylation, suggesting that these three PTMs may coordinately regulate the function of many proteins in common wheat. 36 Genome-Wide Identification and Characterization of Long Non-Coding RNA in Wheat Roots in Response to Ca2+ Channel Blocker It remains unclear whether plant lncRNAs are responsive to Ca2+-channel blocking. When using the Ca2+-channel blocker, LaCl3, to treat germinated wheat seeds for 24 h, we found that both root length and mitosis were inhibited in the LaCl3-treated groups. The effect of the Ca2+-channel blocker was verified in three ways: a cytdecrease detected using Fluo-3/AM staining, a decrease in the Ca content measured using inductively coupled plasma mass spectrometry, and an inhibition of Ca2+influx detected using Non-invasive Micro-test Technology. Genome-wide high throughput RNA-seq and bioinformatical methods were used to identify lncRNAs, and found 177 differentially expressed lncRNAs that might be in responsive to Ca2+-channel blocking. Among these, 108 were up-regulated and 69 were down-regulated. The validity of identified lncRNAs data from RNA-seq was verified using qPCR. GO and KEGG analysis indicated that a number of lncRNAs might be involved in diverse biological processes upon Ca2+-channel blocking. Further GO analysis showed that 23 lncRNAs might play roles as transcription factor (TF); Moreover, eight lncRNAs might participate in cell cycle regulation, and their relative expressions were detected using qPCR. This study also provides diverse data on wheat lncRNAs that can deepen our understanding of the function and regulatory mechanism of Ca2+-channel blocking in plants. 36 First report of Fusarium pseudograminearum causing crown rot of wheat in Europe
\0 2018年第11周小麦文献推荐（3.17） 3/ 17 本期作者：麦萌 今天一早在朋友圈看到有人发了一张秀恩爱截图，我拿给胖丫看。胖丫不屑的说，这都是多老的段子了，还拿来秀。 好吧，话说到这份上，我只能转身离开了。 Hi，大家好!我是麦萌，周末愉快！大家的基金都已经交了吧。使用下面的网站可以搜索公众号里的文章，重要的是还可以指定要搜索的公众号，所以赶紧试一试吧。http://search.xmt.cn/#/wxsearch。 现在就让我们来盘点下过去一周与小麦有关的文献更新。 1 Genetic Diversity and Population Structure of F3:6 Nebraska Winter Wheat Genotypes Using Genotyping-By-Sequencing https://doi.org/10.3389/fgene.2018.00076 The availability of information on the genetic diversity and population structure in wheat ( Triticum aestivum L.) breeding lines will help wheat breeders to better use their genetic resources and manage genetic variation in their breeding program. The recent advances in sequencing technology provide the opportunity to identify tens or hundreds of thousands of single nucleotide polymorphism (SNPs) in large genome species (e.g., wheat). These SNPs can be utilized for understanding genetic diversity and performing genome wide association studies (GWAS) for complex traits. In this study, the genetic diversity and population structure were investigated in a set of 230 genotypes (F3:6) derived from various crosses as a prerequisite for GWAS and genomic selection. Genotyping-by-sequencing provided 25,566 high-quality SNPs. The polymorphism information content (PIC) across chromosomes ranged from 0.09 to 0.37 with an average of 0.23. The distribution of SNPs markers on the 21 chromosomes ranged from 319 on chromosome 3D to 2,370 on chromosome 3B. The analysis of population structure revealed three subpopulations (G1, G2, and G3). Analysis of molecular variance identified 8% variance among and 92% within subpopulations. Of the three subpopulations, G2 had the highest level of genetic diversity based on three genetic diversity indices: Shannon’s information index ( I ) = 0.494, diversity index ( h ) = 0.328 and unbiased diversity index (uh) = 0.331, while G3 had lowest level of genetic diversity ( I = 0.348, h = 0.226 and uh = 0.236). This high genetic diversity identified among the subpopulations can be used to develop new wheat cultivars. 2 Plant and Floret Growth at Distinct Developmental Stages During the Stem Elongation Phase in Wheat https://doi.org/10.3389/fpls.2018.00330 Floret development is critical for grain setting in wheat ( Triticum aestivum ), but more than 50% of grain yield potential (based on the maximum number of floret primordia) is lost during the stem elongation phase (SEP, from the terminal spikelet stage to anthesis). Dynamic plant (e.g., leaf area, plant height) and floret (e.g., anther and ovary size) growth and its connection with grain yield traits (e.g., grain number and width) are not clearly understood. In this study, for the first time, we dissected the SEP into seven stages to investigate plant (first experiment) and floret (second experiment) growth in greenhouse- and field-grown wheat. In the first experiment, the values of various plant growth trait indices at different stages were generally consistent between field and greenhouse and were independent of the environment. However, at specific stages, some traits significantly differed between the two environments. In the second experiment, phenotypic and genotypic similarity analysis revealed that grain number and size corresponded closely to ovary size at anthesis, suggesting that ovary size is strongly associated with grain number and size. Moreover, principal component analysis (PCA) showed that the top six principal components PCs explained 99.13, 98.61, 98.41, 98.35, and 97.93% of the total phenotypic variation at the green anther, yellow anther, tipping, heading, and anthesis stages, respectively. The cumulative variance explained by the first PC decreased with floret growth, with the highest value detected at the green anther stage (88.8%) and the lowest at the anthesis (50.09%). Finally, ovary size at anthesis was greater in wheat accessions with early release years than in accessions with late release years, and anther/ovary size shared closer connections with grain number/size traits at the late vs. early stages of floral development. Our findings shed light on the dynamic changes in plant and floret growth-related traits in wheat and the effects of the environment on these traits. 3 Utilization of a Wheat55K SNP Array for Mapping of Major QTL for Temporal Expression of the Tiller Number https://doi.org/10.3389/fpls.2018.00333 Maximum tiller number and productive tiller number are important traits for wheat grain yield, but research involving the temporal expression of tiller number at different quantitative trait loci (QTL) levels is limited. In the present study, a population set of 371 recombined inbred lines derived from a cross between Chuan-Nong18 and T1208 was used to construct a high-density genetic map using a Wheat55K SNP Array and to perform dynamic QTL analysis of the tiller number at four growth stages. A high-density genetic map containing 11,583 SNP markers and 59 SSR markers that spanned 4,513.95 cM and was distributed across 21 wheat chromosomes was constructed. A total of 28 single environmental QTL were identified in the recombined inbred lines population, and among these, seven QTL were stable and used for multi-environmental and dynamic analysis. These QTL were mapped to chromosomes 2D, 4A, 4D, 5A, 5D, and 7D, respectively. Each QTL explained 1.63–21.22% of the observed phenotypic variation, with an additive effect from -20.51 to 11.59. Dynamic analysis showed that cqTN-2D.2 can be detected at four growth stages of tillering, explaining 4.92–17.16% of the observed phenotypic variations and spanning 13.71 Mb ( AX-109283238-AX-110544009 : 82189047-95895626) according to the physical location of the flanking markers. The effects of the stable QTL were validated in the recombined inbred lines population, and the beneficial alleles could be utilized in future marker-assisted selection. Several candidate genes for MTN and PTN were predicted. The results provide a better understanding of the QTL selectively expressing the control of tiller number and will facilitate future map-based cloning. 9.17% SNP markers showed best hits to the Chinese Spring contigs. It was indicated that Wheat55K Array was efficient and valid to construct a high-density wheat genetic map. 4 The Role of Hydrogen Peroxide in Mediating the Mechanical Wounding-Induced Freezing Tolerance in Wheat https://doi.org/10.3389/fpls.2018.00327 Systemic wound response (SWR), a well-characterized systemic signaling response, plays crucial roles in plant defense responses. Progress in understanding of the SWR in abiotic stress has also been aided by the researchers. However, the function of SWR in freezing stress remains elusive. In this study, we showed that local mild mechanical wounding enhanced freezing tolerance in newly occurred systemic leaves of wheat plants ( Triticum aestivum L.). Wounding significantly increased the maximal photochemical efficiency of photosystem II, net photosynthetic rate, and the activities of the antioxidant enzymes under freezing stress. Wounding also alleviated freezing-induced chlorophyll decomposition, electrolyte leakage, water lose, and membrane peroxidation. In addition, wounding-induced freezing stress mitigation was closely associated with the ratio between reduced glutathione (GSH) and oxidized glutathione (GSSG), and the ratio between ascorbate (AsA) and dehydroascorbate (DHA), as well as the contents of total soluble sugars and free amino acids. Importantly, pharmacological study showed that wounding-induced freezing tolerance was substantially arrested by pretreatment of wheat leaves with the scavenger of hydrogen peroxide (H2O2) or the inhibitor of NADPH oxidase (RBOH). These results support the hypothesis that local mechanical wounding-induced SWR in newly occurred leaves is largely attributed to RBOH-dependent H2O2production, which may subsequently induce freezing tolerance in wheat plants. This mechanism may have a potential application to reduce the yield losses of wheat under late spring freezing conditions. 5 Identification and Characterization of Wheat Yellow Striate Virus, a Novel Leafhopper-Transmitted Nucleorhabdovirus Infecting Wheat https://doi.org/10.3389/fmicb.2018.00468 A new wheat viral disease was found in China. Bullet-shaped viral particles within the nucleus of the infected wheat leave cells, which possessed 180–210 nm length and 35–40 nm width, were observed under transmission electron microscopy. A putative wheat-infecting rhabdovirus vectored by the leafhopper Psammotettix alienus was identified and tentatively named wheat yellow striate virus (WYSV). The full-length nucleotide sequence of WYSV was determined using transcriptome sequencing and RACE analysis of both wheat samples and leafhoppers P. alienus . The negative-sense RNA genome of WYSV contains 14,486 nucleotides (nt) and seven open reading frames (ORFs) encode deduced proteins in the order N-P-P3-M-P6-G-L on the antisense strand. In addition, WYSV genome has a 76-nt 3′ leader RNA and a 258-nt 5′ trailer, and the ORFs are separated by conserved intergenic sequences. The entire genome sequence shares 58.1 and 57.7% nucleotide sequence identity with two strains of rice yellow stunt virus (RYSV-A and RYSV-B) genomes, respectively. The highest amino acid sequence identity was 63.8% between the L proteins of the WYSV and RYSV-B, but the lowest was 29.5% between the P6 proteins of these viruses. Phylogenetic analysis firmly established WYSV as a new member of the genus Nucleorhabdovirus . Collectively, this study provided evidence that WYSV is likely the first nucleorhabdovirus described infecting wheat via leafhopper P. alienus transmission. 6 Genetic dissection of interactions between wheat flour starch and its components in two populations using two QTL mapping methods https://doi.org/10.1007/s11032-018-0797-y Starch content and its components are important for determining wheat end-use quality and yield. However, little information is available about their interactions at the QTL/gene level in more than one population using different QTL mapping methods. Therefore, to dissect these interactions, two mapping populations from two locations over 2 years were used. The QTLs for the populations were analyzed by unconditional and conditional QTL mapping by two different analysis methods. In the two populations, there were a total of 24 unconditional additive QTLs detected for flour amylose (FAMS), flour amylopectin (FAMP), flour total starch (FTSC), and the ratio of FAMS to FAMP using ICIMapping4.1 methods, but 26 unconditional QTLs were found using QTLNetwork2.0 methods. Of these QTLs, 10 stable major additive QTLs were identified in more than one environment, mainly distributed on chromosomes 3B, 4A, 5A, and 7D. The maximum percentage of phenotypic variance explained (PVE) reached 54.31%. Two new unconditional major additive QTLs on chromosome 3B ( Qftsc3B and Qfamp3B ) were found. A total of 23 and 19 conditional additive QTLs were identified in the two populations using two different methods, respectively. Of which, eight and six stable major conditional QTLs were detected on chromosomes 3B, 4A, and 7D, respectively. New repressed QTLs were identified, such as Qftsc / fams5B-1 and Qftsc/fams5B-2 . There were 20 epistatic unconditional and 15 conditional QTLs detected. In all, important QTLs on chromosomes 3B, 4A, and 7A were found in both populations. However, the number of important QTLs in the special recombinant inbred line (RIL) population was higher than that in the double haploid (DH) population, especially on chromosomes 7D and 5B. Moreover, the QTLs on chromosomes 4A, 7A, and 7D were close to the Wx-1 loci in the RIL population. These indicated better results can be obtained by a special population to target traits than by a common population. The important QTLs on key chromosomes can always be detected no matter what kinds of populations are used, such as the QTLs on chromosome 4A. In addition, QTL clusters were found on chromosomes 4A, 3B, 7A, 7D, and 5A in the two populations, indicating these chromosome regions were very important for starch biosynthesis. 7 Zinc-biofortified seeds improved seedling growth under zinc deficiency and drought stress in durum wheat 10.1002/jpln.201800014 High zinc (Zn) concentration of seeds has beneficial effects both on seed vigor and human nutrition. This study investigated the effect of Zn biofortification on growth of young durum wheat ( Triticum durum cv. Yelken) seedlings under varied Zn and water supply. The seeds differing in Zn concentrations were obtained by spraying ZnSO4 to durum wheat plants at different rates under field conditions. Three groups of seeds were obtained with the following Zn concentrations: 9, 20, and 50 mg Zn kg−1. The seeds differing in Zn were tested for germination rate, seedling height, shoot dry matter production, and shoot Zn concentration under limited and well irrigated conditions in a Zn-deficient soil with and without Zn application. In an additional experiment carried out in solution culture, root and shoot growth and superoxide dismutase activity (SOD) of seedlings were studied under low and adequate Zn supply. Low seed Zn concentration resulted in significant decreases in seedling height both in Zn-deficient and sufficient soil, but more clearly under water-limited soil condition. Decrease in seed germination due to low seed Zn was also more evident under limited water supply. Increasing seed Zn concentration significantly restored impairments in seedling development. Drought-induced decrease in seedling growth at a given seed Zn concentration was much higher when soil was Zn-deficient. Increasing seed Zn concentration also significantly improved SOD activity in seedlings grown under low Zn supply, but not under adequate Zn supply. The results suggest that using Zn-biofortified seeds assures better seed vigor and seedling growth, particularly when Zn and water are limited in the growth medium. The role of a higher antioxidative potential ( i.e ., higher SOD activity) is discussed as a possible major factor in better germination and development of seedlings resulting from Zn-biofortified seeds. 8 QTL mapping for seedling morphology under drought stress in wheat cross synthetic (W7984)/Opata https://doi.org/10.1017/S1479262118000023 Drought stress ‘particularly at seedling stage’ causes morpho-physiological differences in wheat which are crucial for its survival and adaptability. In the present study, 209 recombinant inbred lines (RILs) from synthetic wheat (W7984)× ‘Opata’ (also known as SynOpRIL) population were investigated under well-watered and water-limited conditions to identify quantitative trait loci (QTL) for morphological traits at seedling stage. Analysis of variance revealed significant differences (P 0.01) among RILs, and water treatments for all traits with moderate to high broad sense heritability. Pearson's coefficient of correlation revealed positive correlation among all traits except dry root weight that showed poor correlation with fresh shoot weight (FSW) under water-limited conditions. A high-density linkage map was constructed with 2639 genotyping-by-sequencing markers and covering 5047 cM with an average marker density of 2 markers/cM. Composite interval mapping identified 16 QTL distributed over nine chromosomes, of which six were identified under well-watered and 10 in water-limited conditions. These QTL explained from 4 to 59% of the phenotypic variance. Six QTL were identified on chromosome 7B; three for shoot length under water-limited conditions (QSL.nust-7B) at 64, 104 and 221 cM, two for fresh root weight (QFRW.nust-7B) at 124 and 128 cM, and one for root length (QRL.nust-7B) at 122 cM positions. QFSW.nust-7B appeared to be the most significant QTL explaining 59% of the phenotypic variance and also associated with FSW at well-watered conditions. These QTL could serve as target regions for candidate gene discovery and marker-assisted selection in wheat breeding. 9 The wheat multidomain cystatin TaMDC1 displays antifungal, antibacterial, and insecticidal activities in planta Cystatins are the polypeptides with cysteine proteinase inhibitory activities. Plant cystatins or phytocystatins are known to contribute to plant resistance against insect pests. Recently, increasing data proved that some of the phytocystatins also have antifungal activities in vitro. Here, we functionally characterized a wheat multidomain cystatin, TaMDC1, using in planta assays. Expression of TaMDC1 in wheat seedlings is up-regulated in response to methyl jasmonate and salicylic acid, indicating that TaMDC1 is involved in biotic stress responses mediated by these plant hormones. The TaMDC1 cDNA was integrated in tomato genome and expressed under cauliflower mosaic virus 35S promoter. Four transgenic plants that show high level of the transgene expression were selected by RNA gel blot and immunoblot analysis and utilized to assess biotic stress resistance against the bacterial pathogen Pseudomonas syringae , the fungal pathogens Botrytis cinerea and Alternaria alternata , and the insect pest Colorado potato beetle (CPB, Leptinotarsa decemlineata ). Detached leaf inoculation assays revealed that the tomato plants expressing TaMDC1 showed high levels of resistance against P. syringae and A. alternata , and elevated tolerance against B. cinerea . Sustenance of L. decemlineata larvae to the transgenic plants demonstrated inhibition of CPB larvae growth. Inhibitory activity of TaMDC1 against selected pathogens was also demonstrated by in vitro assays with total protein extracted from transgenic tomato plants. Taken together, the presented data suggest that TaMDC1 is involved in a broad spectrum biotic stress resistance in planta. 10 Identification and validation of a major chromosome region for high grain number per spike under meiotic stage water stress in wheat ( Triticum aestivum L.) https://doi.org/10.1371/journal.pone.0194075 Grain number is a major trait for wheat yield under dryland farming. An International Triticeae Mapping Initiative (ITMI) mapping population comprising 105 recombinant inbred lines (RIL) developed from a cross between a Synthetic hexaploid wheat ( Triticum aestivum ) ‘W7984’ and a spring wheat variety ‘Opata M85’ was used to identify quantitative trait loci (QTL) associated with grain number per spike under two treatment conditions, normal watering and water stress during meiosis. Two major QTL for grain number per spike on the main stem Q . Gnu . uwa-5A-1 and Q . Gnu . uwa-5A-2 with phenotypic variations of 25.71% and 24.93%, respectively, were detected on the long arm of chromosome 5A when plants were exposed to water stress during meiosis. One QTL ( Q . Gnu . uwa-2A ) with a LOD score of 2.8 was detected on the long arm of chromosome 2A under normal watering condition. The alleles associated with higher grain number per spike under different treatment conditions came from the Synthetic W7984 parent. Two populations developed from crosses Synthetic W7984 × Lang and Synthetic W7984 × Westonia were used to validate the identified QTL under water stress during meiosis. SSR markers Xbarc230 and Xbarc319 linked with the identified QTL on chromosome 5AL were validated in the two F2:4 segregating populations. These closely linked SSR markers could potentially be utilized in marker-assisted selection to reduce yield loss in regions where water stress during meiosis occurs frequently. The identified QTL can be incorporated into elite lines / cultivars to improve wheat grain yield. 11 The impacts of phosphorus deficiency on the photosynthetic electron transport chain https://doi.org/10.1104/pp.17.01624 Phosphorus (P) is an essential macronutrient, and P deficiency limits plant productivity. Recent work showed that P deficiency affects electron transport to photosystem I (PSI), but the underlying mechanisms are unknown. Here, we present a comprehensive biological model describing how P deficiency disrupts the photosynthetic machinery and the electron transport chain through a series of sequential events in barley (Hordeum vulgare). Phosphorus deficiency reduces the orthophosphate (Pi) concentration in the chloroplast stroma to levels that inhibit ATP synthase activity. Consequently, protons accumulate in the thylakoids and cause lumen acidification, which inhibits linear electron flow. Limited plastoquinol (PQH2) oxidation retards electron transport to the cytochrome (Cyt) b6f complex, yet the electron transfer rate of PSI is increased under steady-state growth light and is limited under high light conditions. Under P deficiency, the enhanced electron flow through PSI increases the levels of NADPH, whereas ATP production remains restricted and hence reduces CO2 fixation. In parallel, lumen acidification activates the qE component of the non-photochemical quenching (NPQ) mechanism and prevents over-excitation of photosystem II (PSII) and damage to the leaf tissue. Consequently, plants can be severely affected by P deficiency for weeks without displaying any visual leaf symptoms. All of the processes in the photosynthetic machinery influenced by P deficiency appear to be fully reversible and can be restored in less than 60 min after resupply of Pi to the leaf tissue. 12 Differential Expression Profiling of Microspores During the Early Stages of Isolated Microspore Culture Using the Responsive Barley Cultivar Gobernadora https://doi.org/10.1534/g3.118.200208 In barley, it is possible to induce embryogenesis in the haploid and uninucleate microspore to obtain a diploid plant that is perfectly homozygous. To change developmental fates in this fashion, microspores need to engage in cellular de-differentiation, interrupting the pollen formation, and restore totipotency prior to engaging in embryogenesis. In this work, we used the barley cultivar Gobernadora to characterize the transcriptome of microspores prior to (day 0) and immediately after (days 2 and 5) the application of a stress pretreatment. A deep RNA-seq analysis revealed that microspores at these three time points exhibit a transcriptome of ~14k genes, ~90% of which were shared. An expression analysis identified a total of 3,382 differentially expressed genes (DEGs); of these, 2,155 and 2,281 DEGs were respectively identified when contrasting expression at days 0 and 2 and at days 2 and 5. These define 8 expression profiles in which DEGs share a common up- or down-regulation at these time points. Up-regulation of numerous glutathione S-transferase and heat shock protein genes as well as down-regulation of ribosomal subunit protein genes was observed between days 0 and 2. The transition from microspores to developing embryos (days 2 vs 5) was marked by the induction of transcription factor genes known to play important roles in early embryogenesis, numerous genes involved in hormone biosynthesis and plant hormonal signal transduction in addition to genes involved in secondary metabolism. This work sheds light on transcriptional changes accompanying an important developmental shift and provides candidate biomarkers for embryogenesis in barley. 13 Targeted resequencing reveals genomic signatures of barley domestication DOI: 10.1111/nph.15077 Barley ( Hordeum vulgare ) is an established model to study domestication of the Fertile Crescent cereals. Recent molecular data suggested that domesticated barley genomes consist of the ancestral blocks descending from multiple wild barley populations. However, the relationship between the mosaic ancestry patterns and the process of domestication itself remained unclear. To address this knowledge gap, we identified candidate domestication genes using selection scans based on targeted resequencing of 433 wild and domesticated barley accessions. We conducted phylogenetic, population structure, and ancestry analyses to investigate the origin of the domesticated barley haplotypes separately at the neutral and candidate domestication loci. We discovered multiple selective sweeps that occurred on all barley chromosomes during domestication in the background of several ancestral wild populations. The ancestry analyses demonstrated that, although the ancestral blocks of the domesticated barley genomes were descended from all over the Fertile Crescent, the candidate domestication loci originated specifically in its eastern and western parts. These findings provided the first molecular evidence implicating multiple wild or protodomesticated lineages in the process of barley domestication initiated in the Levantine and Zagros clusters of the origin of agriculture. 14 Transcriptome Analysis of a Premature Leaf Senescence Mutant of Common Wheat ( Triticum aestivum L.) https://doi.org/10.3390/ijms19030782 Leaf senescence is an important agronomic trait that affects both crop yield and quality. In this study, we characterized a premature leaf senescence mutant of wheat ( Triticum aestivum L.) obtained by ethylmethane sulfonate (EMS) mutagenesis, named m68 . Genetic analysis showed that the leaf senescence phenotype of m68 is controlled by a single recessive nuclear gene. We compared the transcriptome of wheat leaves between the wild type (WT) and the m68 mutant at four time points. Differentially expressed gene (DEG) analysis revealed many genes that were closely related to senescence genes. Gene Ontology (GO) enrichment analysis suggested that transcription factors and protein transport genes might function in the beginning of leaf senescence, while genes that were associated with chlorophyll and carbon metabolism might function in the later stage. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the genes that are involved in plant hormone signal transduction were significantly enriched. Through expression pattern clustering of DEGs, we identified 1012 genes that were induced during senescence, and we found that the WRKY family and zinc finger transcription factors might be more important than other transcription factors in the early stage of leaf senescence. These results will not only support further gene cloning and functional analysis of m68 , but also facilitate the study of leaf senescence in wheat. 15 Transcriptome Analysis Identifies a 140 kb Region of Chromosome 3B Containing Genes Specific to Fusarium Head Blight Resistance in Wheat https://doi.org/10.3390/ijms19030852 Fusarium head blight (FHB), mainly caused by Fusarium graminearum , is one of the most destructive fungal diseases of wheat ( Triticum aestivum L.). Because of the quantitative nature of FHB resistance, its mechanism is poorly understood. We conducted a comparative transcriptome analysis to identify genes that are differentially expressed in FHB-resistant and FHB-susceptible wheat lines grown under field conditions for various periods after F. graminearum infection and determined the chromosomal distribution of the differentially expressed genes (DEGs). For each line, the expression in the spike (which exhibits symptoms in the infected plants) was compared with that in the flag leaves (which do not exhibit symptoms in the infected plants). We identified an island of 53 constitutive DEGs in a 140 kb region with high homology to the FhbL693b region on chromosome 3B. Of these genes, 13 were assigned to specific chloroplast-related pathways. Furthermore, one gene encoded inositol monophosphate (IMPa) and two genes encoded ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Our findings suggest that the temporary susceptibility in locally infected spikes results from the cross-talk between RuBisCO and IMPa, which blocks secondary signaling pathways mediated by salicylic acid and induces a systemic acquired resistance in the distant leaf tissue. 16 Effects of water deficit on breadmaking quality and storage protein compositions in bread wheat (Triticum aestivum L.) DOI: 10.1002/jsfa.8968 Water deficiency produced a shorten grain-filling period and a decrease in grain number, grain weight and grain yield, a reduced starch granule; increased protein content and glutenin macropolymer contents, resulting in superior dough properties and breadmaking quality. Reversed-phase ultra-performance liquid chromatography analysis showed that the total gliadin and glutenin content as well as the accumulation of individual composition were significantly increased by water deficiency. Two-dimensional gel electrophoresis detected 144 individual storage protein spots with significant accumulation changes in developing grains under water deficit. The comparative proteomics analysis revealed that water deficiency resulted in significant upregulation of 12 gliadins, 12 HMW-GSs, and 46 LMW-GSs. Quantitative real-time polymerase chain reaction analysis revealed that the expression of two storage protein biosynthesis related transcription factors Dof and Spa was upregulated by water deficiency. \0 \0 欢迎关注 “ 小麦研究联盟 ”, 了解小麦新进展 投稿、转载、合作以及信息分布等请联系： wheatgenome
小麦里导入的外源染色体片段对小麦基因组的影响远小于小麦基因组对它的影响 本期作者：Neal 胖丫最近看到WHH大学一教授被爆出硕士期间发表的多篇文章造假。胖丫说，这个真的是青史留名啊。是呀，作为老师，一定要在学生入门时强调好这一点，同时老师也要做好把关。不过作为老师，也要以身作则，少搞哪些拿不上台面的事情。最近看到《钱氏家训》里的两句话说的特别好“心术不可得罪于天地 言行皆当无愧于圣贤。利在一身勿谋也，利在天下必谋之”。怪不得钱氏家族“出了很多名人，人家的格局在哪里了。 今天我们打算聊一聊这一篇文章，题目是“ Transcriptome reprogramming due to the introduction of a barley telosome into bread wheat affects more barley genes than wheat ”，发表在 Plant Biotechnology Journal 上面。作者信息如下： 我看到这个题目很惊喜，主要是他的研究思路。所以今天我们就来说说这一篇文章。小麦族有很多近缘物种，在小麦育种上，我们可以将这些近缘物种的染色体片段导入普通小麦里，创建新的种质，但是在实际利用过程中却要面临诸多困难。连锁累赘和不完全的遗传补偿效应是主要的原因。我们对导入的外源染色质影响植物表型的分子机制也了解甚少。本文利用一个含有大麦7H染色体长臂的普通小麦附加系、正常的普通小麦和供体大麦。对这个三个材料进行进行转录组测序，每个样品是6个重复。 对测序结果进行分析发现，大麦有约2.4%，中国春有小于1%的reads 映射至非期望基因组上。中国春或者附加系有35031个基因是转录的，而大麦7H染色体区间339-656Mbp（也即染色体长臂）有923个基因表达。在中国春和附加系之间，97.3%的基因没有差异表达，也就是有960个基因是差异表达的。差异表达的基因中，509下调表达，451上调表达。大麦和附加系比较，7HL上表达的923个基因中，389个基因（42%）是差异表达的，包括233个在附加系里下调表达的基因和156个在附加系里上调表达的基因。由此作者得出结论“These greatly differing proportions of differential transcription (DT) implied that the effect of a non-native genetic background was much greater than the effect of the presence of an exotic telosome”。在附加系材料里，外源7HL片段导入后对背景基因组上的基因影响要远远小于背景基因组对导入的7HL上基因的影响。 上述结果也就是我们常说的人容易受到周围环境的影响。打个比方说，我们往平静的湖面上上扔了一块大石头，引起水面波动，随后石头沉入湖底，而水面再次平静。对湖水来说，仿佛从没有一块石头来过；而对这块石头来讲，从此将暗无天日。所以相对来讲，石头的变化很大，而湖水变化不大。这里湖水就是中国春六倍体基因组，而石头就是大麦7H染色体长臂。这个结果让我很意外，照常理来讲，7HL导入进去之后，应该是对位于7AL,7BL和7DL的基因的影响要大于其他部分同源上的影响。 话又说回来了，实际上没有这么简单，7HL的导入还引起了小麦7AL上的一个染色体片段缺失（700-736 Mbp）。这样的缺失也存在于其他6个CS/B整条染色体的附加系。缺失的基因，7HL上的基因可以部分补偿。 另外作者还分析了差异表达基因在染色体上的分布特点，这种分析就类似于14年发表的3B参考基因组上基因转座子等在染色体上的分布特点的分析。所以这里我们就不在分析了。后面的差异表达基因的功能富集分析也没啥好说的。这里作者只分析了苗期的一个阶段，也许分析更多发育阶段的转录组，或者选择减数分裂阶段也好，不知道结论是否一样呢？ 参照文章的思路，我们在六倍体里其实也是可以比较不同亚基因组之间的基因表达上的差异的。比方说，干旱处理后，我们鉴定出来一批差异表达基因。分析这些差异表达的基因中，其对应的亚基因组上的基因是如何变化的。这样的结果其实还是挺有意思的。还可以进一步分析那些A/B/D之间表达模式不同的基因，看看能否找出一定的规律来。现在小麦转录组里这样分析的还比较少，但15年孙其信组发表了一篇题为“Temporal transcriptome profiling reveals expression partitioning of homeologous genes contributing to heat and drought acclimation in wheat (Triticum aestivum L.)”的文章，里面有专门分析A/B/D之间的差异。以后这也许是小麦转录组分析的必备项了。这才是我们小麦的特色啊。这种思路还可以拓展，研究转座子对不同亚基因组上基因表达/翻译的影响，对甲基化的影响。 欢迎关注 “ 小麦研究联盟 ”， 了解小麦新进展 投稿、转载、合作以及信息分布等请联系： wheatgenome
本期作者：Meng Wang 编者按： 尽管近两年的IF不是很理想，Plant Cell（下简称PC）无疑仍是也将会继续是植物学研究的殿堂级期刊。从11月28日小编推送PC上小麦种子萌发/休眠的QTL文章开始，接下来每周周二，我们会将2005年以后在PC上发表的小麦领域研究论文进行逐一梳理和推送，以飨读者。需要特别指出的是，本合辑题为“我要上PC”，是比照“我要上春晚”而诙谐命名；由于对研究内容要求较系统、文章发表要求较高和审稿机制较严格，PC上面的文章确实值得深入学习；但我们公众号倡导大家把更多的目光放在学习这些文章的思路、内容和意义上，而不是只看重和崇拜高影响因子^_^。 面包小麦作为六倍体作物，其祖先种（除了B组的）是已知且尚存的，所以进化脉络比较清晰；目前各种组合的人工合成六倍体小麦的创制也都可以实现，可以用来模拟小麦的多倍体化过程；同时小麦是比较年轻的作物，又富含转座子和重复序列，基因组相对活跃-综合这些因素， 小麦可以算的上研究植物进化（多倍体化）比较理想的材料。 上周小编解读了小麦籽粒重要性状遗传位点 Hardness locus的进化方面的PC文章，从一个个例的角度小试牛刀（ 小麦籽粒硬度Hardness Locus的进化研究—小麦领域Plant Cell上论文合辑（十二） ）。本周咱们扩大一下尺度，从全基因的角度，看一下PC上的三篇讲小麦进化方面的文章。这涉及到很多全基因组测序和生物信息学方面的内容，由于小编不是这个方向的，所以解读难免较浅，权当抛砖引玉，欢迎大家留言讨论或撰稿补充。 按照时间顺序，第一篇是2008年在PC上题为“Identification and Characterization of Shared Duplications between Rice and Wheat Provide New Insight into Grass Genome Evolution”的文章，通讯作者是法国INRA研究所（上周那篇也是这个研究所，所以我说是小麦研究重镇喽~）的Catherine Feuillet教授。 敲黑板： 不知大家留意了没，我们“我要上PC”系列在介绍PC上小麦研究文章的同时，也顺便给大家简单介绍了不少小麦研究的重镇和大牛教授，所以多多关注我们推送的文章，不仅可以了解小麦研究的最新进展，也会为您申请国际访问学者、出国读博后或博士，抑或寻求国际合作，提供了很多有用的信息。Feuillet教授就是这样一位大牛，为小麦的全基因组测序做出了重要的贡献。 书归正传，2008年，小麦全基因组测序尚刚起步，所以本研究用的是水稻的全基因测序信息和小麦的EST数据（主要基于当时The International Triticeae EST Cooperative这个组织的数据库）。研究人员根据研究时发现的实际问题，首先对序列比对和统计分析的参数进行了优化升级。利用这套优化的参数，他们发现了水稻基因组中的29个染色体间的复制事件（interchromosomal duplications）和小麦基因组中的10个染色体间的复制事件（是否还记得 Ph1 的解读文章我们也提到小麦中的类似事件？）。作者又对水稻和小麦的基因组进行了共线性分析，发现其中七个复制事件具有共线性。进一步的，借助高粱和玉米的基因组数据，作者发现禾本科的物种或许最初只有五个染色体，然后通过染色体（片段）复制、融合和易位等事件，进化成各个物种的完整染色体。 哈哈，是不是有点绕。再来看下一篇，题为“Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces”，10年发表在PC，通讯作者，也是Catherine Feuillet教授；不过这次是国际团队（IWGSC）一起合作完成。 这篇文章主要是分析小麦3B染色体的测序数据。小麦的3B染色体是测序最早、最好的亚染色体，关于它的故事，我们有机会可以好好讲一讲，也欢迎大家投稿。这篇文章通过测序和注释呢，将3B染色体上的基因、转座子等进行了具体的分析，得出了一个最重要的结论就是： 通过分析3B上的基因数目，预测二倍体小麦全基因中的基因数目会远远大于其他作物。 这貌似也很好理解，毕竟小麦的全基因组要比其他作物大得多，且存在高频的序列重复现象。但，真的是这样么？ 不同观点来了，也就是2011年在PC上题为“Frequent Gene Movement and Pseudogene Evolution Is Common to the Large and Complex Genomes of Wheat, Barley, and Their Relatives”的文章，通讯作者为Nils Stein，Catherine Feuillet教授也参与了本研究。 本研究基于Jaroslav独家的染色体（臂）筛选技术，对小麦的1号染色体和大麦对应的1H染色体进行了筛选和测序，通过比对分析后得出了新的一个结论：由于大量存在的转座子等的作用，小麦基因组确实容易产生序列复制事件，从而产生了更多的、与其他禾本科物种基因组不具有共线性的序列，但是这些序列包含的基因大多为假基因，所以， 小麦全基因组中的基因总数量与其他作物是差不多的 。 这两个观点，在人类全基因组测序完成的前后，也都被提出过，最终的结论是人类基因组虽然比小白鼠等的基因组大，但是基因数目是差不多的。最近小麦的多个全基因组图谱得到公布，基于全基因组信息的高通量、高分辨率小麦转录组也越来越多，那么对于这两个观点，读者们怎么看？ 欢迎关注 “小麦研究联盟”， 了解小麦新进展投稿、转载、合作以及信息发布等请联系： wheatgenome
2018年第10周小麦文献推荐（3.11） 正式开始前，先说说我们前面举办的一个答题赢话费活动，前几日我们公布了获奖名单（），对这份名单的前6名的成绩存有疑问，根据题目数量与他们的答题日期和完成时间，初步判断是作弊行为。当然，咱们也不能一棍子打死，给人家一个机会解释，另外我也想认识这几位大神，对我们小麦和我们公众号了解这么多，一定是非凡人。 后面那个排名第一自称李周的人联系我们。他开门见山就说我就是第一名，凭什么质疑他之类的话。我说，你报下你的手机号，我稍后会核实你与那个第一名是否是同一人。结果人家不理我，自顾自的在喷我。我看这态势不像是来解决问题的，我索性就拉黑了。真要感谢微信的拉黑功能，世界顿时清静了。 后面Google他们的手机号之后，发现网上有人举报他们是骗子，同时在防骗数据库查也能查到他们的电话（ http://new.fpsjk.cn/searchList_Detail.aspx?date=2017-04-05 ）（下图是曝光的骗子电话，希望能够帮助后来人），另外也可能是羊毛党。我不是反对薅羊毛，但请低调点不要被看出来。至此事情对我来说已告一段落。现在网络发达，也提醒大家注意网上防骗。我其实感到挺高兴，毕竟他们不是我们小麦人。我对我们这样一个群体是抱有预想的，或者说我们这样一个群体其实是有共同目标的。也因为有这样的共同目标和追求，我们才能聚集在一起。在我们群体里，不会容忍造假行为。这就是为什么我会感到高兴的主要原因。 说完了骗子，我们再说说这次真正的前十名，名单见下图。恭喜这些小伙伴，今天有时间的时候留意下话费是否到账。 终于，让我们进入正题，这一周有几篇文献还是不错的，思路和方法上值得学习和借鉴。 1 Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies Bread wheat ( Triticum aestivum L.) is a staple food for a significant part of the world’s population. The growing demand on its production can be satisfied by improving yield and resistance to biotic and abiotic stress. Knowledge of the genome sequence would aid in discovering genes and QTLs underlying these traits and provide a basis for genomics-assisted breeding. Physical maps and BAC clones associated with them have been valuable resources from which to generate a reference genome of bread wheat and to assist map-based gene cloning. As a part of a joint effort coordinated by the International Wheat Genome Sequencing Consortium, we have constructed a BAC-based physical map of bread wheat chromosome arm 7DS consisting of 895 contigs and covering 94% of its estimated length. By anchoring BAC contigs to one radiation hybrid map and three high resolution genetic maps, we assigned 73% of the assembly to a distinct genomic position. This map integration, interconnecting a total of 1,713 markers with ordered and sequenced BAC clones from a minimal tiling path, provides a tool to speed up gene cloning in wheat. The process of physical map assembly included the integration of the 7DS physical map with a whole-genome physical map of Aegilops tauschii and a 7DS Bionano genome map, which together enabled efficient scaffolding of physical-map contigs, even in the non-recombining region of the genetic centromere. Moreover, this approach facilitated a comparison of bread wheat and its ancestor at BAC-contig level and revealed a reconstructed region in the 7DS pericentromere. 2 Transcriptome reprogramming due to the introduction of a barley telosome into bread wheat affects more barley genes than wheat Despite a long history, the production of useful alien introgression lines in wheat remains difficult mainly due to linkage drag and incomplete genetic compensation. In addition, little is known about the molecular mechanisms underlying the impact of foreign chromatin on plant phenotype. Here, a comparison of the transcriptomes of barley, wheat and a wheat barley 7HL addition line allowed the transcriptional impact both on 7HL genes of a non-native genetic background, and on the wheat gene complement as a result of the presence of 7HL to be assessed. Some 42% (389/923) of the 7HL genes assayed were differentially transcribed, which was the case for only 3% (960/35,301) of the wheat gene complement. The absence of any transcript in the addition line of a suite of chromosome 7A genes implied the presence of a 36 Mbp deletion at the distal end of the 7AL arm; this deletion was found to be in common across the full set of Chinese Spring/Betzes barley addition lines. The remaining differentially transcribed wheat genes were distributed across the whole genome. The up-regulated barley genes were mostly located in the proximal part of the 7HL arm, while the down-regulated ones were concentrated in the distal part; as a result, genes encoding basal cellular functions tended to be transcribed, while those encoding specific functions were suppressed. An insight has been gained into gene transcription in an alien introgression line, thereby providing a basis for understanding the interactions between wheat and exotic genes in introgression materials. 3 Zinc and Iron Concentration as Affected by Nitrogen Fertilization and Their Localization in Wheat Grain Nearly half of the world cereal production comes from soils low or marginal in plant available zinc, leading to unsustainable and poor quality grain production. Therefore, the effects of nitrogen (N) rate and application time on zinc (Zn) and iron (Fe) concentration in wheat grain were investigated. Wheat ( Triticum aestivum var. Krabat) was grown in a growth chamber with 8 and 16 h of day and night periods, respectively. The N rates were 29, 43, and 57 mg N kg-1 soil, equivalent to 80, 120, and 160 kg N ha-1. Zinc and Fe were applied at 10 mg kg-1 growth media. In one of the N treatments, additional Zn and Fe through foliar spray (6 mg of Zn or Fe in 10 ml water/pot) was applied. Micro-analytical localization of Zn and Fe within grain was performed using scanning macro-X-ray fluorescence (MA-XRF) and laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS). The following data were obtained: grain and straw yield pot-1, 1000 grains weight, number of grains pot-1, whole grain protein content, concentration of Zn and Fe in the grains. Grain yield increased from 80 to 120 kg N ha-1 rates only and decreased at 160 kg N ha-1 g. Relatively higher protein content and Zn and Fe concentration in the grain were recorded with the split N application of 160 kg N ha-1. Soil and foliar supply of Zn and Fe (Zn + Fes+f), with a single application of 120 kg N ha-1N at sowing, increased the concentration of Zn by 46% and of Fe by 35%, as compared to their growth media application only. Line scans of freshly cut areas of sliced grains showed co-localization of Zn and Fe within germ, crease and aleurone. We thus conclude that split application of N at 160 kg ha-1 at sowing and stem elongation, in combination with soil and foliar application of Zn and Fe, can be a good agricultural practice to enhance protein content and the Zn and Fe concentration in grain. 5 Genetic Dissection of End-Use Quality Traits in Adapted Soft White Winter Wheat Soft white wheat is used in domestic and foreign markets for various end products requiring specific quality profiles. Phenotyping for end-use quality traits can be costly, time-consuming and destructive in nature, so it is advantageous to use molecular markers to select experimental lines with superior traits. An association mapping panel of 469 soft white winter wheat cultivars and advanced generation breeding lines was developed from regional breeding programs in the U.S. Pacific Northwest. This panel was genotyped on a wheat-specific 90 K iSelect single nucleotide polymorphism (SNP) chip. A total of 15,229 high quality SNPs were selected and combined with best linear unbiased predictions (BLUPs) from historical phenotypic data of the genotypes in the panel. Genome-wide association mapping was conducted using the Fixed and random model Circulating Probability Unification (FarmCPU). A total of 105 significant marker-trait associations were detected across 19 chromosomes. Potentially new loci for total flour yield, lactic acid solvent retention capacity, flour sodium dodecyl sulfate sedimentation and flour swelling volume were also detected. Better understanding of the genetic factors impacting end-use quality enable breeders to more effectively discard poor quality germplasm and increase frequencies of favorable end-use quality alleles in their breeding populations. 6 Expression of TpNRAMP5, a metal transporter from Polish wheat ( Triticum polonicum L.), enhances the accumulation of Cd, Co and Mn in transgenic Arabidopsis plants Numerous natural resistance-associated macrophage proteins (NRAMPs) have been functionally identified in various plant species, including Arabidopsis , rice, soybean and tobacco, but no information is available on NRAMP genes in wheat. In this study, we isolated a TpNRAMP5 from dwarf Polish wheat (DPW, Triticum polonicum L.), a species with high tolerance to Cd and Zn. Expression pattern analysis revealed that TpNRAMP5 is mainly expressed in roots and basal stems of DPW. TpNRAMP5 was localized at the plasma membrane of Arabidopsis leaf protoplast. Expression of TpNRAMP5 in yeast significantly increased yeast sensitivity to Cd and Co, but not Zn, and enhanced Cd and Co concentrations. Expression of TpNRAMP5 in Arabidopsis significantly increased Cd, Co and Mn concentrations in roots, shoots and whole plants, but had no effect on Fe and Zn concentrations. These results indicate that TpNRAMP5 is a metal transporter enhancing the accumulation of Cd, Co and Mn, but not Zn and Fe. Genetic manipulation of TpNRAMP5 can be applied in the future to limit the transfer of Cd from soil to wheat grains, thereby protecting human health. 7 Molecular profiling of a y-type high molecular weight glutenin subunit at Glu-D1 locus from a North Korean landrace wheat ( Triticum aestivum L.) The objective of this study is to demonstrate characteristics of a y-type high molecular weight glutenin subunit (D1y HMW-GS) at Glu-D1 found in IT212991, a North Korean landrace wheat compared to Dy12 and Dy12.K as a novel HMW-GS in JB20, a Korean wheat line onto molecular analyses as PCR, cloning, DNA sequencing, and RP-HPLC and proteomic analyses as sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS–PAGE), two-dimensional electrophoresis (2-DE), Fourier-transform mass spectrometry (LTQ-FT-MS). The D1y of IT212991 was identified to have faster electrophoretic mobility than that of Dy12 by SDS–PAGE. HMW-GS components of IT212991 were identified to be different from Chinese Spring (CS) and JB20, a Korean wheat line by RP-HPLC. The result of mass spectrometric analysis, the D1y of IT212991 (68510.8 Da) was similar to that of Dy12.K of JB20 (68514.4 Da), and lower than Dy12 of CS (69151.2 Da). The result of LTQ-FT-MS based on 2-DE, the D1y of IT212991 was identified to be similar with Dy12 corresponding to the protein function as ‘Glutenin, high molecular weight subunit 12’. The D1y encoding the D1y of IT212991 was identified to consist of 652 amino acid sequences corresponding to 1962 bp according to DNA sequencing. The gene was identified to have a insertion and deletion (InDel) corresponding to 18 bp sequences ‘AACAGGACAAGGGCAACA’ compared to ordinary Dy12 gene. It was demonstrated that the D1y of IT212991 is the same as Dy12.K. 8 Responses of seminal wheat seedling roots to soil water deficits The aims of this paper are to develop our understanding of the ways by which soil water deficits influence early wheat root growth responses, particularly how seminal roots respond to soil drying and the extent to which information on differences in soil water content are conveyed to the shoot and their impact on shoot behaviour. To achieve this, wheat seedlings have been grown, individually for around 25 days after germination in segmented soil columns within vertical plastic compartments. Roots were exposed to different soil volumetric moisture contents (SVMC) within the two compartments. Experiments where the soil in the lower compartment was allowed to dry to different extents, while the upper was maintained close to field capacity, showed that wheat seedlings allocated proportionally more root dry matter to the lower drier soil compartment. The total production of root, irrespective of the upper or lower SVMC, was similar and there were no detected effects on leaf growth rate or gas exchange. The response of seminal roots to proportionally increase their allocation of dry matter, to the drier soil was unexpected with such plasticity of roots system development traditionally linked to heterogeneous nutrient distribution than accessing soil water. In experiments where the upper soil compartment was allowed to dry, root growth slowed and leaf growth and gas exchange declined. Subsequent experiments used root growth rates to determine when seminal root tips first came into contact with drying soil, with the intentions of determining how the observed root growth rates were maintained as an explanation for the observed changes in root allocation. Measurements of seminal root ABA and ethylene from roots within the drying soil are interpreted with respect to what is known about the physiological control of root growth in drying soil. 9 A wheat gene TaSAP17-D encoding an AN1/AN1 zinc finger protein improves salt stress tolerance in transgenic Arabidopsis The stress-associated protein (SAP) multigene family is conserved in both animals and plants. Its function in some animals and plants are known, but it is yet to be deciphered in wheat ( Triticum aestivum L.). We identified the wheat gene TaSAP17-D, a member of the SAP gene family with an AN1/AN1 conserved domain. Subcellular localization indicated that TaSAP17-D localized to the nucleus, cytoplasm, and cell membrane. Expression pattern analyses revealed that TaSAP17-D was highly expressed in seedlings and was involved in NaCl response, polyethylene glycol (PEG), cold, and exogenous abscisic acid (ABA). Constitutive expression of TaSAP17-D in transgenic Arabidopsis resulted in enhanced tolerance to salt stress, confirmed by improved multiple physiological indices and significantly upregulated marker genes related to salt stress response. Our results suggest that TaSAP17-D is a candidate gene that can be used to protect crop plants from salt stress. 10 Light interception and radiation use efficiency response to tridimensional uniform sowing in winter wheat improving radiation use efficiency (RUE) of the canopy is necessary to increase wheat ( Triticum aestivum ) production. Tridimensional uniform sowing (U) technology has previously been used to construct a uniformly distributed population structure that increases RUE. In this study, we used tridimensional uniform sowing to create a wheat canopy within which light was spread evenly to increase RUE. This study was done during 2014–2016 in the Shunyi District, Beijing, China. The soil type was sandy loam. Wheat was grown in two sowing patterns: (1) tridimensional uniform sowing (U); (2) conventional drilling (D). Four planting densities were used: 1.8, 2.7, 3.6, and 4.5 million plants ha−1. Several indices were measured to compare the wheat canopies: photosynthetic active radiation intercepted by the canopy (IPAR), leaf area index (LAI), leaf mass per unit area (LMA), canopy extinction coefficient (K), and RUE. In two sowing patterns, the K values decreased with increasing planting density, but the K values of U were lower than that of D. LMA and IPAR were higher for U than for D, whereas LAI was nearly the same for both sowing patterns. IPAR and LAI increased with increasing density under the same sowing pattern. However, the difference in IPAR and LAI between the 3.6 and 4.5 million plants ha−1 treatments was not significant for both sowing patterns. Therefore, LAI within the same planting density was not affected by sowing pattern. RUE was the largest for the U mode with a planting density of 3.6 million plants ha−1 treatment. For the D sowing pattern, the lowest planting density (1.8 million plants ha−1) resulted in the highest yield. Light radiation interception was minimal for the D mode with a planting density of 1.8 million plants ha−1 treatment, but the highest RUE and highest yield were observed under this condition. For the U sowing pattern, IPAR increased with increasing planting density, but yield and RUE were the highest with a planting density of 3.6 million plants ha−1. These results indicated that the optimal planting density for improving the canopy light environment differed between the sowing patterns. The effect of sowing pattern×planting density interaction on grain yield, yield components, RUE, IPAR, and LMA was significant ( P 0.05). Correlation analysis indicated that there is a positive significant correlation between grain yield and RUE ( r =0.880, P 0.01), LMA ( r =0.613, P 0.05), and spike number ( r =0.624, P 0.05). These results demonstrated that the tridimensional uniform sowing technique, particularly at a planting density of 3.6 million plants ha−1, can effectively increase light interception and utilization and unit leaf area. This leads to the production of more photosynthetic products that in turn lead to significantly increased spike number ( P 0.05), kernel number, grain weight, and an overall increase in yield. 11 Evaluating the Profitability of Foliar Fungicide Programs in Mid-Atlantic Soft-Red Winter Wheat Production In mid-Atlantic soft-red winter wheat (SRWW) production, the standard timing for a fungicide application is between flag leaf emergence (Feekes growth stage 8) and heading (FGS 10.5). However, two-pass and anthesis (FGS 10.5.1) applications are becoming common, yet these programs have not been thoroughly evaluated for disease control, yield, and profitability. Experiments were conducted in the mid-Atlantic in 2015 and 2016 to evaluate fungicide programs with applications at FGS 8, FGS 10.5.1, and two-pass programs with an early application at green-up (FGS 5) followed by (FB) applications at either FGS 8 or FGS 10.5.1. Fungicide programs including an application at FGS 10.5.1 resulted in the highest probability of no disease on the flag leaf (0.29-0.40). The estimated mean yield increases (D ̅) relative to the non-treated check ranged from 253.65 to 634.16 kg ha-1. Using a grain price of 5 bu-1), probabilities were similar between applications at FGS 8 (0.49 to 0.56) and FGS 10.5.1 (0.53). The probability of profitability ranged from 0.48 to 0.57 for FGS 5 FB FGS 8 applications and 0.52 to 0.59 for FGS 5 FB FGS 10.5.1 applications, indicating limited benefit to two-pass programs. 12 Epigenetic perspectives on the evolution and domestication of polyploid plant and crops Polyploidy or whole genome duplication (WGD) is a prominent feature for genome evolution of some animals and all flowering plants, including many important crops such as wheat, cotton, and canola. In autopolyploids, genome duplication often perturbs dosage regulation on biological networks. In allopolyploids, interspecific hybridization could induce genetic and epigenetic changes, the effects of which could be amplified by genome doubling (ploidy changes). Albeit the importance of genetic changes, some epigenetic changes can be stabilized and transmitted as epialleles into the progeny, which are subject to natural selection, adaptation, and domestication. Here we review recent advances for general and specific roles of epigenetic changes in the evolution of flowering plants and domestication of agricultural crops. 13 Wheat stripe rust resistance gene Yr24/Yr26 : A retrospective review The objective of this review is to describe events in China and elsewhere that are related to the discovery, genetic identification, use, and ultimate break-down of a single wheat gene for resistance to stripe rust, namely Yr24/Yr26 . In our retrospective analysis there was an early assumption of at least three genes at or near the locus, which caused an erroneous presumption of genetic diversity for resistance. It is an example of another boom and bust cycle in plant breeding with races virulent to Yr26 (V26 races) now being the majority race group in the Chinese Pst population. We have attempted to present our story in a historical and personal context demonstrating research inputs from different national and international groups, as well as some significant contemporary side issues. It covers the period from the late 1980s to 2017, during which significant rapid advances in the molecular biology of host: pathogen genetics occurred. We attempt to describe both successes and drawbacks in our work. 14 Mapping a leaf senescence gene els1 by BSR-seq in common wheat Leaf senescence is normally the last stage of plant development. Early senescence of functional leaves significantly reduces the photosynthetic time and efficiency, seriously affecting grain yield and quality in wheat. Discovering genes responsible for early leaf senescence ( els ) are necessary for developing novel germplasms and cultivars with delayed leaf-senescence through molecular manipulation and marker assisted selection. In this study, we identified an early leaf senescence line M114 in a derivative of a wheat breeding population. Genetic analysis indicated that early leaf senescence in M114 is controlled by a single recessive gene, provisionally designated els1 . By applying bulked segregant analysis and RNA-Seq (BSR-Seq), seven polymorphic markers linked to els1 were developed and the gene was located on chromosome arm 2BS in a 1.5 cM genetic interval between markers WGGB303 and WGGB305 . A co-segregating marker, WGGB302 , provide a starting point for fine mapping and map-based cloning of els1 . 15 Effects of sulfur fertilization and short-term high temperature on wheat grain production and wheat flour proteins The content of wheat flour proteins affects the quality of wheat flour. Sulfur nutrition in wheat can change the protein content of the flour. The inconsistency and instability of wheat grain quality during grain filling under high temperature stress (HTS) are a major challenge to the production of high-quality wheat. The effects of sulfur fertilization and HTS on wheat flour protein and its components are unknown. In this study, treatments varying two factors: sulfur fertilization and exposure to short-term HTS, at 20 days post-anthesis, were applied to two wheat cultivars with differing gluten types. Plants of a strong-gluten wheat (Gaoyou 2018) and a medium-gluten wheat (Zhongmai 8) were grown in pots in Beijing in 2015–2017. HTS significantly increased the contents of total protein, albumin, gliadin, glutenin, Cys, and Met in wheat kernels, but reduced grain yield, grain weight, protein yield, globulin content, and total starch accumulation. The HTS-induced increase in total protein amount was closely associated with nitrate reductase (NR) and glutamine synthetase (GS) activities in flag leaves. Sulfur fertilization increased grain and protein yields; grain weight; total protein, albumin, gliadin, glutenin, and globulin contents; protein yield; total starch; Cys, Met; and NR and GS activities. HTS and sulfur fertilization had larger effects on the strong- than on the medium-gluten cultivar. Sulfur fertilization also alleviated the negative effects of HTS on grain yield, protein yield, and starch content. Thus, growing wheat with additional soil sulfur can improve the quality of the flour. 16 Low pH stress responsive transcriptome of seedling roots in wheat ( Triticum aestivum L.) Soil acidification is one of major problems limiting crop growth and especially becoming increasingly serious in China owing to excessive use of nitrogen fertilizer. Only the STOP1 of Arabidopsis was identified clearly sensitive to proton rhizotoxicity and the molecular mechanism for proton toxicity tolerance of plants is still poorly understood. The main objective of this study was to investigate the transcriptomic change in plants under the low pH stress. The low pH as a single factor was employed to induce the response of the wheat seedling roots. Wheat cDNA microarray was used to identify differentially expressed genes (DEGs). A total of 1057 DEGs were identified, of which 761 genes were up-regulated and 296 were down-regulated. The greater percentage of up-regulated genes involved in developmental processes, immune system processes, multi-organism processes, positive regulation of biological processes and metabolic processes of the biological processes. The more proportion of down-regulation genes belong to the molecular function category including transporter activity, antioxidant activity and molecular transducer activity and to the extracellular region of the cellular components category. Moreover, most genes among 41 genes involved in ion binding, 17 WAKY transcription factor genes and 17 genes related to transport activity were up-regulated. KEGG analysis showed that the jasmonate signal transduction and flavonoid biosynthesis might play important roles in response to the low pH stress in wheat seedling roots. Based on the data, it is can be deduced that WRKY transcription factors might play a critical role in the transcriptional regulation, and the alkalifying of the rhizosphere might be the earliest response process to low pH stress in wheat seedling roots. These results provide a basis to reveal the molecular mechanism of proton toxicity tolerance in plants. 17 High Relative Parasitic Fitness of G22 Derivatives is Associated with the Epidemic Potential of Wheat Stripe Rust in China In total, 13 commercial wheat cultivars around China and four races of Puccinia striiformis f. sp. tritici (namely, CYR32, CYR33, G22-9, and G22-14) were employed for a test of relative parasitic fitness (RPF) using the drop method. The RPF values were measured, including the urediniospore germination rate, the latent period, the uredinial length, the uredinial density, the infection area, the sporulation intensity, the lesion expansion speed, and the sporulation period. The results indicated that the parameters of relative parasitic fitness of the four P. striiformis f. sp. tritici races on the 13 wheat cultivars were significantly different ( P = 0.00) in sporulation intensity, lesion expansion speed, uredinial length, sporulation period, uredinial density, and latent period. The urediniospore germination rates of the four P. striiformis f. sp. tritici races for the test were significantly different ( P = 0.00), whereas no correlation with the different cultivars was observed ( P = 1.00). The infection areas of the tested races on the different cultivars were significantly different ( P = 0.00) but there were no obvious manifestations among the various races ( P = 0.20). Principal component analysis (PCA) showed that the sporulation intensity represented sporulation capacity and scalability, the latent period indicated infection ability, and the urediniospore germination rate represented urediniospore vigor, all of which fully contributed to the RPF in the interaction of the four races and 13 wheat cultivars, which was calculated by the following formula: RPF = (sporulation intensity × urediniospore germination rate)/latent period. The sporulation and infection of G22-9 on the 13 large-scale cultivated cultivars were the highest, and the RPF of G22-9 was higher than that of the predominant races, CYR32 and CYR33. This result suggested that G22-9 could become a new predominant race and potentially cause epidemics of wheat stripe rust in China. To prevent potential epidemics, susceptible wheat cultivars should be withdrawn from production and breeding programs should reduce the use of Yr10 and Yr26 and use other more effective resistance genes in combination with nonrace-specific resistance for developing wheat cultivars with durable resistance to stripe rust. 18 Genome-Wide Identification and Characterization of Long Non-Coding RNA in Wheat Roots in Response to Ca2+Channel Blocker It remains unclear whether plant lncRNAs are responsive to Ca2+-channel blocking. When using the Ca2+-channel blocker, LaCl3, to treat germinated wheat seeds for 24 h, we found that both root length and mitosis were inhibited in the LaCl3-treated groups. The effect of the Ca2+-channel blocker was verified in three ways: a cyt decrease detected using Fluo-3/AM staining, a decrease in the Ca content measured using inductively coupled plasma mass spectrometry, and an inhibition of Ca2+ influx detected using Non-invasive Micro-test Technology. Genome-wide high throughput RNA-seq and bioinformatical methods were used to identify lncRNAs, and found 177 differentially expressed lncRNAs that might be in responsive to Ca2+-channel blocking. Among these, 108 were up-regulated and 69 were down-regulated. The validity of identified lncRNAs data from RNA-seq was verified using qPCR. GO and KEGG analysis indicated that a number of lncRNAs might be involved in diverse biological processes upon Ca2+-channel blocking. Further GO analysis showed that 23 lncRNAs might play roles as transcription factor (TF); Moreover, eight lncRNAs might participate in cell cycle regulation, and their relative expressions were detected using qPCR. This study also provides diverse data on wheat lncRNAs that can deepen our understanding of the function and regulatory mechanism of Ca2+-channel blocking in plants. 19 Simultaneous improvement of grain yield and protein content in durum wheat by different phenotypic indices and genomic selection Grain yield and protein content are of major importance in durum wheat breeding, but their negative correlation has hampered their simultaneous improvement. To account for this in wheat breeding, the grain protein deviation (GPD) and the protein yield were proposed as targets for selection. The aim of this work was to investigate the potential of different indices to simultaneously improve grain yield and protein content in durum wheat and to evaluate their genetic architecture towards genomics-assisted breeding. To this end, we investigated two different durum wheat panels comprising 159 and 189 genotypes, which were tested in multiple field locations across Europe and genotyped by a genotyping-by-sequencing approach. The phenotypic analyses revealed significant genetic variances for all traits and heritabilities of the phenotypic indices that were in a similar range as those of grain yield and protein content. The GPD showed a high and positive correlation with protein content, whereas protein yield was highly and positively correlated with grain yield. Thus, selecting for a high GPD would mainly increase the protein content whereas a selection based on protein yield would mainly improve grain yield, but a combination of both indices allows to balance this selection. The genome-wide association mapping revealed a complex genetic architecture for all traits with most QTL having small effects and being detected only in one germplasm set, thus limiting the potential of marker-assisted selection for trait improvement. By contrast, genome-wide prediction appeared promising but its performance strongly depends on the relatedness between training and prediction sets. 20 RNAi-Mediated Downregulation of Inositol Pentakisphosphate Kinase ( IPK1 ) in Wheat Grains Decreases Phytic Acid Levels and Increases Fe and Zn Accumulation Enhancement of micronutrient bioavailability is crucial to address the malnutrition in the developing countries. Various approaches employed to address the micronutrient bioavailability are showing promising signs, especially in cereal crops. Phytic acid (PA) is considered as a major antinutrient due to its ability to chelate important micronutrients and thereby restricting their bioavailability. Therefore, manipulating PA biosynthesis pathway has largely been explored to overcome the pleiotropic effect in different crop species. Recently, we reported that functional wheat inositol penta kis phosphate kinase ( TaIPK1 ) is involved in PA biosynthesis, however, the functional roles of the IPK1 gene in wheat remains elusive. In this study, RNAi-mediated gene silencing was performed for IPK1 transcripts in hexaploid wheat. Four non-segregating RNAi lines of wheat were selected for detailed study (S3-D-6-1; S6-K-3-3; S6-K-6-10 and S16-D-9-5). Homozygous transgenic RNAi lines at T4 seeds with a decreased transcript of TaIPK1 showed 28–56% reduction of the PA. Silencing of IPK1 also resulted in increased free phosphate in mature grains. Although, no phenotypic changes in the spike was observed but, lowering of grain PA resulted in the reduced number of seeds per spikelet. The lowering of grain PA was also accompanied by a significant increase in iron (Fe) and zinc (Zn) content, thereby enhancing their molar ratios (Zn:PA and Fe:PA). Overall, this work suggests that IPK1 is a promising candidate for employing genome editing tools to address the mineral accumulation in wheat grains. 21 Evaluation of end use quality and root traits in wheat cultivars associated with 1RS.1BL translocation 1RS.1BL translocation in wheat, exploited for its multiple disease resistance ( Lr26, Yr9, Sr31 and Pm8 ), has maintained significance due to its agronomical advantages. However, this translocation exhibits serious defects in dough quality due to the presence of Sec - 1 loci on 1RS arm. In the present investigation micro SDS sedimentation test (MST), high molecular weight glutenin subunits (HMWGS) and bread making analysis of 26 genotypes were studied along with their root phenotyping in the field and under hydroponic culture system. The MST values showed that genotypes having Sec -1 loci had low MST values but in the presence of Glu-D1 (5 + 10) with Glu-B1 (7 + 9) and (7 + 8) they had high MST values, thus overcoming the negative effects of secalin on dough quality. The loaf volume showed positive correlation with MST values of the genotypes. The translocation of 1RS arm led to higher root biomass and longer root length than Pavon 76 without 1RS. Better root traits in recombinant 1RS 44:38 and 1B + 38 than Pavon 1RS.1BL suggested the role of negative epistatic effects between different QTL regions in 1RS arm. The results suggest that it should be possible to harness the useful alleles associated with good dough quality, better root traits, high yield and stress tolerance with or without secalin. 22 Three endoplasmic reticulum-associated fatty acyl-coenzyme a reductases were involved in the production of primary alcohols in hexaploid wheat ( Triticum aestivum L.) We reported the cloning and characterization of three TaFARs, namely TaFAR6 , TaFAR7 and TaFAR8 , encoding fatty acyl-coenzyme A reductases (FAR) in wheat leaf cuticle. Expression analysis revealed that TaFAR6 , TaFAR7 and TaFAR8 were expressed at the higher levels in the seedling leaf blades, and were expressed moderately or weakly in stamen, glumes, peduncle, flag leaf blade, sheath, spike, and pistil. The heterologous expression of three TaFARs in yeast ( Saccharomyces cerevisiae ) led to the production of C24:0 and C26:0 primary alcohols. Transgenic expression of the three TaFARs in tomato ( Solanum lycopersicum ) and rice ( Oryza sativa ) led to increased accumulation of C24:0–C30:0 primary alcohols. Transient expression of GFP protein-tagged TaFARs revealed that the three TaFAR proteins were localized to the endoplasmic reticulum (ER), the site of wax biosynthesis. The three TaFAR genes were transcriptionally induced by drought, cold, heat, powdery mildew ( Blumeria graminis ) infection, abscisic acid (ABA) and methyl jasmonate (MeJa) treatments. 23 Analysis of MAPK and MAPKK gene families in wheat and related Triticeae species The work presented here focuses on two subfamilies of Triticeae MAPKs, the MAP kinases (MPKs), and the MAPK kinases (MKKs) whose members phosphorylate the MPKs. In silico analysis of multiple Triticeae sequence databases led to the identification of 152 MAPKs belonging to these two sub-families. Some previously identified MAPKs were renamed to reflect the literature consensus on MAPK nomenclature. Two novel MPKs, MPK24 and MPK25, have been identified, including the first example of a plant MPK carrying the TGY activation loop sequence common to mammalian p38 MPKs. An EF-hand calcium-binding domain was found in members of the Triticeae MPK17 clade, a feature that appears to be specific to Triticeae species. New insights into the novel MEY activation loop identified in MPK11s are offered. When the exon-intron patterns for some MPKs and MKKs of wheat, barley and ancestors of wheat were assembled based on transcript data in GenBank, they showed deviations from the same sequence predicted in Ensembl. The functional relevance of MAPKs as derived from patterns of gene expression, MPK activation and MKK-MPK interaction is discussed. 24 Transcriptome analysis of wheat seedling and spike tissues in the hybrid Jingmai 8 uncovered genes involved in heterosis Heterosis, known as one of the most successful strategies for increasing crop yield, has been widely exploited in plant breeding systems. Despite its great importance, the molecular mechanism underlying heterosis remains elusive. In the present study, RNA sequencing (RNA-seq) was performed on the seedling and spike tissues of the wheat ( Triticum aestivum ) hybrid Jingmai 8 (JM8) and its homozygous parents to unravel the underlying mechanisms of wheat heterosis. In total, 1686 and 2334 genes were identified as differentially expressed genes (DEGs) between the hybrid and the two inbred lines in seedling and spike tissues, respectively. Gene Ontology analysis revealed that DEGs from seedling tissues were significantly enriched in processes involved in photosynthesis and carbon fixation, and the majority of these DEGs expressed at a higher level in JM8 compared to both inbred lines. In addition, cell wall biogenesis and protein biosynthesis-related pathways were also significantly represented. These results confirmed that a combination of different pathways could contribute to heterosis. The DEGs between the hybrid and the two inbred progenitors from the spike tissues were significantly enriched in biological processes related to transcription, RNA biosynthesis and molecular function categories related to transcription factor activities. Furthermore, transcription factors such as NAC , ERF , and TIF-IIA were highly expressed in the hybrid JM8. These results may provide valuable insights into the molecular mechanisms underlying wheat heterosis. 25 A Comparison Between Genotyping-by-sequencing and Array-based Scoring of SNPs for Genomic Prediction Accuracy in Winter Wheat The utilization of DNA molecular markers in plant breeding to maximize selection response via marker-assisted selection (MAS) and genomic selection (GS) has revolutionized plant breeding. A key factor affecting GS applicability is the choice of molecular marker platform. Genotyping-by-sequencing scored SNPs (GBS-scored SNPs) provides a large number of markers, albeit with high rates of missing data. Array scored SNPs are of high quality, but the cost per sample is substantially higher. The objectives of this study were 1) compare GBS-scored SNPs, and array scored SNPs for genomic selection applications, and 2) compare estimates of genomic kinship and population structure calculated using the two marker platforms. SNPs were compared in a diversity panel consisting of 299 hard winter wheat ( Triticum aestivum L.) accessions that were part of a multi-year, multi-environments association mapping study. The panel was phenotyped in Ithaca, Nebraska for heading date, plant height, days to physiological maturity and grain yield in 2012 and 2013. The panel was genotyped using GBS-scored SNPs, and array scored SNPs. Results indicate that GBS-scored SNPs is comparable to or better than Array-scored SNPs for genomic prediction application. Both platforms identified the same genetic patterns in the panel where 90% of the lines were classified to common genetic groups. Overall, we concluded that GBS-scored SNPs have the potential to be the marker platform of choice for genetic diversity and genomic selection in winter wheat. 26 Isochorismate-based salicylic acid biosynthesis confers basal resistance to Fusarium graminearum in barley Salicylic acid (SA) plays an important role in signal transduction and disease resistance. In Arabidopsis , SA can be made by either of two biosynthetic branches, one involving isochorismate synthase (ICS) and the other involving phenylalanine ammonia lyase (PAL). However, the biosynthetic pathway and the importance of SA remains largely unknown in Triticeae. Here, we cloned one ICS and seven PAL genes from barley, and studied their functions by overexpressing and suppressing them in that plant. Suppression of the ICS gene significantly delayed plant growth, while PAL genes, both overexpressed and suppressed, had no significant effect on plant growth. Similarly, suppression of the ICS compromised plant resistance to Fusarium graminearum , while similar suppression of PAL genes had no significant effect. We then focused on transgenic plants with ICS . In a leaf-based test with F. graminearum , transgenic plants with an upregulated ICS were comparable to the wild-type control plants. By contrast, transgenic plants with a suppressed ICS lost the ability to accumulate SA during pathogen infection and were also more susceptible to Fusarium than the wild-type controls. This suggests that ICS plays a unique role in SA biosynthesis in barley, which in turn confers a basal resistance to F. graminearum by modulating the accumulation of H2O2, O2-, and reactive-oxygen associated enzymatic activities. Although SA mediates systemic acquired resistance (SAR) in dicots, there was no comparable SAR response to F. graminearum in barley. This study expands our knowledge about SA biosynthesis in barley and proves that SA confers basal resistance for fungal pathogens. This article is protected by copyright. All rights reserved. 27 Barley yellow dwarf virus Infection Leads to Higher Chemical Defense Signals and Lower Electrophysiological Reactions in Susceptible Compared to Tolerant Barley Genotypes Barley yellow dwarf virus (BYDV) is a phloem limited virus that is persistently transmitted by aphids. Due to huge yield losses in agriculture, the virus is of high economic relevance. Since the control of the virus itself is not possible, tolerant barley genotypes are considered as the most effective approach to avoid yield losses. Although several genes and quantitative trait loci are known and used in barley breeding for virus tolerance, little is known about molecular and physiological backgrounds of this trait. Therefore, we compared the anatomy and early defense responses of a virus susceptible to those of a virus-tolerant cultivar. One of the very early defense responses is the transmission of electrophysiological reactions. Electrophysiological reactions to BYDV infection might differ between susceptible and tolerant cultivars, since BYDV causes disintegration of sieve elements in susceptible cultivars. The structure of vascular bundles, xylem vessels and sieve elements was examined using microscopy. All three were significantly decreased in size in infected susceptible plants where the virus causes disintegration of sieve elements. This could be associated with an uncontrolled ion exchange between the sieve-element lumen and apoplast. Further, a reduced electrophysiological isolation would negatively affect the propagation of electrophysiological reactions. To test the influence of BYDV infection on electrophysiological reactions, electropotential waves (EPWs) induced by leaf-tip burning were recorded using aphids as bioelectrodes. EPWs in infected susceptible plants disappeared already after 10 cm in contrast to those in healthy susceptible or infected tolerant or healthy tolerant plants. Another early plant defense reaction is an increase in reactive oxygen species (ROS). Using a fluorescent dye, we found a significant increase in ROS content in infected susceptible plants but not in infected tolerant plants. Similar results were found for the phytohormones abscisic acid and three jasmonates. Salicylic acid levels were generally higher after BYDV infection compared to uninfected plants. Heat stimulation caused an increase in jasmonates. By shedding light on the plant defense mechanisms against BYDV, this study, provides further knowledge for breeding virus tolerant plants. 28 Polymorphism of floral type gene Cly1 and its association with thermal stress in barley Cleistogamy refers to a type of sexual breeding system with closed flowers. Cleistogamous flowers shed their pollen before flower opening, which leads to autogamy. Two SNPs in the open reading frame region of the Cly1 gene are associated with floral type. In the present study, we investigated the floral type of 436 barley accessions. Molecular markers were developed to genotype these barley accessions based on the two SNPs in the Cly1 gene region. The molecular markers explained floral type in 90% of the accessions. The Cly1 gene was sequenced in accessions with inconsistent genotype and phenotype. Thirteen SNPs were detected with ten new SNPs in the gene region. We further investigated whether floral type was associated with temperature stress tolerance in four field trials. One site experienced frost stress with a minimum temperature of -3.4°C during flowering. Grain fertility rates as low as 85% were observed at this site but ranged from 92–96% at the other three sites. The relationship between grain fertility rate and floral type under temperature stress was inconclusive. Some lines with higher grain fertility rates were identified under frost stress, and would be useful for frost stress studies in barley.
本期作者：Rui Wang 今天会涉及到三篇文章，前两篇我们一月份在 漫谈小麦赤霉病 中介绍过，其中包括2016年NG上的Fhb1 gene克隆文章以及南农马老师课题组2017年在The Crop Journal上发表的一篇综述，第三篇是最近发表在Phytopathology 上的 PFT gene验证文章。 首先Nature Genetics上的基因克隆文章，题目是Wheat Fhb1 encodes a chimericlectin with agglutinin domains and a pore-forming toxin-like domain conferring resistance to Fusarium head blight。这篇文章的重要性以及各个精彩的实验过程我就不再赘述了。总体来说，作为一篇中规中矩的基因克隆文章，在拿到基因后用三方面来验证，包括mutation analysis , RNAi-induced gene-silencing studies，以及overexpression with transformation of wheat。按说是没有什么可挑剔的，可是文章刚一发出来，就立即引起一些争议，其中小编亲耳听到的一点就是：通过测序，这个基因的抗性allele在美国，欧洲很多的小麦材料中都有出现，而客观情况是我们都知道美国以及欧洲的材料很少有 Fhb1 抗性的，事实上美国很多实际应用的抗性都是来源于望水白和苏麦3号。 现在回过头来看NG这篇文章，其实作者们已经预料到了类似的问题，所以文章中有一个Supplementary Table 6，作者们挑了40个不同抗性水平的cultivar和 l andrace，其中也包括国内的很多材料，而得到的结果也堪称完美：22个抗性材料都含有 PFT gene 的抗性allele，而其余的18个感性材料都在这个PFT位点存在变异或者是null allele。 请点击输入图片描述 可是问题就出在这：首先说，这四十个材料是怎么选的，文章没有提及，其次，作者在原文中说用这40个材料做了一个association study。 可是对于一个association study来说，40个材料是不是有点少？材料中的diversity是不是足够？这些都没有交代。 联系到我在上文所提到的争议，NG这篇文章能得到这么完美的结果真的是太不容易（诡异）了！因为其他课题组用PFT去筛选不同种质资源的时候，得到的表型和基因型的相关性其实是非常差的。其中就包括我们要说到的南农马老师的这篇综述，题目是A journey to understand wheat Fusarium head blight resistance in the Chinese wheat landrace Wangshuibai，关于表型和基因型的非相关性，作者列举了三种情况： 1. PFT 基因序列在感病材料PH691和抗性材料望水白、苏麦3号之间完全一致； 2. 在某组重组自交系里，一个具有望水白 PFT 类型的家系却是感病； 3. 44个地方品种材料的 PFT 基因序列与望水白和苏麦3号一致，然而却只有12个表现为抗病类型 总结来说就是：有PFT基因也不一定是抗病的！！！ 然后接下来就是最新发表的文章，题目是Molecular Characterization and Expression of PFT, an FHB Resistance Gene at the Fhb1 QTL in Wheat，完成单位是江苏农科院粮食作物研究所，第一作者是Yi He，通讯作者是Hongxiang Ma。文章的内容还是比较丰富的，比如有很多gene表达数据，但是我只节选了gene 在不同种质资源中验证这部分。 材料和方法： 348个材料：A total of 348 wheat accessions originating from China (293), Japan (14), U.S.A. (7), Mexico (6), Australia (4), Canada(4), Italy (3), Brazil (2) and 15 unknown origin accessions。 重要结论： 1. Four haplotypes were found in the 348accessions by the above sequence analysis: Hap-W, Hap-S1, Hap-S2, and Hap-N. 2. However, unlike previous researchers, we found the wild-type PFT sequence existed not only in resistant accessions but also insusceptible accessions such as Nonglin 67, Chuannong 42and Xiaoyan 54. 还是那句话，有这个gene，也不一定抗病。 3. Furthermore, five moderatelyresistant accessions, such as CA25, Ningyan 1 and Zhenmai 6 had mutant instead of wild-type PFT sequences. 4. For the 184 PFT negative accessions, only 102 accessionswere susceptible to FHB, while the remaining 82 accessions demonstrated moderateor high FHB resistance. 第三点和第四点说明没有这个PFT gene，也照样是抗病的。这点不一定跟PFT有关系，毕竟这些种植资源中有可能有其它的抗病基因。 以上的结果根据的就是这个图。说实话，这个图做为一个已克隆基因的验证结果，完全是不可以接受的（如果认为这个基因没有其它互作基因的话）。另外，这个图有一些细节也值得再深挖一些：比如说这个S2的haplotype 虽然呈现出非常感病，但是这种haplotype 却只有四个line；另外，Wild type 和S1 的haplotype 虽说在表型上有差异，但貌似也没有那么明显。（文中只给了平均数，没有Std和p value.但文章附加了原始数据，有兴趣的小伙伴可以下载）。 稍有遗憾的是，作者既然有这些line的origin，按照origin来分析一下结果应该会很有意思。还有，这300多个种质资源和NG文章中的40个材料有什么不同或者相同点呢（比如从origin和育种谱系来分析），为什么他们得到的结果是完全对应，而本文得到的结果却不一样（当然，从文章的题目可以看出，这篇文章的出发点和逻辑结构跟我的出发点不一样，所以可能也没打算在这方面多下功夫）。 根据以上结果，作者提出FHB抗性可能是多基因复合体： We speculate that wheat resistance to FHB is a multigenic complex trait, and PFT represents one of the genes to assist FHB resistance. Additional efforts are still needed to reveal the mechanisms of Fhb1 in FHB resistance. 最后，小编想说，虽然说后续的研究对NG那篇文章的结果都不能完美验证，但我还是对这篇文章充满敬意的，起码从那篇文章的结构和逻辑来说，确实是没有问题的。可是作者们也确实忽略或者说无意中错过了提出不确定性这样一个机会。我不知道如果这个研究在Supplementary Table 6 （40个line）的基础上再多选几个材料或者说没有那么“运气好”的话，发现几个有基因却不抗病，或者没基因也却抗病的情况，然后在文章中提出还有其它的基因也可能参与PFT复合体，是不是就更好一些。就像文中所提出的，Our discovery identifies a new type of durable plant resistance geneconferring quantitative disease resistance to plants against Fusarium species. 既然作者已经意识到这个gene是个quantitative resistance，提出还有其它基因参与抗性其实也算是顺理成章吧。不过要真是这种情况的话，文章是不是还能发在NG上就真不好说了。 总之，我们期待关于 Fhb1 更多更精彩的研究，有争议不可怕，解决争议的过程也就是走向真理的过程。
明确和准确判断小麦花药发育的不同时期对研究小麦花药或花粉发育至关重要。今天和大家一块分享一篇刚发表在Frontiers in Plant Science上的文章： Anther Morphological Development and Stage Determination in Triticum aestivum (doi: 10.3389/fpls.2018.00228) 该文章将小麦花药发育的整个过程分为15个时期，并且研究了叶环距、穗长、小花长度、花药长度和宽度与花药发育不同时期的相关性。研究发现叶环距和和穗长可以作为不同花药发育时期的快速鉴定指标，而花药长度可进一步对不同的发育时期进行精准鉴定。另外，小麦花药发育到四分体末期和小孢子产生的早期（第8-9期），绒毡层开始出现PCD（programmed cell death），并一致持续到第11期（ vacuolate pollen stage）。小麦绒毡层细胞的PCD与水稻相比开始稍晚，但比拟南芥要早两个时期。 小麦花药发育15个不同时期的界定及形态徐特点可以参见下表（左划可看全文）： Stage Stage name Description 1 Stamen primordia stage Anther is round or oval, with epidermis clear. Inner tissue comprised of primordial cells with little or no differentiation. 2 Archesporial stage Anther becomes oval in shape. Archesporial tissue begins to form the connective tissue to separate the theca of the anther. 3 Sporogenous tissue stage Four independent lobes begin to form, with parietal and sporogenous tissue present at corners of anther. Vascular region begins to form. 4 Lobe formation stage Four lobes are separate and clearly defined, each containing an endothecium and middle layer. Sporogenous tissue is still present. Vascular tissue is more highly developed. 5 Pre-callose stage Tapetal layer is present around the locules. Upper and lower locules separate at the stomium region and maintain distinct epidermal layers. 6 Central callose stage Tapetal cells grow larger as tapetum becomes complete and uniform. Microspore Mother Cells form from sporogenous tissue. Callose is visible in the center of the locules, encasing the MMCs. 7 Meiotic stage MMCs begin to undergo meiosis as the tapetum continues to grow and vacuolate. Anther size increases and meiotic microspores move to wall of tapetum, leaving a hollow region in the center of the locules. Meiotic cells exhibit globular shape as they move toward tapetal wall. 8 Tetrad stage Meiotic cells break apart to form tetrads. Middle layer begins to be crushed between tapetum and outer layers. 9 Young microspore stage Callose wall surrounding tetrads degrades and tetrads are released as young microspores. Middle layer is barely present and tapetum is at its largest and most swollen size. Young microspores are loose within the locules. 10 Vacuolate microspore stage Microspores become vacuolate and press into tapetal wall. An exine layer begins to develop on the now vacuolate microspores. Orbicules are visible between tapetum and microspores at high magnification. Tapetum begins to reduce in size as anther grows larger. 11 Vacuolate pollen stage Microspores grow larger and more spherical, becoming multi-nucleate. Two nuclei are visible in microspores. Tapetal layer is thinner and uneven as tapetal degeneration is at its peak. 12 3-nucleate pollen stage Pollen grains become round and starch filled. Gametes develop within pollen grains. Tapetum is very minimal or completely gone. The anther is at its largest point. 13 Bilocular stage Pollen grains dehydrate and contract. The septal region separating the upper and lower locules degrades, causing the anther to become bilocular. 14 Dehiscence Epidermal cells at stomium region degrade, causing locules to open and the now mature pollen grains to be released. 15 Senescence Pollen continues to be released as the anther becomes brittle and degrades. Eventually the senescing anther will release from the filament and fall from the flower. 作者同时研究了叶环距（auricle distance）、穗长（spike length）、小花长度（spikelet length）、花药长度（anther length）和宽度（anther width）五个指标与花药发育时期之间的相关性。每个指标的定义可参见下图： 简单概括一下（具体细节可以参见原文）： 叶环距： 由于不同材料之间的株高差异较大，相应地叶环距（旗叶叶耳到倒二叶叶耳的距离）的变化也就较大，在同一材料中叶环距的大小与花药发育时期的线性关系较好，可用于同一品种内花药发育时期的鉴定，但其绝对长度并不适合株高差异明显的不同材料之间的判断。 花药长度： 在花药发育的第4-10期，花药长度可以作为一个相对准确的参数来确定不同品种的发育时期，但在花药发育的后期准确性下降。 花药宽度： 在花药发育的第8-10期，花药宽度变化并不明显（停止变宽），因此并不适合作为花药发育时期的判断指标。 穗长和小花长度： 除了花药发育的第8和第9期之外，穗长和小花长度在第4-12期基本是线性增加的，但在不同品种中又存在差异，因此可以作为同一品种内部花药发育时期判定的指标。 这篇文章应该是首次对小麦花药发育的不同时期进行了全面而详细的定义和介绍，并给我们提供了一个相对准确地判断花药发育时期的方法：我们可以通过花药的长度对某个材料的发育阶段进行判断，不同材料之间花药绝对长度的变化不明显；叶环距和穗长在同一材料内部还是与花药发育阶段有较好的相关性，是一个简单有效地判断指标，但在评价之前需要提前建立一个标准。
2018年第八周小麦文献推荐（2.25） 终于又回来了，胖丫说每次要出远门的前两天总是心慌慌的，干啥也没心思，还老容易生病。只有坐到熟悉的位置上才有平时的那种感觉，打开电脑的同时也在心里默默想着今年要完成哪些工作。可是，一想到去年打算完成的事，又不得不拖到今年来完成，心里难免要苦笑一下。 本周的文献推荐拖到现在才更新，首先说声抱歉，由于个人身心原因没能按时完成一周的文献更新。好了，我们言归正传，来看看本周有哪些与小麦有关的文献更新！ 1Exploring and exploiting the boundaries of host specificity using the cereal rust and mildew models Individual plants encounter a vast number of microbes including bacteria, viruses, fungi and oomycetes through their growth cycle, yet few of these pathogens are able to infect them. Plant species have diverged over millions of years, co-evolving with few specific pathogens. The host boundaries of most pathogen species can be clearly defined. In general, the greater the genetic divergence from the preferred host, the less likely that pathogen would be able to infect that plant species. Co-evolution and divergence also occur within pathogen species, leading to highly specialized subspecies with narrow host ranges. For example, cereal rust and mildew pathogens ( Puccinia and Blumeria spp.) display high host specificity as a result of ongoing co-evolution with a narrow range of grass species. In rare cases, however, some plant species are in a transition from host to nonhost or are intermediate hosts (near nonhost). Barley was reported as a useful model for genetic and molecular studies of nonhost resistance due to rare susceptibility to numerous heterologous rust and mildew fungi. This review evaluates host specificity in numerous Puccinia/Blumeria –cereal pathosystems and discusses various approaches for transferring nonhost resistance (NHR) genes between crop species to reduce the impact of important diseases in food production. 2 Elucidation of the origin of “ agriocrithon ” based on domestication genes questions the hypothesis that Tibet is one of the centers of barley domestication Wild barley forms a two-rowed spike with a brittle rachis, whereas domestic barley has two- or six-rowed spikes with a tough rachis. As does domestic barley, “ agriocrithon” forms a six-rowed spike; however the spike is brittle the same as wild barley, which makes the origin of agriocrithon obscure. Haplotype analysis of the Six-rowed spike 1 ( vrs1 ) and the Non-brittle rachis 1 (btr1 ) and 2 ( btr2 ) genes was conducted to infer the origin of agriocrithon barley. Some agriocrithon barley accessions ( eu-agriocrithon ) carried Btr1 and Btr2 haplotypes that are not found in any cultivars, implying that they are directly derived from wild barley through a mutation at the vrs1 locus. Other agriocrithon barley accessions ( pseudo-agriocrithon ), carried Btr1 or Btr2 from cultivated barley, thus implying that they originated from hybridization between six-rowed landraces carrying btr1Btr2 and Btr1btr2 genotypes followed by recombination to produce Btr1Btr2 . All materials we collected from Tibet belong to pseudo-agriocrithon and thus do not support the Tibetan Plateau as a center of barley domestication. Tracing the evolutionary history of these allelic variants revealed that eu-agriocrithon represented six-rowed barley lineages that were selected by early farmers; once in south-eastern Turkmenistan ( vrs1.a1 ) and again in the eastern part of Uzbekistan ( vrs1.a4 ). 3 Distinct domains of the AVRPM3A2/F2 avirulence protein from wheat powdery mildew are involved in immune receptor recognition and putative effector function Recognition of the AVRPM3A2/F2 avirulence protein from powdery mildew by the wheat PM3A/F immune receptor induces a hypersensitive response after co-expression in Nicotiana benthamiana . The molecular determinants of this interaction and how they shape natural AvrPm3**a2/f2 allelic diversity are unknown. We sequenced the AvrPm3**a2/f2 gene in a worldwide collection of 272 mildew isolates. Using the natural polymorphisms of AvrPm3**a2/f2 as well as sequence information from related gene family members, we tested 85 single-residue-altered AVRPM3A2/F2 variants with PM3A, PM3F and PM3FL456P/Y458H(modified for improved signaling) in Nicotiana benthamiana for effects on recognition. An intact AvrPm3**a2/f2 gene was found in all analyzed isolates and the protein variant recognized by PM3A/F occurred globally at high frequencies. Single-residue alterations in AVRPM3A2/F2 mostly disrupted, but occasionally enhanced, the recognition response by PM3A, PM3F and PM3FL456P/Y458H. Residues enhancing hypersensitive responses constituted a protein domain separate from both naturally occurring polymorphisms and positively selected residues of the gene family. These results demonstrate the utility of using gene family sequence diversity to screen residues for their role in recognition. This approach identified a putative interaction surface in AVRPM3A2/F2 not polymorphic in natural alleles. We conclude that molecular mechanisms besides recognition drive AvrPm3**a2/f2 diversification. 4 TaNAC2 is a negative regulator in the wheat-stripe rust fungus interaction at the early stage NAC transcription factors play important roles in plant response to various stresses. In this study, the roles of TaNAC2 in wheat against biotic and abiotic stresses were investigated. The expression of TaNAC2 was highly induced in wheat- Puccinia striiformis ( Pst ) interactions and ABA treatment. TaNAC2 was localized in the nuclei of Arabidopsis protoplasts. The C-terminus of TaNAC2 was necessary for transcriptional activation by the yeast one-hybrid assay. Furthermore, silencing of TaNAC2 enhanced tolerance to Pst via a significant increase of H2O2 generation and suppressing hyphal growth at the early interaction stage. 5 Mapping of HKT1;5 Gene in Barley Using GWAS Approach and Its Implication in Salt Tolerance Mechanism Studies of salinity tolerance in the diploid wheat ancestor Triticum monococcum showed that HKT1;5 -like gene was a major gene in the QTL for salt tolerance, named Nax2 . In the present study, we were interested in investigating the molecular mechanisms underpinning the role of the HKT1;5 gene in salt tolerance in barley ( Hordeum vulgare ). A USDA mini-core collection of 2,671 barley lines, part of a field trial was screened for salinity tolerance, and a Genome Wide Association Study (GWAS) was performed. Our results showed important SNPs that are correlated with salt tolerance that mapped to a region where HKT1;5 ion transporter located on chromosome four. Furthermore, sodium (Na+) and potassium (K+) content analysis revealed that tolerant lines accumulate more sodium in roots and leaf sheaths, than in the sensitive ones. In contrast, sodium concentration was reduced in leaf blades of the tolerant lines under salt stress. In the absence of NaCl, the concentration of Na+ and K+were the same in the roots, leaf sheaths and leaf blades between the tolerant and the sensitive lines. In order to study the molecular mechanism behind that, alleles of the HKT1;5 gene from five tolerant and five sensitive barley lines were cloned and sequenced. Sequence analysis did not show the presence of any polymorphism that distinguishes between the tolerant and sensitive alleles. Our real-time RT-PCR experiments, showed that the expression of HKT1;5 gene in roots of the tolerant line was significantly induced after challenging the plants with salt stress. In contrast, in leaf sheaths the expression was decreased after salt treatment. In sensitive lines, there was no difference in the expression of HKT1;5 gene in leaf sheath under control and saline conditions, while a slight increase in the expression was observed in roots after salt treatment. These results provide stronger evidence that HKT1;5 gene in barley play a key role in withdrawing Na+ from the xylem and therefore reducing its transport to leaves. Given all that, these data support the hypothesis that HKT1;5 gene is responsible for Na+unloading to the xylem and controlling its distribution in the shoots, which provide new insight into the understanding of this QTL for salinity tolerance in barley. 6 Association of yield-related traits in founder genotypes and derivatives of common wheat ( Triticum aestivum L.) The genotypes of 215 wheat cultivars including 11 founder parents and 106 derivatives were analyzed by the 9 K wheat SNP iSelect assay. A total of 4138 polymorphic single nucleotide polymorphism (SNP) loci were detected on 21 chromosomes, of which 3792 were mapped to single chromosome locations. All genotypes were phenotyped for six yield-related traits including plant height (PH), spike length (SL), spikelet number per spike (SNPS), kernel number per spike (KNPS), kernel weight per spike (KWPS), and thousand kernel weight (TKW) in six irrigated environments. Genome-wide association analysis detected 117 significant associations of 76 SNPs on 15 chromosomes with phenotypic explanation rates ( R 2 ) ranging from 2.03 to 12.76%. In comparing allelic variation between founder parents and their derivatives (106) and other cultivars (98) using the 76 associated SNPs, we found that the region 116.0–133.2 cM on chromosome 5A in founder parents and derivatives carried alleles positively influencing kernel weight per spike (KWPS), rarely found in other cultivars. 7 Rht24 reduces height in the winter wheat population ‘Solitär × Bussard’ without adverse effects on Fusarium head blight infection 思路可以关注一下 The introduction of the Reduced height ( Rht )- B1 and Rht - D1 semi-dwarfing genes led to remarkable increases in wheat yields during the Green Revolution. However, their utilization also brings about some unwanted characteristics, including the increased susceptibility to Fusarium head blight. Thus, Rht loci that hold the potential to reduce plant height in wheat without concomitantly increasing Fusarium head blight (FHB) susceptibility are urgently required. The biparental population ‘Solitär × Bussard’ fixed for the Rht - 1 wild-type alleles, but segregating for the recently described gibberellic acid (GA)-sensitive Rht24 gene, was analyzed to identify quantitative trait loci (QTL) for FHB severity, plant height, and heading date and to evaluate the effect of the Rht24 locus on these traits. The most prominent QTL was Rht24 on chromosome 6A explaining 51% of genotypic variation for plant height and exerting an additive effect of − 4.80 cm. For FHB severity three QTL were detected, whereas five and six QTL were found for plant height and heading date, respectively. No FHB resistance QTL was co-localized with QTL for plant height. Unlike the Rht - 1 semi-dwarfing alleles, Rht24b did not significantly affect FHB severity. This demonstrates that the choice of semi-dwarfing genes used in plant breeding programs is of utmost consideration where resistance to FHB is an important breeding target. 8 Novel sources of resistance to Septoria nodorum blotch in the Vavilov wheat collection identified by genome-wide association studies The fungus Parastagonospora nodorum is the causal agent of Septoria nodorum blotch (SNB) of wheat. The pathosystem is mediated by multiple fungal necrotrophic effector–host sensitivity gene interactions that include SnToxA– Tsn1 , SnTox1– Snn1, and SnTox3– Snn3 . A P. nodorum strain lacking SnToxA , SnTox1, and SnTox3 ( toxa13 ) retained wild-type-like ability to infect some modern wheat cultivars, suggesting evidence of other effector-mediated susceptibility gene interactions or the lack of host resistance genes. To identify genomic regions harbouring such loci, we examined a panel of 295 historic wheat accessions from the N. I. Vavilov Institute of Plant Genetic Resources in Russia, which is comprised of genetically diverse landraces and breeding lines registered from 1920 to 1990. The wheat panel was subjected to effector bioassays, infection with P. nodorum wild type (SN15) and toxa13 . In general, SN15 was more virulent than toxa13. Insensitivity to all three effectors contributed significantly to resistance against SN15, but not toxa13 . Genome-wide association studies using phenotypes from SN15 infection detected quantitative trait loci (QTL) on chromosomes 1BS ( Snn1 ), 2DS, 5AS, 5BS ( Snn3 ), 3AL, 4AL, 4BS, and 7AS. For toxa13 infection, a QTL was detected on 5AS (similar to SN15), plus two additional QTL on 2DL and 7DL. Analysis of resistance phenotypes indicated that plant breeders may have inadvertently selected for effector insensitivity from 1940 onwards. We identify accessions that can be used to develop bi-parental mapping populations to characterise resistance-associated alleles for subsequent introgression into modern bread wheat to minimise the impact of SNB. 9 Genetic dissection of wheat panicle traits using linkage analysis and a genome-wide association study The panicle traits of wheat, such as grain number per spike and 1000-grain weight, are closely correlated with grain yield. Superior and effective alleles at loci related to panicles developments play a crucial role in the progress of molecular improvement in wheat yield breeding. Here, we revealed several notable allelic variations of seven panicle-related traits through an integration of genome-wide association mapping and a linkage analysis. The linkage analysis was performed using a recombinant inbred line (RIL) population (173 lines of F8:9) with a high-density genetic map constructed with 90K SNP arrays, Diversity Arrays Technology (DArT) and simple sequence repeat (SSR) markers in five environments. Thirty-five additive quantitative trait loci (QTL) were discovered, including eleven stable QTLs on chromosomes 1A, 2D, 4B, 5B, 6B, and 6D. The marker interval between EX_C101685 and RAC875_C27536 on chromosome 4B exhibited pleiotropic effects for GW, SL, GNS, FSN, SSN, and TSS, with the phenotypic variation explained (PVE) ranging from 5.40 to 37.70%. In addition, an association analysis was conducted using a diverse panel of 205 elite wheat lines with a composite map (24,355 SNPs) based on the Illumina Infinium assay in four environments. A total of 73 significant marker-trait associations (MTAs) were detected for panicle traits, which were distributed across all wheat chromosomes except for 4D, 5D, and 6D. Consensus regions between RAC875_C27536_611 and Tdurum_contig4974_355 on chromosome 4B for GW in multiple environments, between QTSS5A.7 - 43 and BS00021805_51 on 5A for SD and TSS, and between QSD3A.2 - 164 and RAC875_c17479_359 on 3A for SL and GNS in multiple environments were detected through linkage analysis and a genome-wide association study (GWAS). In addition, six stable QTL clusters on chromosomes 2D, 3A, 4B, 5A, and 6A were identified with high PVE% on a composite map. This study provides potentially valuable information on the dissection of yield-component traits and valuable genetic alleles for molecular-design breeding or functional gene exploration. 10 Precise identification of wheat-Thinopyrum intermedium translocation chromosomes carrying resistance to wheat stripe rust in line Z4 and its derived progenies The wheat- Thinopyrum intermedium derived line Z4 has displayed novel and effective stripe rust resistance for over 40 years. This study aimed to precisely identify the chromosome constitution of Z4 and determine the stripe rust resistance contribution using multicolor fluorescent in situ hybridization (FISH) and molecular marker analysis. The results indicated that the Z4 line (2n=44) contained two pairs of non-Robertsonian translocations without the 3A chromosomes of wheat. FISH karyotypes of F3 progenies derived from crosses between Z4 and MY11 indicated that the transmission of the translocated chromosomes appeared normal and the number of wheat chromosomes 3A and 3D frequently varied. The FISH signal distribution of a new repetitive probe named Oligo-3A1 confirmed the physical breakage points on chromosome 3AL incorporated into translocated chromosomes. PLUG markers revealed the breakage points on chromosomes 3A, 7JS and 3D invloved in the translocated chromosomes and they were designated as T3DS-3AS.3AL-7JSS and T3AL-7JSS.7JSL. Stripe rust resistances surveys indicated that the proximal region of 7JSS or 7JSL may confer the resistance at the adult plant stage. The precise characterization of the chromosome complements of wheat-Th. intermedium Z4 and derived progenies has demonstrated the importance of combining cytogenetic and molecular approaches in the genomics era for further wheat genetic manipulation and breeding purposes 11 Combining High-Throughput Phenotyping and Genomic Information to Increase Prediction and Selection Accuracy in Wheat Breeding Genomics and phenomics have promised to revolutionize the field of plant breeding. The integration of these two fields has just begun and is being driven through big data by advances in next-generation sequencing and developments of field-based high-throughput phenotyping (HTP) platforms. Each year the International Maize and Wheat Improvement Center (CIMMYT) evaluates tens-of-thousands of advanced lines for grain yield across multiple environments. To evaluate how CIMMYT may utilize dynamic HTP data for genomic selection (GS), we evaluated 1170 of these advanced lines in two environments, drought (2014, 2015) and heat (2015). A portable phenotyping system called ‘Phenocart’ was used to measure normalized difference vegetation index and canopy temperature simultaneously while tagging each data point with precise GPS coordinates. For genomic profiling, genotyping-by-sequencing (GBS) was used for marker discovery and genotyping. Several GS models were evaluated utilizing the 2254 GBS markers along with over 1.1 million phenotypic observations. The physiological measurements collected by HTP, whether used as a response in multivariate models or as a covariate in univariate models, resulted in a range of 33% below to 7% above the standard univariate model. Continued advances in yield prediction models as well as increasing data generating capabilities for both genomic and phenomic data will make these selection strategies tractable for plant breeders to implement increasing the rate of genetic gain. 12 Estimating wheat and maize daily evapotranspiration using artificial neural network In this research, artificial neural network (ANN) is used for estimating wheat and maize daily standard evapotranspiration. Ten ANN models with different structures were designed for each crop. Daily climatic data , leaf area index (LAI), and plant height ( h ) were used as inputs. For five structures of ten, the evapotranspiration (ETC) values calculated by ETC = ET0 × K C equation (ET0 from Penman-Monteith equation and K C from FAO-56, ANNC) were used as outputs, and for the other five structures, the ETC values measured by weighing lysimeter (ANNM) were used as outputs. In all structures, a feed forward multiple-layer network with one or two hidden layers and sigmoid transfer function and BR or LM training algorithm was used. Favorite network was selected based on various statistical criteria. The results showed the suitable capability and acceptable accuracy of ANNs, particularly those having two hidden layers in their structure in estimating the daily evapotranspiration. Best model for estimation of maize daily evapotranspiration is «M»ANN1C (8-4-2-1), with T max, T min, RHmax, RHmin, U 2, n , LAI, and h as input data and LM training rule and its statistical parameters (NRMSE, d , and R2) are 0.178, 0.980, and 0.982, respectively. Best model for estimation of wheat daily evapotranspiration is «W»ANN5C (5-2-3-1), with T max, T min, Rn, LAI, and h as input data and LM training rule, its statistical parameters (NRMSE, d , and R 2) are 0.108, 0.987, and 0.981 respectively. In addition, if the calculated ETCused as the output of the network for both wheat and maize, higher accurate estimation was obtained. Therefore, ANN is suitable method for estimating evapotranspiration of wheat and maize. 13 Evaluation of Yield, Processing Quality, and Nutritional Quality in Different-Colored Wheat Grains under Nitrogen and Phosphorus Fertilizer Application Increased grain yield and improved processing and nutritional quality are important factors in wheat ( Triticum aestivum L.) production. Six wheat cultivars with different-colored grains (white, red, and purple) were used to investigate the effect of combined N (N1: 90 kg N ha−1; N2: 240 kg N ha−1) and P fertilizer (P1: 60 kg P2O5 ha−1; P2: 209 kg P2O5 ha−1) on yield, dough rheological properties, grain Fe and Zn content, and phenolic acid content in two sowing years. Fertilization, cultivar, and its interactions all had a significant effect on most of the tested parameters. Both purple cultivars had a higher average protein content (14.46 and 14.13%), total insoluble phenolic acid content (840.24 and 778.46 μg g−1) and antioxidant activity (16.16 and 13.94 μmol FeSO4 g−1) than the red and white cultivars. Meanwhile, the two red cultivars had the highest total soluble phenolic acid content. High N application increased grain yield, protein content, dough rheological properties, grain Fe and Zn, and accumulative contents. Highest insoluble ferulic acid and total insoluble phenolic acid contents were observed under high P (N1P2 or N2P2) treatment, whereas the highest total soluble phenolic acid contents were observed under low-N treatment. High combined N and P fertilizer application also resulted in higher antioxidant activity. Wheat cultivars with a medium to strong dough strength would benefit from N2P2 treatment in terms of yield, processing quality, and nutritional quality. This is especially true for purple cultivars, which have a high nutritional quality. In contrast, soft gluten cultivars would benefit from N1P2 treatment. 14 Isolation of Mutations Conferring Increased Glyphosate Resistance in Spring Wheat A mutation breeding approach was used to explore the feasibility of isolating glyphosate-resistant (GR) wheat ( Triticum aestivum L.) lines. Although transgenic GR wheat cultivars were developed, they were never introduced due to lack of consumer acceptance and concern over management of volunteer wheat in rotation. Large-scale screening experiments recovered ethyl methanesulfonate mutants able to resist 360 to 480 g acid equivalent (ae) ha−1 glyphosate in four spring wheat cultivars, ‘Hollis’, ‘Louise’, ‘Macon’, and ‘Tara2002’, indicating that it is possible to recover resistance in a wide range of genetic backgrounds (glyphosate is typically applied at 840 g ae ha−1 in transgenic crops). Glyphosate rates of 420 to 530 g ae ha−1 were sufficient to kill the susceptible wild-type parents. Seven GR mutants were characterized: GRH9-5, GRH9-8, GRL1, GRL33, GRL65, GRM14, and GRT20. Glyphosate resistance was examined at the whole-plant level in dose–response experiments. Three mutant lines—GRL33, GRH9-5, and GRT20—exhibited resistance based on a significant increase in the dose required to retard growth compared with the corresponding susceptible wild type. According to F2 segregation analysis, GRL1, GRL65, and GRT20 segregated as a single dominant gene, whereas GRL33, GRH9-5, and GRH9-8 appeared to be either a single semidominant or polygenic trait. Although GRL1 was associated with an amino acid substitution (L239F) in TaEPSPS-7D1 , no nucleotide changes were observed in the coding regions of wheat 5-enolpyruvylshikimate-3-phosphate synthase ( EPSPS ) gene in GRL33 and GRH9-8. Results suggest that glyphosate resistance can result from multiple genetic mechanisms in wheat. 15 Reciprocal Hosts' Responses to Powdery Mildew Isolates Originating from Domesticated Wheats and Their Wild Progenitor The biotroph wheat powdery mildew, Blumeria graminis (DC.) E.O. Speer, f. sp. tritici Em. Marchal ( Bgt ), has undergone long and dynamic co-evolution with its hosts. In the last 10,000 years, processes involved in plant evolution under domestication, altered host-population structure. Recently both virulence and genomic profiling separated Bgt into two groups based on their origin from domestic host and from wild emmer wheat. While most studies focused on the Bgt pathogen, there is significant knowledge gaps in the role of wheat host diversity in this specification. This study aimed to fill this gap by exploring qualitatively and also quantitatively the disease response of diverse host panel to powdery mildew . A set of eight Bgt isolates, originally collected from domesticated and wild wheat was used for screening this wheat collection. The isolates from domesticated wheat elicited susceptible to moderate plant responses on domesticated wheat lines and high resistance on wild genotypes (51.7% of the tested lines were resistant). Isolates from wild emmer elicited reciprocal disease responses: high resistance of domesticated germplasm and high susceptibility of the wild material (their original host). Analysis of variance of the quantitative phenotypic responses showed a significant Isolates × Host species interaction and further supported these findings. Furthermore, analysis of the range of disease severity values showed that when the group of host genotypes was inoculated with Bgt isolate from the reciprocal host, coefficient of variation was significantly higher than when inoculated with its own isolates. This trend was attributed to the role of major resistance genes in the latter scenario (high proportion of complete resistance). By testing the association between disease severity and geographical distance from the source of inoculum, we have found higher susceptibility in wild emmer close to the source. Both qualitative and quantitative assays showed a reciprocal resistance pattern in the wheat host and are well aligned with the recent findings of significant differentiation into wild-emmer and domesticated-wheat populations in the pathogen. 16 Anther Morphological Development and Stage Determination in Triticum aestivum Anther development progresses through 15 distinct developmental stages in wheat, and accurate determination of anther developmental stages is essential in anther and pollen studies. A detailed outline of the development of the wheat anther through its entire developmental program, including the 15 distinct morphological stages, is presented. In bread wheat ( Triticum aestivum ), anther developmental stages were correlated with five measurements, namely auricle distance, spike length, spikelet length, anther length and anther width. Spike length and auricle distance were shown to be suitable for rapid anther staging within cultivars. Anther length is an accurate measurement in determining anther stages and may be applicable for use between cultivars. Tapetal Programmed Cell Death (PCD) in wheat begins between late tetrad stage (stage 8) and the early young microspore stage (stage 9) of anther development. Tapetal PCD continues until the vacuolate pollen stage (stage 11), at which point the tapetum fully degrades. The timing of tapetal PCD initiation is slightly delayed compared to that in rice, but is two stages earlier than in the model dicot Arabidopsis. The MYB80 gene, which encodes a transcription factor regulating the timing of tapetal PCD, reaches its peak expression at the onset of tapetal PCD in wheat. 17 Genomic-Enabled Prediction Kernel Models with Random Intercepts for Multi-environment Trials In this study, we compared the prediction accuracy of the main genotypic effect model (MM) without G×E interactions, the multi-environment single variance G×E deviation model (MDs), and the multi-environment environment-specific variance G×E deviation model (MDe) where the random genetic effects of the lines are modeled with the markers (or pedigree). With the objective of further modeling the genetic residual of the lines, we incorporated the random intercepts of the lines (l) and generated another three models . Each of these 6 models were fitted with a linear kernel method (Genomic Best unbiased predictor, GB) and a Gaussian Kernel (GK) method. We compared these 12 model-method combinations with another two multi-environment G×E interactions models with unstructured variance-covariances (MUC) using GB and GK kernels (4 model-method). Thus, we compared the genomic-enabled prediction accuracy of a total of 16 model-method combinations on two maize data sets with positive phenotypic correlations among environments, and on two wheat data sets with complex G×E that includes some negative and close to zero phenotypic correlations among environments. The two models (MDs and MDE with the random intercept of the lines and the GK method) were computationally efficient and gave high prediction accuracy in the two maize data sets. Regarding the more complex G×E wheat data sets, the prediction accuracy of the model-method combination with G×E, MDs and MDe, including the random intercepts of the lines with GK method had important savings in computing time as compared with the G×E interaction multi-environment models with unstructured variance-covariances but with lower genomic prediction accuracy. 18 Probabilities of having minimum amounts of available soil water at wheat planting Winter wheat ( Triticum aestivum L.)-fallow (WF) remains a prominent cropping system throughout the Central Great Plains despite documentation confirming the inefficiency of precipitation storage during the summer fallow period. Wheat yield is greatly influenced by available soil water at planting, and that quantity is influenced by cropping intensity, tillage intensity, crop grown prior to winter wheat planting, and length of the non-crop period prior to winter wheat planting. The objective of this study was to determine the effect of cropping system intensity, tillage, and crop prior to wheat planting on available soil water at planting and the probabilities of having certain minimum amounts of available soil water at wheat planting. Available soil water was measured at wheat planting for nine cropping systems varying in fallow frequency, tillage intensity, and crop prior to wheat over a 25-yr period at Akron, CO. Available soil water at wheat planting was found to be greatest (average 218 mm) for no-tillage (NT) and reduced-tillage (RT) systems in which a fallow period of 12–14 months preceded wheat planting. The lowest amounts of available soil water at wheat planting were found for the continuously cropped rotations (average 100 mm). The cumulative probability exceedance graphs of available soil water at planting fell into three groupings: 1) the five rotations that had a NT or RT fallow period prior to the next wheat crop; 2) the WF (conventional till) rotation; 3) the three rotations with either pea ( Pisum sativum L.) or proso millet ( Panicum miliaceum L.) prior to the next wheat crop. These graphs provide a valuable decision support tool for helping farmers assess risk in moving from a WF cropping system to a system of greater cropping intensity and diversity. 19 Fast-Forwarding Genetic Gain ‘Speed breeding’ enables scientists to exploit gene bank accessions and mutant collections for an unparalleled rapid gene discovery and gene deployment. Combining speed breeding and other leading-edge plant breeding technologies with strategic global partnerships, has the potential to achieve the genetic gain targets required to deliver our future crops.
2 12 本期作者：Rui Wang 春节马上就要到了！希望大家都过一个好年！还继续奋斗在实验室的小伙伴也不要孤单，大部分的异乡游子都是没有春节假期的，你不是一个人在战斗！ 今天咱们继续聊聊小麦生信常用数据库和网站- 基因表达数据库，首先还是回到我们的Case Study 上，我们鉴定到一个QTL ，也找到了flanking marker 的具体物理位置，而且发现线性相关还不错，QTL 被定位到了10M 的一个距离。那下一步就是看看这10M 的区间都有哪些基因呢，它们的表达量又怎样呢？这就要用到我们今天介绍的gene 表达数据库了。当然，10M 距离之内基因数目还是很多的，想就此把candidate gene 找到是不大可能的，但是做一下初步的筛选对我们以后的精细定位或者说发一篇不错的QTL mapping 文章还是很有帮助的！ 按照惯例，我们先从背景介绍和基本应用开始，已经熟知以下两个数据库的小伙伴可以点个赞直接去看春晚了，我们下次再详细聊怎样玩转这两个表达数据库。 首先，我们从下面这个网页开始，已经开始用RefSeq v1.0 的小伙伴应该看到过这个网站了吧，不过你有没有继续深入的点进去呢？比如我们要谈的Expression！ https://wheat-urgi.versailles.inra.fr/Seq-Repository/Expression 从这个网页可以轻易找到小麦基因表达的两个重要数据库，一个是WheatExp，另一个是ExpVIP（Wheat expression browser）。 第一个WheatExp ： http://wheat.pw.usda.gov/WheatExp/ Quality and adapter-trimmed RNA seq reads were mapped to the full cDNA set of wheat transcripts from the International Wheat Genome SequencingConsortium which are hosted by the Ensembl database. Diploid datasets were mapped to A-genome (32,091cDNAs), tetraploid datasets were mapped to the A- and B-genomes (68,166 cDNAs)and hexaploid datasets were mapped to the A-, B- and D- genomes (101,245cDNAs). Current expression data is generated from Ensembl release 26. ReferenceFASTA and GTF files, as well as all expression data in tabular format, are available for download from the following FTP site. 这个数据库对应的文献于 2015 年 12 月发表在 BMC Plant Biology 上面。 目前这个数据库包括七套数据，第一个是跟发育期有关的，第二三个是跟小麦籽粒发育有关的，第五个数据是跟抗旱和热击有关的。 具体的应用有两种方法，第一种是用序列进行 BLAST ，第二种是直接输入基因的名字（大家看看这个 example 基因是 based on 哪个版本的 annotation ？）。 我输入了一个根部发育 QTL 所对应区间的 gene ，出来的结果非常直观，下图是不同发育期的表达量，不过基本可以排除这不是我要找的 candidate gene 了（大家可以根据结果分析一下）。 这个是在籽粒不同 layers 的表达量变化 第二个 expVIP ： http://www.wheat-expression.com/ 这个数据库跟上一个最大的不同在于数据种类增多了，包含 16 个研究（小麦中的不同发育时间，组织，病原体感染和非生物胁迫）的 418 个 RNA-seq 样品的重新分析。比如最重要的是它有 FHB ， Rust ，白粉病，和 Septoriatritici blotch 侵染后不同时期的基因表达量，这对于做抗病的小伙伴还是很有用的！这些数据不仅可以帮我们正向筛选想要的基因，有的时候也可以帮我们反向排除很多基因。 相对应的文章于2016年2月发表在 PlantPhysiology 。 这个数据库应用起来就没有 BLAST 的功能了，只能输入基因的名字，可以输一个，也可以两个，用最下面的框框最多可以输 50 个。基因的名字可以用 TCAG 版本，也可以用 CSS 版本（就是下图所展示的 IWGSC2.26 版本）。 比如有一个QTL是跟穗子发育相关的，把对应的gene输入查询，结果如下，看到这个结果还是可以小兴奋一下的，因为这个gene在spike的表达远比在其它组织中要高，而且在spike中不同时期表达量也不一样，这样就可以根据我具体的trait来细致的分析。 另外，在表达量的上方会有针对 16 个 studies 的选项，大家可以根据自己所做的 trait 来选择，比如抗病的就选第 7 个， Stress-disease ，当然也可以全选。 好了，今天的介绍就到这，其实对于这两个数据库，最主要问题还是基因注释名字版本的问题，有兴趣的小伙伴可以自己先玩一下。然后就是如何能把 candidateregion 内的所有 gene 一次性都调出来，这也是需要一些技巧的，我们下次在介绍。
2018年第六周小麦文献推荐（2.11） 本期作者 麦萌 今天是第六周的周末了，相信大部分人回家过春节了，不过春节期间我们应该不打烊，不过可能会更新不准时。回家了，就不要心心念念工作上的事了，抛到脑后，好好休息和放松，来年好好干，一定也差不了。 我读研第一年的春节，回家之前，特地打印了几篇文献带回家，希望在家可以好好学习下。至于结果嘛，你们你猜到了，怎么带回去的又怎么带回来的。其实，中间还是拿出来一次，奈何家里太冷了，坐不住啊，于是作罢。从此以后放假再也不会带任何学习的东西了。不过，现在好了，手机越来越好了，貌似一部手机走天下。过年，带个手机回去就好了，文献的事交给我们吧。好吧，这是又给自己立了一个flag，但愿今年不会荒废。 回家之后大家也要注意身体，千万不要胡吃海喝。酒呢，也要适可而止，也不要劝别人酒，大家随意就好。多陪陪父母说会话，父母唠叨就听着，不要和家里人争长短，辨是非。胖丫说我年龄大了，这种话说了也没人听。我嘿嘿一笑，其实吧，这是回家之前，我说给自己的。 如果家里下载文献不方便，可以在群里求助，我知道还是有不少小伙伴奋斗在工作第一线的。 1 Analysis of the Genetic Diversity and Population Structure of Austrian and Belgian Wheat Germplasm within a Regional Context Based on DArT Markers Analysis of crop genetic diversity and structure provides valuable information needed to broaden the narrow genetic base as well as to enhance the breeding and conservation strategies of crops. In this study, 95 Austrian and Belgian wheat cultivars maintained at the Centre for Genetic Resources (CGN) in the Netherlands were characterised using 1052 diversity array technology (DArT) markers to evaluate their genetic diversity, relationships and population structure. The rarefacted allelic richness recorded in the Austrian and Belgian breeding pools ( A 25 = 1.396 and 1.341, respectively) indicated that the Austrian germplasm contained a higher genetic diversity than the Belgian pool. The expected heterozygosity ( HE ) values of the Austrian and Belgian pools were 0.411 and 0.375, respectively. Moreover, the values of the polymorphic information content (PIC) of the Austrian and Belgian pools were 0.337 and 0.298, respectively. Neighbour-joining tree divided each of the Austrian and Belgian germplasm pools into two genetically distinct groups. The structure analyses of the Austrian and Belgian pools were in a complete concordance with their neighbour-joining trees. Furthermore, the 95 cultivars were compared to 618 wheat genotypes from nine European countries based on a total of 141 common DArT markers in order to place the Austrian and Belgian wheat germplasm in a wider European context. The rarefacted allelic richness ( A 10) varied from 1.224 (Denmark) to 1.397 (Austria). Cluster and principal coordinates (PCoA) analyses divided the wheat genotypes of the nine European countries into two main clusters. The first cluster comprised the Northern and Western European wheat genotypes, whereas the second included the Central European cultivars. The structure analysis of the 618 European wheat genotypes was in a complete concordance with the results of cluster and PCoA analyses. Interestingly, a highly significant difference was recorded between regions (26.53%). In conclusion, this is the first study to reveal the high diversity levels and structure of the uncharacterised Austrian and Belgian wheat germplasm maintained at the CGN as well as place them in a wider European context. The results should help plant breeders to utilise the most promising wheat genotypes of this study in future breeding programmes for enhancing wheat cultivars. 2 Fast modification on wheat straw outer surface by water vapor plasma and its application on composite material The presence of non-poplar extracts, cutin, and wax layer in the wheat straw outer surface (WOS) greatly limit its application in bio-composite preparation. In this study, a dielectric-barrier-discharge plasma using water vapor as feeding gas was used to fast modify the WOS. The morphology, free radical concentrations, surface chemical components, and contact angles of WOS before and after plasma modification were investigated. Wheat straw was further prepared into wheat straw-based composites (WSC) and its bonding strength was evaluated by a paper tension meter. The results showed that water vapor plasma leads to the appearance of surface roughness, the generation of massive free radicals, and the introduction of oxygen-containing groups. In addition, both initial and equilibrium contact angle and the surface total free energy were significantly increased after plasma modification. These results synergistically facilitate the spread and permeation of adhesive onto the WOS and thus improve the bonding strength of all prepared WSCs. A good linear relationship between bonding strength and surface roughness parameters, contact angles, and total free energy were observed. In general, this study provided a time-saving and cost-effective modification method to realize WSC manufacture. 4 Genetic mapping of a novel recessive allele for non-glaucousness in wild diploid wheat Aegilops tauschii: implications for the evolution of common wheat Cuticular wax on the aerial surface of plants has a protective function against many environmental stresses. The bluish–whitish appearance of wheat leaves and stems is called glaucousness. Most modern cultivars of polyploid wheat species exhibit the glaucous phenotype, while in a wild wheat progenitor, Ae. tauschii , both glaucous and non-glaucous accessions exist. Iw2 , a wax inhibitor locus on the short arm of chromosome 2D, is the main contributor to this phenotypic variation in Ae. tauschii , and the glaucous/non-glaucous phenotype of Ae. tauschii is usually inherited by synthetic hexaploid wheat. However, a few synthetic lines show the glaucous phenotype although the parental Ae. tauschii accessions are non-glaucous. Molecular marker genotypes indicate that the exceptional non-glaucous Ae. tauschii accessions share the same genotype in the Iw2 chromosomal region as glaucous accessions, suggesting that these accessions have a different causal locus for their phenotype. This locus was assigned to the long arm of chromosome 3D using an F2 mapping population and designated W4 , a novel glaucous locus in Ae. tauschii . The dominant W4 allele confers glaucousness, consistent with phenotypic observation of Ae. tauschii accessions and the derived synthetic lines. These results implied that glaucous accessions of Ae. tauschii with the W2W2iw2iw2W4W4 genotype could have been the D-genome donor of common wheat. 5 Comparison of a one- and two-stage mixed model analysis of Australia’s National Variety Trial Southern Region wheat data A one-stage analysis of a series of variety trials involves a combined analysis of the individual plot data across trials. Together with prudent modelling of the genetic effects across trials, this is considered to be the gold standard analysis of multi-environment field trial data. An alternative is a two-stage approach in which the variety means from an analysis of the individual trials in stage one are combined into a weighted mixed model analysis in stage two to give the full set of predicted variety by environment effects and an estimate of their associated variance structure. The two-stage analysis will exactly reproduce the one-stage analysis if the full variance-covariance matrix of the means from stage one is known and is utilised in stage two. Typically the full matrix is not stored and a diagonal approximation is used. This introduces a compromise to the full analysis. The impacts of a diagonal approximation are greater in the presence of sophisticated models for the genetic effects. A second compromise is through a loss of information in estimating the non-genetic variance parameters using the two-stage approach. In this paper we draw a direct link between the one and two-stage analysis approaches for crop variety evaluation data in Australia. We now have the computing power to analyse large and complex multi-environment variety trial data sets using the one-stage approach without the need for a two-stage approximation. This should motivate a move away from the two-stage approach in a range of contexts. 6 Genetic Dissection of Wheat Kernel Hardness Using Conditional QTL Mapping of Kernel Size and Protein-Related Traits Kernel hardness (KH) is one of the primary quality parameters for common wheat ( Triticum aestivum L.) and has a major impact on milling, flour quality, and end-product properties. In addition to Puroindoline ( Pin ) mutations and differences in Pin expression, other factors, such as kernel size and protein-related traits, play noticeable roles in determining hardness, but at the quantitative trait locus (QTL) level, the influence of these factors remains unclear. In this study, genetic relationships between KH and kernel size traits and between KH and protein-related traits were demonstrated by unconditional and conditional mapping using a wheat 90K genotyping assay with a segregating population of 173 recombinant inbred lines in four environments. Eight additive QTL for KH were detected using unconditional QTL mapping analysis; these QTL were primarily distributed on chromosomes 4B, 5A, 5B, and 6D, with phenotypic variation that ranged from 0.2 to 17.7%. In addition, one pair of epistatic QTL ( QKH3B.4-65 / QKH4B.6-2 ) was identified by unconditional mapping, and this pair accounted for 1.6% of the phenotypic variation. Through conditional mapping, after excluding the influences of kernel size and protein-related traits, 14 QTL were discovered and accounted for 0.6–18.5% of the phenotypic variation. Of them, the stable QTL QKH4B.4-17 made the largest contribution, which was partially contributed by the kernel length (KL), kernel thickness (KT), and dry gluten content (DGC). Furthermore, QKH4B.4-17 was crucially contributed by the kernel width (KW), kernel diameter (KD), kernel protein content (KPC), and wet gluten content (WGC) and was independent of the sedimentation volume (SV) and gluten index (GI). Another major QTL, QKH5B.10-63 , was independent of the KW and KT; partly due to the variations in KL, KD, DGC, and WGC; and conclusively contributed by the KPC, SV, and GI. Seven additional QTL were only detected in the conditional analysis and were crucially contributed by kernel size or protein-related traits. These results demonstrated that kernel size and protein-related traits play significant roles in determining KH. The present study increases the understanding of the relationships between KH and kernel size and between KH and protein-related traits at the QTL level. 7 Introgression of Aegilops mutica genes into common wheat genome Introgression of genetic material from wheat wild relatives into the common wheat genome remains important. This is a natural and inexhaustible source of enrichment of the wheat gene pool with genes that improve wheat’s adaptive potential. Hexaploid lines F4–F5 of wheat type were developed via hybridization of common wheat Aurora (AABBDD) and genome-substituted amphidiploid Aurotica (AABBTT). The hexaploid genome of the latter includes the diploid genome TT from wheat relative Aegilops mutica instead of subgenome DD of common wheat. F1–F3 hybrids had limited self-fertility, which had substantially increased for some derivatives in F4–F5. For all generations, development of the lines was accompanied by cytogenetic control of the chromosome numbers. The chromosome numbers varied in general from 33 to 46 depending upon generation. In most descendants, that number was 42 chromosomes in F4when plants with chromosome numbers 40–44 were selected in each generation. F5 lines originate from nine selffertile F2 plants, differ from Aurora according to some morphological characters, and have alien DNA in their genome as was demonstrated by DNA dot-blot hybridization with genomic DNA of Aegilops mutica as a probe. 8 GABA Shunt in Durum Wheat Plant responses to salinity are complex, especially when combined with other stresses, and involve many changes in gene expression and metabolic fluxes. Until now, plant stress studies have been mainly dealt only with a single stress approach. However, plants exposed to multiple stresses at the same time, a combinatorial approach reflecting real-world scenarios, show tailored responses completely different from the response to the individual stresses, due to the stress-related plasticity of plant genome and to specific metabolic modifications. In this view, recently it has been found that γ-aminobutyric acid (GABA) but not glycine betaine (GB) is accumulated in durum wheat plants under salinity only when it is combined with high nitrate and high light. In these conditions, plants show lower reactive oxygen species levels and higher photosynthetic efficiency than plants under salinity at low light. This is certainly relevant because the most of drought or salinity studies performed on cereal seedlings have been done in growth chambers under controlled culture conditions and artificial lighting set at low light. However, it is very difficult to interpret these data. To unravel the reason of GABA accumulation and its possible mode of action, in this review, all possible roles for GABA shunt under stress are considered, and an additional mechanism of action triggered by salinity and high light suggested. 9 Simultaneous Transfer of Leaf Rust and Powdery Mildew Resistance Genes from Hexaploid Triticale Cultivar Sorento into Bread Wheat Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici , and wheat leaf rust, caused by Puccinia triticina Eriks, are two important diseases that severely threaten wheat production. Sorento, a hexaploid triticale cultivar from Poland, shows high resistance to the wheat powdery mildew isolate E09 and the leaf rust isolate PHT in Beijing, China. To introduce resistance genes into common wheat, Sorento was crossed with wheat line Xuezao, which is susceptible to both diseases, and the F1 hybrids were then backcrossed with Xuezao as the recurrent male parent. By marker analysis, we demonstrate that the long arm of the 2R (2RL) chromosome confers resistance to both the leaf rust and powdery mildew isolates at adult-plant and seedling stages, while the long arm of 4R (4RL) confers resistance only to powdery mildew at both stages. The chromosomal composition of BC2F3 plants containing 2R or 2RL and 4R or 4RL in the form of substitution and translocation were confirmed by GISH (genomic in situ hybridization) and FISH (fluorescence in situ hybridization). Monosomic and disomic substitutions of a wheat chromosome with chromosome 2R or 4R, as well as one 4RS-4DL/4DS-4RL reciprocal translocation homozigote and one 2RL-1DL translocation hemizigote, were recovered. Such germplasms are of great value in wheat improvement. 10 Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome evolution between two wheat cultivars (周五辉哥刚介绍过) Background: Recent improvements in DNA sequencing and genome scaffolding have paved the way to generate high-quality de novo assemblies of pseudomolecules representing complete chromosomes of wheat and its wild relatives. These assemblies form the basis to compare the evolutionary dynamics of wheat genomes on a megabase-scale. Results: Here, we provide a comparative sequence analysis of the 700-megabase chromosome 2D between two bread wheat genotypes, the old landrace Chinese Spring and the elite Swiss spring wheat line CH Campala Lr22a. Both chromosomes were assembled into megabase-sized scaffolds. There was a high degree of sequence conservation between the two chromosomes. Analysis of large structural variations revealed four large insertions/deletions (InDels) of 100 kb. Based on the molecular signatures at the breakpoints, unequal crossing over and double-strand break repair were identified as the evolutionary mechanisms that caused these InDels. Three of the large InDels affected copy number of NLRs, a gene family involved in plant immunity. Analysis of single nucleotide polymorphism (SNP) density revealed three haploblocks of 8 Mb, 9 Mb and 48 Mb with a 35-fold increased SNP density compared to the rest of the chromosome. Gene content across the two chromosomes was highly conserved. Ninety-nine percent of the genic sequences were present in both genotypes and the fraction of unique genes ranged from 0.36 to 0.63%. Conclusions: This comparative analysis of two high-quality chromosome assemblies enabled a comprehensive assessment of large structural variations and gene content. The insight obtained from this analysis will form the basis of future wheat pan-genome studies. 11 Characterization of gluten proteins and celiac disease-related immunogenic epitopes in the Triticeae: cereal domestication and breeding contributed to decrease the content of gliadins and gluten Wheat proteins are important for the physico-chemical properties of bread-dough and contribute to the protein intake in the human diet. In certain individuals, an immunological reactivity of the gluten protein family is strongly implicated in the etiology of celiac disease (CD) and non-celiac wheat sensitivity (NCWS). There is evidence that gluten-related disorders have increased in frequency in recent years. Gluten proteins were characterized and quantified by reversed-phase high-performance liquid chromatography (RP-HPLC) while the occurrence of CD immunogenic epitopes was searched in the gliadin sequences of Triticeae within the NCBI database. We have observed a tendency toward low content of gliadins in cultivated species compared to that of the wild ancestors in all Triticeae members. Regarding the glutenin subunits, there was no clear trend, but levels tended to be higher in cultivated species. Thousand-kernel weight is higher for domesticated and cultivated species. Quantification of DQ2- and DQ8-restricted epitopes in gliadin sequences showed a great variability in the number of CD epitopes per species and genome. A higher frequency of immunnogenic epitopes was found to be associated with genomes of the DD, BBAADD, and RR type. Durum wheats tend to have a lower content of gluten and CD immunogenic epitopes. Cultivated barley could be an alternative cereal with low immunogenic epitopes and low gluten. The results reported in this study suggest that domestication and breeding have contributed to a decrease in the content of gliadins and total gluten in the Triticeae species over time. 12 Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array Polypoid species play significant roles in agriculture and food production. Many crop species are polyploid, such as potato, wheat, strawberry, and sugarcane. Genotyping has been a daunting task for genetic studies of polyploid crops, which lags far behind the diploid crop species. Single nucleotide polymorphism (SNP) array is considered to be one of, high-throughput, relatively cost-efficient and automated genotyping approaches. However, there are significant challenges for SNP identification in complex, polyploid genomes, which has seriously slowed SNP discovery and array development in polyploid species. Ploidy is a significant factor impacting SNP qualities and validation rates of SNP markers in SNP arrays, which has been proven to be a very important tool for genetic studies and molecular breeding. In this review, we (1) discussed the pros and cons of SNP array in general for high throughput genotyping, (2) presented the challenges of and solutions to SNP calling in polyploid species, (3) summarized the SNP selection criteria and considerations of SNP array design for polyploid species, (4) illustrated SNP array applications in several different polyploid crop species, then (5) discussed challenges, available software, and their accuracy comparisons for genotype calling based on SNP array data in polyploids, and finally (6) provided a series of SNP array design and genotype calling recommendations. This review presents a complete overview of SNP array development and applications in polypoid crops, which will benefit the research in molecular breeding and genetics of crops with complex genomes. 13 Decomposing Additive Genetic Variance Revealed Novel Insights into Trait Evolution in Synthetic Hexaploid Wheat Whole genome duplication (WGD) is an evolutionary phenomenon, which causes significant changes to genomic structure and trait architecture. In recent years, a number of studies decomposed the additive genetic variance explained by different sets of variants. However, they investigated diploid populations only and none of the studies examined any polyploid organism. In this research, we extended the application of this approach to polyploids, to differentiate the additive variance explained by the three subgenomes and seven sets of homoeologous chromosomes in synthetic allohexaploid wheat (SHW) to gain a better understanding of trait evolution after WGD. Our SHW population was generated by crossing improved durum parents ( Triticum turgidum; 2n = 4x = 28, AABB subgenomes) with the progenitor species Aegilops tauschii (syn Ae. squarrosa, T. tauschii ; 2n = 2x = 14, DD subgenome). The population was phenotyped for 10 fungal/nematode resistance traits as well as two abiotic stresses. We showed that the wild D subgenome dominated the additive effect and this dominance affected the A more than the B subgenome. We provide evidence that this dominance was not inflated by population structure, relatedness among individuals or by longer linkage disequilibrium blocks observed in the D subgenome within the population used for this study. The cumulative size of the three homoeologs of the seven chromosomal groups showed a weak but significant positive correlation with their cumulative explained additive variance. Furthermore, an average of 69% for each chromosomal group's cumulative additive variance came from one homoeolog that had the highest explained variance within the group across all 12 traits. We hypothesize that structural and functional changes during diploidization may explain chromosomal group relations as allopolyploids keep balanced dosage for many genes. Our results contribute to a better understanding of trait evolution mechanisms in polyploidy, which will facilitate the effective utilization of wheat wild relatives in breeding. 14 The Effect of Grain Position on Genetic Improvement of Grain Number and Thousand Grain Weight in Winter Wheat in North China Genetic improvements have significantly contributed to wheat production. Five wheat cultivars—widely grown in north China in the 1950s, 1990s, or 2010s—were grown in field experiments conducted in the 2014–2015 and 2015–2016 growing seasons. This study evaluated the genetic progress in wheat grain yield and its related traits in north China and explored how breeding and selection have influenced grain numbers and weights within spikelets in the past 60 years. The results showed that the significant increases in grain yield in the past 60 years were mainly due to increases in grain number per spike and grain weight, while spike number per m2 has not changed significantly. Improvements in thousand grain weight (TGW) from the 1950s to 2010s have occurred at four grain positions (G1 to G4). The relative contribution of G4 to TGW increased over time, but was much less than the contributions of G1, G2, and G3. Indeed, the average grain weight at G4 was much less than that of 1000 grains. The increase in grain number per spike since the 1950s was mainly due to an increase in grain number at G1, G2 and G3, with the relative contribution of grain position to grain number being G1 G2 G3 G4. Dwarfing genes increased grain number per spike and grain number at G3 and G4, but not TGW. In future, yields could be boosted by enhancing grain weight at G4 and grain number at G3 and G4, while maintaining those at G1 and G2. 15 Inheritance and Linkage of Virulence Genes in Chinese Predominant Race CYR32 of the Wheat Stripe Rust Pathogen Puccinia striiformis f. sp. tritici Puccinia striiformis f.sp. tritici ( Pst ) is the causal agent of stripe (yellow) rust on wheat. It seriously threatens wheat production worldwide. The obligate biotrophic fungus is highly capable of producing new virulent races that can overcome resistance. Studying the inheritance of Pst virulence using the classical genetic approach was not possible until the recent discovery of its sexual stage on barberry plants. In the present study, 127 progeny isolates were obtained by selfing a representative Chinese Yellow Rust (CYR) race, CYR32, on Berberis aggregate . The parental isolate and progeny isolates were characterized by testing them on 25 wheat lines with different Yr genes for resistance and 10 simple sequence repeat (SSR) markers. The 127 progeny isolates were classified into 27 virulence phenotypes (VPs), and 65 multi-locus genotypes (MLGs). All progeny isolates and the parental isolate were avirulent to Yr5, Yr8, Yr10, Yr15, Yr24, Yr26, Yr32 , and YrTr1 ; but virulent to Yr1, Yr2, Yr3, Yr4, Yr25, Yr44 , and Yr76 . The VPs of the parental isolate to nine Yr genes ( Yr6, Yr7, Yr9, Yr17, Yr27, Yr28, Yr43, YrA , and YrExp2 ) and the avirulence phenotype to YrSP were found to be heterozygous. Based on the segregation of the virulence/avirulence phenotypes, we found that the VPs to Yr7, Yr28, Yr43 , and YrExp2 were controlled by a dominant gene; those to Yr6, Yr9 , and YrA ( Yr73, Yr74 ) by two dominant genes; those to Yr17 and Yr27 by one dominant and one recessive gene; and the avirulence phenotype to YrSP by two complementary dominant genes. Molecular mapping revealed the linkage of 10 virulence/avirulence genes. Comparison of the inheritance modes of the virulence/avirulence genes in this study with previous studies indicated complex interactions between virulence genes in the pathogen and resistance genes in wheat lines. The results are useful for understanding the plant-pathogen interactions and developing wheat cultivars with effective and durable resistance. 16 Genome-Wide Association Analyses Identify QTL Hotspots for Yield and Component Traits in Durum Wheat Grown under Yield Potential, Drought, and Heat Stress Environments Understanding the genetic bases of economically important traits is fundamentally important in enhancing genetic gains in durum wheat. In this study, a durum panel of 208 lines (comprised of elite materials and exotics from the International Maize and Wheat Improvement Center gene bank) were subjected to genome wide association study (GWAS) using 6,211 DArTseq single nucleotide polymorphisms (SNPs). The panel was phenotyped under yield potential (YP), drought stress (DT), and heat stress (HT) conditions for 2 years. Mean yield of the panel was reduced by 72% (to 1.64 t/ha) under HT and by 60% (to 2.33 t/ha) under DT, compared to YP (5.79 t/ha). Whereas, the mean yield of the panel under HT was 30% less than under DT. GWAS identified the largest number of significant marker-trait associations on chromosomes 2A and 2B with p -values 10−06 to 10−03 and the markers from the whole study explained 7–25% variation in the traits. Common markers were identified for stress tolerance indices: stress susceptibility index, stress tolerance, and stress tolerance index estimated for the traits under DT (82 cM on 2B) and HT (68 and 83 cM on 3B; 25 cM on 7A). GWAS of irrigated (YP and HT combined), stressed (DT and HT combined), combined analysis of three environments (YP + DT + HT), and its comparison with trait per se and stress indices identified QTL hotspots on chromosomes 2A (54–70 cM) and 2B (75–82 cM). This study enhances our knowledge about the molecular markers associated with grain yield and its components under different stress conditions. It identifies several marker-trait associations for further exploration and validation for marker-assisted breeding. 17 Intercropping with wheat lowers nutrient uptake and biomass accumulation of maize, but increases photosynthetic rate of the ear leaf Intercropping is an ancient agricultural practice that provides a possible pathway for sustainable increases in crop yields. Here, we determine how competition with wheat affects nutrient uptake (nitrogen and phosphorus) and leaf traits, such as photosynthetic rate, in maize. In a field experiment, maize was planted as a sole crop, in three different intercrop configurations with wheat (a replacement intercrop and two add-row intercrops), and as a skip-row system with one out of each three maize rows omitted. Nitrogen and phosphorus uptake were determined at flowering and maturity. Specific leaf area, leaf nitrogen concentration, chlorophyll content, and photosynthetic rate of the ear leaf were determined at flowering. Nitrogen and phosphorus concentrations were significantly lower in intercropped maize than in sole maize and skip-row maize at flowering, but these differences were smaller at maturity. At flowering, specific leaf area was significantly greater in intercrops than in skip-row maize. Leaf nitrogen concentration was significantly lower in add-row intercrops than in sole maize, skip-row maize or maize in the replacement intercrop. Leaf chlorophyll content was highest in sole and skip-row maize, intermediate in maize in the replacement intercrop, and lowest in maize grown in add-row intercrops. On the contrary, photosynthetic rate was significantly higher in the replacement intercrop than in sole maize, skip-row maize and the intercrop with an additional maize row. The findings indicate that competition with intercropped wheat severely constrained nutrient uptake in maize, while photosynthetic rate of the ear leaf was not negatively affected. Possible mechanisms for higher photosynthesis rate at lower leaf nitrogen content in intercropped maize are discussed. 18 Durum Wheat Landraces from East and West Regions of the Mediterranean Basin Are Genetically Distinct for Yield Components and Phenology Genetic diversity of durum wheat landraces is a powerful tool for the introgression of new alleles of commercial interest in breeding programs. In a previous study, our team structured a collection of 172 durum wheat landraces from 21 Mediterranean countries in four genetic populations related to their geographical origin: east Mediterranean (17), east Balkan and Turkey (23), west Balkan and Egypt (25), and West Mediterranean (73), leaving 34 genotypes as admixed, and association mapping was carried out for important agronomic traits. Using a subset of this collection, the current study identified 23 marker alleles with a differential frequency in landraces from east and west regions of the Mediterranean Basin, which affected important agronomic traits. Eastern landraces had higher frequencies than the western ones of alleles increasing the number of spikes (wPt-5385 on chromosome 1B), grains per m2 (wPt-0841 on chromosome 7B), and grain filling duration (7 significant marker trait associations). Eastern landraces had higher frequencies of marker alleles located on chromosomes 4A, 5B, and 6B associated with reduced cycle length, and lighter grains than the western ones. Also for lower kernel weight, four marker alleles were located on chromosome 1A. Breeders may use the molecular markers identified in the current study for improving yield under specific Mediterranean environments. 19 Influence of cadmium and phosphorus enhance absorption and membrane damage in wheat seedlings grown in nutrient medium The effects of cadmium (Cd) and their amelioration with phosphorus (P) on plant growth, antioxidative components, and accumulation of Cd, iron (Fe), and zinc (Zn) were studied in wheat ( Triticum aestivum L.) seedlings. Reduced biomass and chlorophyll contents under the influence of Cd were observed to be increased on P application. As compared to control, the content of NP-SH, proline, and cysteine were observed to be increased in Cd treated seedlings which was also comparatively higher in Cd with P exposed seedlings. The activities of CAT, POX, SOD, APX, and GR were increased both in root and shoot at lower dose of Cd but reduced at higher dose, while P application enhanced the activity of these enzymes even at higher dose. Application of P, reduced the uptake of Cd but enhanced the accumulation of Fe and Zn both in root and shoot tissue. A close relationship existed between lipid peroxidation and tissue metal concentration.
2/4 本期作者：Rui Wang 本来今天按计划是继续我们生信小菜鸟的养成记，但是今天小菜鸟在窝里不想出来了，我们就来谈谈腐生病原菌的抗病和育种问题。其实真正的起因是昨天我们的主编在群里分享了一篇即将在NG上发表的Septoria tritici blotch (STB) 抗病文章，正好小编自己博士阶段的研究也是相关方面的，现在就借这个机会来谈谈腐生病原菌的致病和抗病机理。今天这一系列文章也算是我们公众号首次正式的跟大家介绍这方面的内容了！ 在开始之前，先概述一下基本的研究背景：大家对于小麦抗病机理的理解大多来自于锈病和白粉病这种危害比较大的疾病，但一定要注意这些疾病都是由一些共生病原菌造成的。这些共生病原菌侵染植物的目的是跟宿主共生，然后宿主最普遍的一种抗病手段就是通过HR反应来杀死自己一些局部的细胞和组织，这样共生病原菌就失去了营养来源，也就被抑制在了这个局部的组织处。而经典的分子抗病模型就是gene-for-gene model，如下图，R gene 识别 Avr gene来诱导抗性。在这个模型中，要想成功侵入宿主，那就要求病原菌没有Avr，而宿主要想抗病，那就必须含有R蛋白，所以这种模型的抗病基因一般都是Dominant Resistance。 但今天介绍的腐生病原菌可就大不相同了，顾名思义，腐生菌就是要生活在死的组织上，所以像上边那种HR反应的手段不仅不能抗病，反而帮助病原菌更好地生存了。事实上，根据研究发现（植病经典文章：The Cysteine Rich Necrotrophic Effector SnTox1 Produced by Stagonospora nodorum Triggers Susceptibility of Wheat Lines Harboring Snn1），腐生菌也就是利用了类似HR的生理过程，在侵染过程中释放一些毒性蛋白，诱导更为激烈的HR，我们称之为细胞程序性死亡Programmed cell death (PCD) 的过程来达到让植物的细胞没有止境的坏死，然后它们从死细胞中吸取营养。这个过程用模型归纳起来有点类似于反着的gene-for-gene model （这个模型目前还不能广泛应用），就如下图所示，在这个模型中，要想植物感病，病原菌首先要有毒素基因，并且植物中必须有能被这个毒素基因结合的蛋白。所以这种病的抗病基因一般是Recessive Resistance（Dominant Susceptibility） 提到这，小编也来炫耀一下，以上这两个model都是我读博所在NDSU和相关美国农部实验室共同提出来的。 相关文献 1. The wheat Stb6 gene controlling agene-for-gene resistance to Zymoseptoria tritici encodes a wall-associated kinase-like protein Nature Genetics Feb. 2018 由于系统问题，现在这篇文章在线查不到了，以下的简介是该文在 2016 年一次会议的摘要。 导读：接下来的前四篇文章都是围绕Septoria tritici blotch (STB)来展开的，第一篇发现抗病基因符合gene-for-gene模型，跟一般的腐生菌抗病“ reverse gene-for-gen”模型不一样，这也就是为什么能发NG的原因吧。 Z. tritici is an ascomycete fungus that causesSeptoria tritici blotch (STB), a globally economically damaging foliar disease of wheat. Resistance to STB is an important target in wheat breeding and during the past several decades at least 18 major resistance loci, most of which confer an isolate-specific resistance, have been identified and genetically mapped. However, none of these have so far been cloned. Stb6 is the most well-characterized resistance gene that controls Z. tritici isolates carrying a matching avirulence gene AvrStb6 via an unknown mechanism not involving HR. Here we report the isolation of Stb6 using a combination of map-based cloning, VIGS, TILLING and stable wheat transformation. We show that Stb6 encodes a transmembrane protein with an extracellular galacturonan-binding domain and a cytoplasmic kinase domain, and thus is a member of the wall-associated receptor kinase(WAK) gene family. This finding is in line with Z. tritici being a pathogen that colonizes leaf apoplast and does not penetrate host plant cells or develop appressoria. We also show that the common disease susceptibility alleles contain non-synonymous mutations corresponding to changes at the conserved amino acid residues in the kinase domain of the encoded protein, suggesting a mechanism of susceptibility which involves a loss of kinase activity. To our knowledge, this is the first report demonstrating control of gene-for-gene resistance by a WAK-like protein in plants. https://www.ismpmi.org/congress/2016/abstracts/pages/abstractdetail.aspx?LID=689 2. A small secreted protein in Zymoseptoria tritici is responsible for avirulence on wheat cultivars carrying the Stb6 resistance gene New Phytologist Feb. 2017 导读：第二篇到第四篇讲的是病原菌这个角度的基因克隆， AvrStb6 正好是上文中跟 Stb6 对应的因子。 Zymoseptoria tritici is the causal agent of Septoria tritici blotch, a major pathogen of wheat globally and the most damaging pathogen of wheat in Europe. A gene-for-gene (GFG) interaction between Z. tritici and wheat cultivars carrying the Stb6 resistance gene has been postulated for many years, but the genes have not been identified. We identified AvrStb6 by combining quantitative trait locus mapping in a cross between two Swiss strains with a genome-wide association study using a natural population of c. 100 strains fromFrance. We functionally validated AvrStb6 using ectopic transformations. AvrStb6 encodes a small, cysteine-rich, secreted protein that produces an avirulence phenotype on wheat cultivars carrying the Stb6 resistance gene. We found 16 nonsynonymous single nucleotide polymorphisms among the tested strains, indicating that AvrStb6 is evolving very rapidly. AvrStb6 is located in a highly polymorphic subtelomeric region and is surrounded by transposable elements, which may facilitate its rapid evolution to overcome Stb6 resistance. AvrStb6 is the first avirulence gene to be functionally validated in Z. tritici, contributing to our understanding of avirulence in apoplastic pathogens and the mechanisms underlying GFGinteractions between Z. tritici and wheat. http://onlinelibrary.wiley.com/wol1/doi/10.1111/nph.14434/full 3. Have we finally opened the door to understanding Septoria tritici blotch disease in wheat? New Phytologist Mar. 2017 这篇是第二篇的评论性文章 The ability of a fungal pathogen to colonize and infect a plant is a special and unique process. Nearly all plant-fungal interactions occur out of sight as plants have evolved complex systems to recognize and resist most pathogens. However, there is a low percentage of fungal species that have evolved tools to circumvent host defense and cause disease, and it is the basis of these interactions which is of intense interest amongst plant and microbe researchers. It is now recognized that pathogens facilitate disease by secreting virulence molecules (also known as effectors) that target and manipulate endogenous host processes. Consequently, the identification and characterization of these effectors has been the focus of the molecular plant pathology field now for several decades, not only to understand the basis of disease, but also to underpin novel disease management strategies. In the study by Zhong et al . in this issue of New Phytologist (pp.619–631), the authors have identified the first effector from the devastating wheat pathogen Zymoseptoria tritici involved in a gene-for-gene interaction with a host resistance protein and, in doing so,have opened the door to finally begin to understand how it inflicts devastating yield losses. http://onlinelibrary.wiley.com/doi/10.1111/nph.14502/full 4. Characterization of an antimicrobial and phytotoxic ribonuclease secreted by the fungal wheat pathogen Zymoseptoria tritici New Phytologist Sept. 2017 导读：第四篇仍然是病原菌角度克隆致病因子，effector Zt6，这个因子应该符合Reverse gene-for-gene model，因为它是一个毒素蛋白，不过这个研究的创新点在于发现这个因子有双重效用，除了做为毒素侵染宿主以外，还能做为antimicrobial因子来抑制其它病原菌的生长进而减少竞争（这些毒素要是能被提纯开发成广谱抗生素或者抗真菌药物，那可是了不得的成果！） The fungus Zymoseptoria tritici is the causal agent of SeptoriaTritici Blotch (STB) disease of wheat leaves. Zymoseptoria tritici secretes many functionally uncharacterized effector proteins during infection. Here, we characterized a secreted ribonuclease (Zt6) with an unusual biphasic expression pattern. Transient expression systems were used to characterize Zt6, and mutants thereof, in both host and non-hostplants. Cell-free protein expression systems monitored the impact of Zt6protein on functional ribosomes, and in vitro assays of cells treated with recombinant Zt6 determined toxicity against bacteria, yeasts, and filamentous fungi. We demonstrated that Zt6 is a functional ribonuclease and that phytotoxicity is dependent on both the presence of a 22-amino-acid N-terminal ‘loop’ region and its catalytic activity.Zt6 selectively cleaves both plant and animal rRNA species and is toxic to wheat, tobacco, bacterial and yeast cells, but not to Z. tritici itself. Zt6 is the first Z. tritici effector demonstrated to have a likely dual functionality. The expression pattern of Zt6 and potent toxicity towards microorganisms suggest that, although it may contribute to the execution of wheat cell death, it is also likely to have an important secondary function in antimicrobial competition and nice protection. http://onlinelibrary.wiley.com/doi/10.1111/nph.14786/full 5. The hijacking of a receptor kinase-driven pathway bya wheat fungal pathogen leads to disease Science Advances Oct. 2016 导读：这篇是经典的reversegene-for-gene model 的研究文章，出自我史大哥之手！ Necrotrophic pathogens live and feed on dying tissue, but their interactions with plants are not well understood compared to biotrophic pathogens. The wheat Snn1 gene confers susceptibility to strains of the necrotrophic pathogen Parastagonospora nodorum that produce the SnTox1 protein. We report the positional cloning of Snn1, a member of the wall-associated kinase class of receptors, which are known to drive pathways for biotrophic pathogen resistance. Recognition of SnTox1by Snn1 activates programmed cell death, which allows this necrotroph to gain nutrients and sporulate. These results demonstrate that necrotrophic pathogens such as P. nodorum hijack host molecular pathways that are typically involved in resistance to biotrophic pathogens, revealing the complex nature of susceptibility and resistance in necrotrophic and biotrophic pathogen interactions with plants. http://advances.sciencemag.org/content/2/10/e1600822 两篇综述性文章： 文章发的再牛，用到田里才算成功！宋老师前天的推送“ 抗病育种之我遐想”我真是感受颇深，我自身其实就是从分子植病的背景转到育种课题组，起初也是不能太理解育种实践中的一些思维和操作，但是现在越来越明白，在小麦研究领域中，理论和应用还是有很大的一个鸿沟的。不过鸿沟越大，我们这些小麦研究者们才越有奋斗的动力和价值 ! 6. Navigating complexity to breed disease-resistant crops Nature Reviews Genetics Jan. 2018 Plant diseases are responsible for substantial crop losses each year and pose a threat to global food security and agricultural sustainability. Improving crop resistance to pathogens through breeding is an environmentally sound method for managing disease and minimizing these losses. However, it is challenging to breed varieties with resistance that is effective, stable and broad-spectrum. Recent advances in genetic and genomic technologies have contributed to a better understanding of the complexity of host-pathogen interactions and have identified some of the genes and mechanisms that underlie resistance. This new knowledge is benefiting crop improvement through better-informed breeding strategies that utilize diverse forms of resistance at different scales, from the genome of a single plant to the plant varieties deployed across a region. https://www.nature.com/articles/nrg.2017.82 7. A review of wheat diseases—a field perspective （这篇我们在 10/24 推送过： 小麦病害综述--除了白粉病 ） Molecular Plant Pathology Dec. 2017 Wheat is one of the primary staple foods throughout the planet.Significant yield gains in wheat production over the past 40 years have resulted in a steady balance of supply versus demand. However, predicted global population growth rates and dietary changes mean that substantial yield gains over the next several decades will be needed to meet this escalating demand. Akey component to meeting this challenge is better management of fungal incited diseases, which can be responsible for 15%–20% yield losses per annum.Prominent diseases of wheat that currently contribute to these losses include the rusts, blotches and head blight/scab. Other recently emerged or relatively unnoticed diseases, such as wheat blast and spot blotch, respectively, also threaten grain production. This review seeks to provide an overview of the impact, distribution and management strategies of these diseases. In addition, the biology of the pathogens and the molecular basis of their interaction with wheat are discussed. http://onlinelibrary.wiley.com/doi/10.1111/mpp.12618/full 欢迎关注 “小麦研究联盟”， 了解小麦新进展投稿、转载、合作以及信息发布等请联系： wheatgenome
2018年第五周小麦文献推荐（2.4） 1 The goat grass genome’s role in wheat improvement Nature plants上面的一篇点评，通讯作者是何中虎老师。 The recently published reference genome of Aegilops tauschii provides new insights into the originator of the D genome donor of hexaploid wheat. This will be a foundation for exploring the genomic diversity underpinning adaptive traits in wheat, and ultimately advance wheat improvement efforts. 2 Identification of QTL conferring resistance to stripe rust (Puccinia striiformis f. sp. hordei) and leaf rust (Puccinia hordei) in barley using nested association mapping (NAM) The biotrophic rust fungi Puccinia hordei and Puccinia striiformis are important barley pathogens with the potential to cause high yield losses through an epidemic spread. The identification of QTL conferring resistance to these pathogens is the basis for targeted breeding approaches aiming to improve stripe rust and leaf rust resistance of modern cultivars. Exploiting the allelic richness of wild barley accessions proved to be a valuable tool to broaden the genetic base of resistance of barley cultivars. In this study, SNP-based nested association mapping (NAM) was performed to map stripe rust and leaf rust resistance QTL in the barley NAM population HEB-25, comprising 1,420 lines derived from BC1S3 generation. By scoring the percentage of infected leaf area, followed by calculation of the area under the disease progress curve and the average ordinate during a two-year field trial, a large variability of resistance across and within HEB-25 families was observed. NAM based on 5,715 informative SNPs resulted in the identification of twelve and eleven robust QTL for resistance against stripe rust and leaf rust, respectively. Out of these, eight QTL for stripe rust and two QTL for leaf rust are considered novel showing no overlap with previously reported resistance QTL. Overall, resistance to both pathogens in HEB-25 is most likely due to the accumulation of numerous small effect loci. In addition, the NAM results indicate that the 25 wild donor QTL alleles present in HEB-25 strongly differ in regard to their individual effect on rust resistance. In future, the NAM concept will allow to select and combine individual wild barley alleles from different HEB parents to increase rust resistance in barley. The HEB-25 results will support to unravel the genetic basis of rust resistance in barley, and to improve resistance against stripe rust and leaf rust of modern barley cultivars. 3 Phosphorus Alters Starch Morphology and Gene Expression Related to Starch Biosynthesis and Degradation in Wheat Grain Phosphorus is an essential plant macronutrient which profoundly affects the yield and quality of wheat starch. In this study, scanning electron microscopy showed that P fertilizer amount (0, 46, and 92 kg P ha−1) had no significant effect on the shape of starch granules in wheat (cv. Xindong 20) grain. However, confocal laser scanning microscopy with 3-(4-carboxybenzoyl) quinoline-2-carboxaldehyde and methanolic merbromin stains indicated that P amount influenced the microstructure of the starch granules. Starch granules from the 46 kg P ha−1 treatment released significantly more reducing sugars than those from the 0 and 92 kg P ha−1 treatments during digestion with alpha-amylase and amyloglucosidase digestion. Phosphorus application (especially the 46 kg P ha−1 treatments) significantly increased the relative expression of genes related to starch synthesis (especially during early to mid-grain filling) and starch degradation (especially during mid- and late grain filling). Phosphorus application also increased the transcript abundance of amylase genes at the periphery of the endosperm. We propose that P application, especially the 46 kg P ha−1 treatment, enhanced channels in wheat starch granules. These channels facilitated the transport of substances required for starch biosynthesis, thus increasing starch accumulation in wheat endosperm. These results provide insight into the potential mechanisms through which P influences the microstructure and biosynthesis of wheat starch. 4 Enhancement of Germination, Seedling Growth, and Oxidative Metabolism of Barley under Simulated Acid Rain Stress by Exogenous Trehalose This study investigated the effects of simulated acid rain on germination, seedling growth, and oxidative metabolism in barley (Hordeum vulgare L.). Barley seeds were separately soaked in trehalose solutions of 5, 10, and 15 mM concentration or distilled water (the control). Results showed inhibited seed germination, increased foliar damage, decreased chlorophyll content, damaged roots, and delayed seedlings growth in barley when exposed to acid rain at pH 3.0. Although the treatment with acid rain increased the activities of peroxidase, catalase, and plasma membrane H+-ATPase, membrane permeability and malondialdehyde content still increased significantly. However, the addition of exogenous trehalose significantly alleviated the negative effect of acid rain on growth inhibition of barley and increased total leaf chlorophyll due to an increase of chlorophyll a content. Trehalose also increased catalase and peroxidase activity, which led to an increase in the antioxidant capacity and a balance in production and scavenging of free radicals. Plasma membrane H+-ATPase activities of roots and leaves also increased with trehalose and maintained stable pH of the cytoplasm of roots and leaf cells under low pH. The 10 mM trehalose pretreatment was enough to alleviative the negative effects of acid rain in barley 5 Genome-Wide Comparative Analysis of Flowering-Related Genes in Arabidopsis, Wheat, and Barley Early flowering is an important trait influencing grain yield and quality in wheat ( Triticum aestivum L.) and barley ( Hordeum vulgare L.) in short-season cropping regions. However, due to large and complex genomes of these species, direct identification of flowering genes and their molecular characterization remain challenging. Here, we used a bioinformatic approach to predict flowering-related genes in wheat and barley from 190 known Arabidopsis ( Arabidopsis thaliana (L.) Heynh.) flowering genes. We identified 900 and 275 putative orthologs in wheat and barley, respectively. The annotated flowering-related genes were clustered into 144 orthologous groups with one-to-one, one-to-many, many-to-one, and many-to-many orthology relationships. Our approach was further validated by domain and phylogenetic analyses of flowering-related proteins and comparative analysis of publicly available microarray data sets for in silico expression profiling of flowering-related genes in 13 different developmental stages of wheat and barley. These further analyses showed that orthologous gene pairs in three critical flowering gene families (PEBP, MADS, and BBX) exhibited similar expression patterns among 13 developmental stages in wheat and barley, suggesting similar functions among the orthologous genes with sequence and expression similarities. The predicted candidate flowering genes can be confirmed and incorporated into molecular breeding for early flowering wheat and barley in short-season cropping regions. 6 Genomic, Biochemical, and Modeling Analyses of Asparagine Synthetases from Wheat Asparagine synthetase activity in cereals has become an important issue with the discovery that free asparagine concentration determines the potential for formation of acrylamide, a probably carcinogenic processing contaminant, in baked cereal products. Asparagine synthetase catalyses the ATP-dependent transfer of the amino group of glutamine to a molecule of aspartate to generate glutamate and asparagine. Here, asparagine synthetase-encoding polymerase chain reaction (PCR) products were amplified from wheat ( Triticum aestivum ) cv. Spark cDNA. The encoded proteins were assigned the names TaASN1, TaASN2, and TaASN3 on the basis of comparisons with other wheat and cereal asparagine synthetases. Although very similar to each other they differed slightly in size, with molecular masses of 65.49, 65.06, and 66.24 kDa, respectively. Chromosomal positions and scaffold references were established for TaASN1, TaASN2 , and TaASN3 , and a fourth, more recently identified gene, TaASN4 . TaASN1, TaASN2 , and TaASN4 were all found to be single copy genes, located on chromosomes 5, 3, and 4, respectively, of each genome (A, B, and D), although variety Chinese Spring lacked a TaASN2 gene in the B genome. Two copies of TaASN3 were found on chromosome 1 of each genome, and these were given the names TaASN3.1 and TaASN3.2 . The TaASN1, TaASN2, and TaASN3 PCR products were heterologously expressed in Escherichia coli ( TaASN4 was not investigated in this part of the study). Western blot analysis identified two monoclonal antibodies that recognized the three proteins, but did not distinguish between them, despite being raised to epitopes SKKPRMIEVAAP and GGSNKPGVMNTV in the variable C-terminal regions of the proteins. The heterologously expressed TaASN1 and TaASN2 proteins were found to be active asparagine synthetases, producing asparagine and glutamate from glutamine and aspartate. The asparagine synthetase reaction was modeled using SNOOPY® software and information from the BRENDA database to generate differential equations to describe the reaction stages, based on mass action kinetics. Experimental data from the reactions catalyzed by TaASN1 and TaASN2 were entered into the model using Copasi, enabling values to be determined for kinetic parameters. Both the reaction data and the modeling showed that the enzymes continued to produce glutamate even when the synthesis of asparagine had ceased due to a lack of aspartate. 7 Comparative Transcriptome Profiles of Near-Isogenic Hexaploid Wheat Lines Differing for Effective Alleles at the 2DL FHB Resistance QTL Fusarium head blight (FHB), caused by the fungus Fusarium graminearum, represents one of the major wheat diseases worldwide, determining severe yield losses and reduction of grain quality due to the accumulation of mycotoxins. The molecular response associated with the wheat 2DL FHB resistance QTL was mined through a comprehensive transcriptomic analysis of the early response to F. graminearum infection, at 3 days post-inoculation, in spikelets and rachis. The analyses were conducted on two near isogenic lines (NILs) differing for the presence of the 2DL QTL (2-2618, resistant 2DL+ and 2-2890, susceptible null). The general response to fungal infection in terms of mRNAs accumulation trend was similar in both NILs, even though involving an higher number of DEGs in the susceptible NIL, and included down-regulation of the primary and energy metabolism, up-regulation of enzymes implicated in lignin and phenylpropanoid biosynthesis, activation of hormons biosynthesis and signal transduction pathways and genes involved in redox homeostasis and transcriptional regulation. The search for candidate genes with expression profiles associated with the 2DL QTL for FHB resistance led to the discovery of processes differentially modulated in the R and S NILs related to cell wall metabolism, sugar and JA signaling, signal reception and transduction, regulation of the redox status and transcription factors. Wheat FHB response-related miRNAs differentially regulated were also identified as putatively implicated in the superoxide dismutase activities and affecting genes regulating responses to biotic/abiotic stresses and auxin signaling. Altered gene expression was also observed for fungal non-codingRNAs. The putative targets of two of these were represented by the wheat gene WIR1A, involved in resistance response, and a gene encoding a jacalin-related lectin protein, which participate in biotic and abiotic stress response, supporting the presence of a cross-talk between the plant and the fungus. 这篇文章有漏引嫌疑，通过转录组研究2DL QTL已经有几篇了，这篇又引用了几篇呢。。。。 8 Impact of Timing and Method of Virus Inoculation on the Severity of Wheat Streak Mosaic Disease Wheat streak mosaic virus (WSMV), transmitted by the wheat curl mite Aceria tosichella , frequently causes significant yield loss in winter wheat throughout the Great Plains of the United States. A field study was conducted in the 2013–14 and 2014–15 growing seasons to compare the impact of timing of WSMV inoculation (early fall, late fall, or early spring) and method of inoculation (mite or mechanical) on susceptibility of winter wheat cultivars Mace (resistant) and Overland (susceptible). Relative chlorophyll content, WSMV incidence, and yield components were determined. The greatest WSMV infection occurred for Overland, with the early fall inoculations resulting in the highest WSMV infection rate (up to 97%) and the greatest yield reductions relative to the control (up to 94%). In contrast, inoculation of Mace resulted in low WSMV incidence (1 to 28.3%). The findings from this study indicate that both method of inoculation and wheat cultivar influenced severity of wheat streak mosaic; however, timing of inoculation also had a dramatic influence on disease. In addition, mite inoculation provided much more consistent infection rates and is considered a more realistic method of inoculation to measure disease impact on wheat cultivars. 9 A Genome-Wide Association Study of Field and Seedling Response to Individual Stem Rust Pathogen Races Reveals Combinations of Race-Specific Genes in North American Spring Wheat Stem rust of wheat caused by the fungal pathogen Puccinia graminis f. sp. tritici historically caused major yield losses of wheat worldwide. To understand the genetic basis of stem rust resistance in contemporary North American spring wheat, genome-wide association analysis (GWAS) was conducted on an association mapping panel comprised of 250 elite lines. The lines were evaluated in separate nurseries each inoculated with a different P. graminis f. sp. tritici race for 3 years (2013, 2015, and 2016) at Rosemount, Minnesota allowing the evaluation of race-specificity separate from the effect of environment. The lines were also challenged with the same four races at the seedling stage in a greenhouse facility at the USDA-ARS Cereal Disease Laboratory. A total of 22,310 high-quality SNPs obtained from the Infinium 90,000 SNPs chip were used to perform association analysis. We observed often negative and sometimes weak correlations between responses to different races that highlighted the abundance of race-specific resistance and the inability to predict the response of the lines across races. Markers strongly associated with resistance to the four races at seedling and field environments were identified. At the seedling stage, the most significant marker-trait associations were detected in the regions of known major genes ( Sr6, Sr7a , and Sr9b ) except for race QFCSC where a strong association was detected on chromosome arm 1AL. We postulated the presence of Sr2, Sr6, Sr7a, Sr8a, Sr9b, Sr11, Sr12, Sr24, Sr25, Sr31 , and Sr57 ( Lr34 ) in this germplasm based on phenotypic and marker data. We found over half of the panel possessed three or more Sr genes, and most commonly included various combinations of Sr6, Sr7a, Sr8a, Sr9b, Sr11, Sr12 , and Sr57 . Most of these genes confer resistance to specific P. graminis f. sp. tritici races accounting for the prevalent stem rust resistance in North American spring wheat. 10 Identification and Expression Analysis of Wheat TaGF14 Genes The 14-3-3 gene family members play key roles in various cellular processes. However, little is known about the numbers and roles of 14-3-3 genes in wheat. The aims of this study were to identify TaGF14 numbers in wheat by searching its whole genome through blast, to study the phylogenetic relationships with other plant species and to discuss the functions of TaGF14s . The results showed that common wheat harbored 20 TaGF14 genes, located on wheat chromosome groups 2, 3, 4, and 7. Out of them, eighteen TaGF14s are non-ε proteins, and two wheat TaGF14 genes, TaGF14i and TaGF14f , are ε proteins. Phylogenetic analysis indicated that these genes were divided into six clusters: cluster 1 ( TaGF14d, TaGF14g, TaGF14j, TaGF14h, TaGF14c , and TaGF14n ); cluster 2 ( TaGF14k ); cluster 3 ( TaGF14b, TaGF14l, TaGF14m , and TaGF14s ); cluster 4 ( TaGF14a, TaGF14e , and TaGF14r ); cluster 5 ( TaGF14i and TaGF14f ); and cluster 6 ( TaGF14o, TaGF14p, TaGF14q , and TaGF14t ). Tissue-specific gene expressions suggested that all TaGF14s were likely constitutively expressed, except two genes, i.e., TaGF14p and TaGF14f . And the highest amount of TaGF14 transcripts were observed in developing grains at 20 days post anthesis (DPA), especially for TaGF14j and TaGF14l. After drought stress, five genes, i.e., TaGF14c , TaGF14d , TaGF14g , TaGF14h , and TaGF14j , were up-regulated expression under drought stress for both 1 and 6 h, suggesting these genes played vital role in combating against drought stress. However, all the TaGF14s were down-regulated expression under heat stress for both 1 and 6 h, indicating TaGF14s may be negatively associated with heat stress by reducing the expression to combat heat stress or through other pathways. These results suggested that cluster 1, e.g., TaGF14j , may participate in the whole wheat developing stages, e.g., grain-filling (starch biosynthesis) and may also participate in combating against drought stress. Subsequently, a homolog of TaGF14j , TaGF14-JM22 , were cloned by RACE and used to validate its function. Immunoblotting results showed that TaGF14-JM22 protein, closely related to TaGF14d , TaGF14g , and TaGF14j , can interact with AGP-L, SSI, SSII, SBEIIa, and SBEIIb in developing grains, suggesting that TaGF14s located on group 4 may be involved in starch biosynthesis. Therefore, it is possible to develop starch-rich wheat cultivars by modifying TaGF14s . 11 Towards a genetic road map of wheat-processing quality The elucidation of wheat-quality genetics may be seen metaphorically as a road map to greater knowledge, and also as an interlocking jigsaw puzzle. Major genes relevant to the attributes needed for wheat-processing quality have been identified, namely, protein content, grain hardness, milling yield, dough strength, dough extensibility, baking quality, starch-paste viscosity and nutritional value . 12 Variation in grain Zn concentration, and the grain ionome, in field-grown Indian wheat Wheat is an important dietary source of zinc (Zn) and other mineral elements in many countries. Dietary Zn deficiency is widespread, especially in developing countries, and breeding (genetic biofortification) through the HarvestPlus programme has recently started to deliver new wheat varieties to help alleviate this problem in South Asia. To better understand the potential of wheat to alleviate dietary Zn deficiency, this study aimed to characterise the baseline effects of genotype (G), site (E), and genotype by site interactions (GxE) on grain Zn concentration under a wide range of soil conditions in India. Field experiments were conducted on a diverse panel of 36 Indian-adapted wheat genotypes, grown on a range of soil types (pH range 4.5–9.5), in 2013–14 (five sites) and 2014–15 (six sites). Grain samples were analysed using inductively coupled plasma-mass spectrometry (ICP-MS). The mean grain Zn concentration of the genotypes ranged from 24.9–34.8 mg kg-1, averaged across site and year. Genotype and site effects were associated with 10% and 6% of the overall variation in grain Zn concentration, respectively. Whilst G x E interaction effects were evident across the panel, some genotypes had consistent rankings between sites and years. Grain Zn concentration correlated positively with grain concentrations of iron (Fe), sulphur (S), and eight other elements, but did not correlate negatively with grain yield, i.e. no yield dilution was observed. Despite a relatively small contribution of genotype to the overall variation in grain Zn concentration, due to experiments being conducted across many contrasting sites and two years, our data are consistent with reports that biofortifying wheat through breeding is likely to be effective at scale given that some genotypes performed consistently across diverse soil types. Notably, all soils in this study were probably Zn deficient and interactions between wheat genotypes and soil Zn availability/management (e.g. the use of Zn-containing fertilisers) need to be better-understood to improve Zn supply in food systems. 13 Fitness traits of deoxynivalenol and nivalenol-producing Fusarium graminearum species complex strains from wheat Fusarium graminearum of the 15-acetyl(A)deoxynivalenol(DON) chemotype is the main cause of Fusarium head blight (FHB) of wheat in south of Brazil. However, 3-ADON and nivalenol(NIV) chemotypes in other members of the species complex have been found in wheat. To improve our understanding of the pathogen biology and ecology, we assessed a range of fitness-related traits in a sample of 30 strains representatives of 15-ADON (F. graminearum), 3-ADON (F. cortaderiae and F. austroamericanum) and NIV (F. meridionale and F. cortaderiae). These included: perithecia formation on three cereal-based substrates, mycelial growth at two suboptimal temperatures, sporulation and germination, pathogenicity towards a susceptible and a moderately resistant cultivar and sensitivity to tebuconazole. The most important trait favoring F. graminearum was a two times higher sexual fertility ( 40% PPI = perithecia production index) than the other species ( 30% PPI); PPI varied among substrates (maize rice wheat). In addition, sensitivity to tebuconazole appeared lower in F. graminearum which had the only strain with EC50 1 ppm. In the pathogenicity assays, the DON-producers were generally more aggressive (1.5 to 2 × higher final severity) towards the two cultivars, with 3-ADON or 15-ADON leading to higher area under the severity curve than the NIV strains in the susceptible and moderately resistant cv., respectively. There was significant variation among strains of a same species with regards asexual fertility (mycelial growth, macroconidia production and germination), which suggested a strain- rather than a species-specific difference. These results contribute new knowledge to improve our understanding of the pathogen-related traits that may explain the dominance of certain members of the species complex in specific wheat agroecosystems. 14 The future of CRISPR technologies in agriculture Conventional plant breeding is unlikely to meet increasing food demands and other environmental challenges. By contrast, CRISPR technology is erasing barriers to genome editing and could revolutionize plant breeding. However, to fully benefit from the CRISPR revolution, we should focus on resolving its technical and regulatory uncertainties. 15 Asparagine synthetase genes (AsnS1 and AsnS2) in durum wheat: structural analysis and expression under nitrogen stress Wheat is one of the most widely grown cereal crops based on the amount of calories it provides in the human diet. Durum wheat ( Triticum turgidum ssp. durum ) is largely used for production of pasta and other products. In order to use genetic knowledge to improve the understanding of N-use efficiency, we carried out, for the first time in durum wheat, the isolation and the characterization of four members of the asparagine synthetase ( AsnS ) gene family. Phylogenetic inference clustered the Ttu - AsnS1 (1.1 and 1.2) and Ttu - AsnS2 (2.1 and 2.2) genes in AsnS gene class I, which is present in monocots and dicots. Class I genes underwent a subsequent duplication leading to the formation of two subgroups. Plants of Svevo cultivar were grown under N-stress conditions and expression of the four AsnS genes was investigated at three developmental stages (seedling, booting, and late milk development), crucial for N absorption, assimilation and remobilization. AsnS1 genes were down-regulated in N-stressed roots, stems and leaves during seedling growth and booting, but seemed to play a role in N remobilization in flag leaves during grain filling. AsnS2 genes were scarcely expressed in roots, stems, and leaves. In N-stressed spikes there was no differential expression in any of the genes. The genes were mapped in silico using a durum wheat SNP map, assigning Ttu - AsnS1 genes to chromosome 5 and Ttu - AsnS2 to chromosome 3. These findings provide a better understanding of the role of ASN genes in response to N stress in durum wheat. 16 A new opening for wheat seed production Crop plant domestication has targeted a variety of traits, including synchronous development of ovules and stamens to maximize fertilization and seed production. In wheat, with its autogamous, or self-fertilizing, flowers, this is very attractive for guaranteeing yield but extremely frustrating for a researcher trying to cross individuals of distinct genotypes, and even more so for a breeder trying to generate hybrids. Now, Okada et al. (2017) have provided a turning point by characterizing the developmental physiology of wheat florets opening after a few days post-anthesis (‘second opening’). This additional opportunity for pollination facilitates out-crossing, and provides a method to further understand the regulation of wheat flower architecture and development. 17 Unfertilized ovary pushes wheat flower open for cross-pollination Bread wheat is strongly autogamous; however, an opportunity for outcrossing occurs when self-pollination fails and florets open. The first phase of floret opening at anthesis is short and induced by lodicule turgidity. Some wheat florets re-open post-anthesis for several days, known as the 'second opening', for which the underlying mechanisms are largely unknown. We performed detailed physiological, anatomical, and histological investigations to understand the biological basis of the flower opening process. Wheat florets were observed open when the ovary was unfertilized. Unfertilized ovaries significantly increased in radial size post-anthesis, pushing the lemma and palea apart to open the florets. The absence of fertile pollen was not directly linked to this, but anther filament elongation coincided with initiation of ovary swelling. The pericarp of unfertilized ovaries did not undergo degeneration as normally seen in developing grains, instead pericarp cells remained intact and enlarged, leading to increased ovary radial size. This is a novel role for the ovary pericarp in wheat flower opening, and the knowledge is useful for facilitating cross-pollination in hybrid breeding. Ovary swelling may represent a survival mechanism in autogamous cereals such as wheat and barley, ensuring seed set in the absence of self-fertilization and increasing genetic diversity through cross-pollination. 18 Mapping and validation of a new QTL for adult-plant resistance to powdery mildew in Chinese elite bread wheat line Zhou8425B Zhou8425B is an elite wheat ( Triticum aestivum L.) line widely used as a parent in Chinese wheat breeding programs. Identification of genes for adult-plant resistance (APR) to powdery mildew in Zhou8425B is of high importance for continued controlling the disease. In the current study, the high-density Illumina iSelect 90K single-nucleotide polymorphism (SNP) array was used to map quantitative trait loci (QTL) for APR to powdery mildew in 244 recombinant inbred lines derived from the cross Zhou8425B/Chinese Spring. Inclusive composite interval mapping identified QTL on chromosomes 1B, 3B, 4B, and 7D, designated as QPm.caas - 1BL . 1 , QPm.caas - 3BS , QPm.caas - 4BL . 2, and QPm.caas - 7DS , respectively. Resistance alleles at the QPm.caas - 1BL.1 , QPm.caas - 3BS, and QPm.caas - 4BL . 2 loci were contributed by Zhou8425B, whereas that at QPm.caas - 7DS was from Chinese Spring. QPm.caas - 3BS , likely to be a new APR gene for powdery mildew resistance, was detected in all four environments. One SNP marker closely linked to QPm.caas - 3BS was transferred into a semi-thermal asymmetric reverse PCR (STARP) marker and tested on 103 commercial wheat cultivars derived from Zhou8425B. Cultivars with the resistance allele at the QPm.caas - 3BS locus had averaged maximum disease severity reduced by 5.3%. This STARP marker can be used for marker-assisted selection in improvement of the level of powdery mildew resistance in wheat breeding. 19 A new leaf rust resistance gene Lr79 mapped in chromosome 3BL from the durum wheat landrace Aus26582 Aus26582, a durum wheat landrace from the A. E. Watkins Collection, showed seedling resistance against durum-specific and common wheat-specific Puccinia triticina (Pt) pathotypes. Genetic analysis using a recombinant inbred line (RIL) population developed from a cross between Aus26582 and the susceptible parent Bansi with Australian Pt pathotype showed digenic inheritance and the underlying loci were temporarily named LrAW2 and LrAW3 . LrAW2 was located in chromosome 6BS and this study focused on characterisation of LrAW3 using RILs lacking LrAW2 . LrAW3 was incorporated into the DArTseq map of Aus26582/Bansi and was located in chromosome 3BL. Markers linked with LrAW3 were developed from the chromosome survey sequence contig 3B_10474240 in which closely-linked DArTseq markers 1128708 and 3948563 were located. Although bulk segregant analysis (BSA) with the 90 K Infinium array identified 51 SNPs associated with LrAW3 , only one SNP-derived KASP marker mapped close to the locus. Deletion bin mapping of LrAW3 -linked markers located LrAW3 between bins 3BL11-0.85-0.90 and 3BL7-0.63. Since no other all stage leaf rust resistance gene is located in chromosome 3BL, LrAW3 represented a new locus and was designated Lr79 . Marker sun786 mapped 1.8 cM distal to Lr79 and Aus26582 was null for this locus. However, the marker can be reliably scored as it also amplifies a monomorphic fragment that serves as an internal control to differentiate the null status of Aus26582 from reaction failure. This marker was validated among a set of durum and common wheat cultivars and was shown to be useful for marker-assisted selection of Lr79 at both ploidy levels. 20 Targeted Haplotype Comparisons between South African Wheat Cultivars Appear Predictive of Pre-harvest Sprouting Tolerance Pre-harvest sprouting (PHS) has been a serious production constraint for over two decades, especially in the summer rainfall wheat production regions of South Africa. It is a complex genetic trait controlled by multiple genes, which are significantly influenced by environmental conditions. This complicates the accurate prediction of a cultivar's stability in terms of PHS tolerance. A number of reports have documented the presence of major QTL on chromosomes 3A and 4A of modern bread wheat cultivars, which confer PHS tolerance. In this study, the SSR marker haplotype combination of chromosomes 3A and 4A of former and current South African cultivars were compared with the aim to select for improved PHS tolerance levels in future cultivars. A total of 101 wheat cultivars, including a susceptible cultivar and five international tolerant sources, were used in this study. These cultivars and donors were evaluated for their PHS tolerance by making use of a rain simulator. In addition, five seeds of each entry were planted out into seedling trays and leaf material harvested for DNA isolation. A modified CTAB extraction method was used before progressing to downstream PCR applications. Eight SSR markers targeted from the well-characterized 3A and 4A QTL regions associated with PHS tolerance, were used to conduct targeted haplotype analysis. Additionally, recently published KASP SNP markers, which identify the casual SNP mutations within the TaPHS1 gene, were used to genotype the germplasm. The haplotype marker data and phenotypic PHS data were compared across all cultivars and different production regions. A relative change in observed phenotypic variation percentage was obtained per marker allele and across marker haplotype combinations when compared to the PHS susceptible cultivar, Tugela-DN. Clear favorable haplotypes, contributing 40–60% of the variation for PHS tolerance, were identified for QTL 3A and 4A. Initial analyses show haplotype data appear to be predictive of PHS tolerance status and germplasm can now be selected to improve PHS tolerance. These haplotype data are the first of its kind for PHS genotyping in South Africa. In future, this can be used as a tool to predict the possible PHS tolerance range of a new cultivar. 21 Irrigation and Nitrogen Regimes Promote the Use of Soil Water and Nitrate Nitrogen from Deep Soil Layers by Regulating Root Growth in Wheat Unreasonably high irrigation levels and excessive nitrogen (N) supplementation are common occurrences in the North China Plain that affect winter wheat production. Therefore, a 6-yr-long stationary field experiment was conducted to investigate the effects of irrigation and N regimes on root development and their relationship with soil water and N use in different soil layers. Compared to the non-irrigated treatment (W0), a single irrigation at jointing (W1) significantly increased yield by 3.6–45.6%. With increases in water (W2, a second irrigation at flowering), grain yield was significantly improved by 14.1–45.3% compared to the W1 treatments during the drier growing seasons (2010–2011, 2012–2013, and 2015–2016). However, under sufficient pre-sowing soil moisture conditions, grain yield was not increased, and water use efficiency (WUE) decreased significantly in the W2 treatments during normal precipitation seasons (2011–2012, 2013–2014, and 2014–2015). Irrigating the soil twice inhibited root growth into the deeper soil depth profiles and thus weakened the utilization of soil water and NO3-N from the deep soil layers. N applications increased yield by 19.1–64.5%, with a corresponding increase in WUE of 66.9–83.9% compared to the no-N treatment (N0). However, there was no further increase in grain yield and the WUE response when N rates exceeded 240 and 180 kg N ha−1, respectively. A N application rate of 240 kg ha−1 facilitated root growth in the deep soil layers, which was conducive to utilization of soil water and NO3-N and also in reducing the residual NO3-N. Correlation analysis indicated that the grain yield was significantly positively correlated with soil water storage (SWS) and nitrate nitrogen accumulation (SNA) prior to sowing. Therefore, N rates of 180–240 kg ha−1 with two irrigations can reduce the risk of yield loss that occurs due to reduced precipitation during the wheat growing seasons, while under better soil moisture conditions, a single irrigation at jointing was effective and more economical. 22 Genome-Wide Association Studies and Comparison of Models and Cross-Validation Strategies for Genomic Prediction of Quality Traits in Advanced Winter Wheat Breeding Lines The aim of the this study was to identify SNP markers associated with five important wheat quality traits (grain protein content, Zeleny sedimentation, test weight, thousand-kernel weight, and falling number), and to investigate the predictive abilities of GBLUP and Bayesian Power Lasso models for genomic prediction of these traits. In total, 635 winter wheat lines from two breeding cycles in the Danish plant breeding company Nordic Seed A/S were phenotyped for the quality traits and genotyped for 10,802 SNPs. GWAS were performed using single marker regression and Bayesian Power Lasso models. SNPs with large effects on Zeleny sedimentation were found on chromosome 1B, 1D, and 5D. However, GWAS failed to identify single SNPs with significant effects on the other traits, indicating that these traits were controlled by many QTL with small effects. The predictive abilities of the models for genomic prediction were studied using different cross-validation strategies. Leave-One-Out cross-validations resulted in correlations between observed phenotypes corrected for fixed effects and genomic estimated breeding values of 0.50 for grain protein content, 0.66 for thousand-kernel weight, 0.70 for falling number, 0.71 for test weight, and 0.79 for Zeleny sedimentation. Alternative cross-validations showed that the genetic relationship between lines in training and validation sets had a bigger impact on predictive abilities than the number of lines included in the training set. Using Bayesian Power Lasso instead of GBLUP models, gave similar or slightly higher predictive abilities. Genomic prediction based on all SNPs was more effective than prediction based on few associated SNPs. 23 Plasma membrane proteome analysis identifies a role of barley Membrane Steroid Binding Protein in root architecture response to salinity Although physiological consequences of plant growth under saline conditions have been well described, understanding the core mechanisms conferring plant salt adaptation has only started. We target the root plasma membrane (PM) proteomes of two barley varieties, cvs. Steptoe and Morex, with contrasting salinity tolerance. In total, 588 PM proteins were identified by mass spectrometry, of which 182 were either cultivar- or salinity stress-responsive. Three candidate proteins with increased abundance in the tolerant cv. Morex were involved either in sterol-binding (a GTPase-activating protein for the ADP ribosylation factor, ZIGA2, and a membrane steroid binding protein, MSBP) or in phospholipid synthesis (phosphoethanolamine methyltransferase, PEAMT). Overexpression of barley MSBP conferred salinity tolerance to yeast cells, while knock-out of the heterologous AtMSBP1 increased salt sensitivity in Arabidopsis. Atmsbp1 plants showed a reduced number of lateral roots under salinity and root tip-specific expression of barley MSBP in Atmsbp1 complemented this phenotype. In barley, an increased abundance of MSBP correlates with reduced root length and lateral root formation as well as increased levels of auxin under salinity being stronger in the tolerant cv. Morex. Hence, we concluded the involvement of MSBP in phytohormone-directed adaptation of root architecture in response to salinity.
2018年第四周文献推荐（1.28） 亲，2018年的第一个月已经快溜走了，打算今年毕业的小伙伴要抓紧了。最近发现竟然还有老外哥们关注我们，我想问一声看得懂吗，Lee？当年浪迹twitter时关注过这位仁兄，他在twitter上非常活跃，如果汉语好，还是非常欢迎加入我们的。可惜19大之后，也就暂时告别一段时间了。 最近TAG貌似打算开通微信公众号，询问我们是否可以协助管理，我说我倒是可以在这里说一说，看看谁有兴趣参与管理，有兴趣的可以联系 13148474750@163.com ，前提是你能上twitter。 接下来，我们就说说本周的文献更新，本周还是有不少优质文献的，欢迎各位老师和同学在这里分享阅读心得。 1 Resistance gene discovery and cloning by sequence capture and association genetics Genetic resistance is the most economic and environmentally sustainable approach for crop disease protection. Disease resistance (R) genes from wild relatives are a valuable resource for breeding resistant crops. However, introgression of R genes into crops is a lengthy process often associated with co-integration of deleterious linked genes and pathogens can rapidly evolve to overcome R genes when deployed singly. Introducing multiple cloned R genes into crops as a stack would avoid linkage drag and delay emergence of resistance-breaking pathogen races. However, current R gene cloning methods require segregating or mutant progenies, which are difficult to generate for many wild relatives due to poor agronomic traits. We exploited natural pan-genome variation in a wild diploid wheat by combining association genetics with R gene enrichment sequencing (AgRenSeq) to clone four stem rust resistance genes in 6 months. RenSeq combined with diversity panels is therefore a major advance in isolating R genes for engineering broad-spectrum resistance in crops. 2 Genome-wide association analyses identify QTL hotspots for yield and component traits in durum wheat grown under yield potential, drought, and heat stress environments Understanding the genetic bases of economically important traits is fundamentally important in enhancing genetic gains in durum wheat. In this study, a durum panel of 208 lines (comprised of elite materials and exotics from the International Maize and Wheat Improvement Center gene bank) were subjected to genome wide association study (GWAS) using 6,211 DArTseq single nucleotide polymorphisms (SNPs). The panel was phenotyped under yield potential (YP), drought stress (DT), and heat stress (HT) conditions for two years. Mean yield of the panel was reduced by 72% (to 1.64 t/ha) under HT and by 60% (to 2.33 t/ha) under DT, compared to YP (5.79 t/ha). Whereas, the mean yield of the panel under HT was 30% less than under DT. GWAS identified the largest number of significant marker-trait associations on chromosomes 2A and 2B with p-values 10-06 to 10-03 and the markers from the whole study explained 7 to 25% variation in the traits. Common markers were identified for stress tolerance indices: stress susceptibility index, stress tolerance, and stress tolerance index estimated for the traits under DT (82 cM on 2B) and HT (68 and 83 cM on 3B; 25 cM on 7A). GWAS of irrigated (YP and HT combined), stressed (DT and HT combined), combined analysis of three environments (YP + DT + HT), and its comparison with trait per se and stress indices identified QTL hotspots on chromosomes 2A (54 to 70 cM) and 2B (75 to 82 cM). This study enhances our knowledge about the molecular markers associated with grain yield and its components under different stress conditions. It identifies several marker-trait associations for further exploration and validation for marker-assisted breeding. 3 QTL mapping of flag leaf-related traits in wheat (Triticum aestivum L.) QTL controlling flag leaf length, flag leaf width, flag leaf area and flag leaf angle were mapped in wheat. This study aimed to advance our understanding of the genetic mechanisms underlying morphological traits of the flag leaves of wheat (Triticum aestivum L.). A recombinant inbred line (RIL) population derived from ND3331 and the Tibetan semi-wild wheat Zang1817 was used to identify quantitative trait loci (QTLs) controlling flag leaf length (FLL), flag leaf width (FLW), flag leaf area (FLA), and flag leaf angle (FLANG). Using an available simple sequence repeat genetic linkage map, 23 putative QTLs for FLL, FLW, FLA, and FLANG were detected on chromosomes 1B, 2B, 3A, 3D, 4B, 5A, 6B, 7B, and 7D. Individual QTL explained 4.3-68.52% of the phenotypic variance in different environments. Four QTLs for FLL, two for FLW, four for FLA, and five for FLANG were detected in at least two environments. Positive alleles of 17 QTLs for flag leaf-related traits originated from ND3331 and 6 originated from Zang1817. QTLs with pleiotropic effects or multiple linked QTL were also identified on chromosomes 1B, 4B, and 5A; these are potential target regions for fine-mapping and marker-assisted selection in wheat breeding programs. 4 Relationship between QTL for grain shape, grain weight, test weight, milling yield, and plant height in the spring wheat cross RL4452/‘AC Domain’ Kernel morphology characteristics of wheat are complex and quantitatively inherited. A doubled haploid (DH) population of the cross RL4452/‘AC Domain’ was used to study the genetic basis of seed shape. Quantitative trait loci (QTL) analyses were conducted on a total of 18 traits: 14 grain shape traits, flour yield (Fyd), and three agronomic traits (Plant height , 1000 Grain weight , Test weight ), using data from trial locations at Glenlea, Brandon, and Morden in Manitoba, Canada, between 1999 and 2004. Kernel shape was studied through digital image analysis with an Acurum® grain analyzer. Plht, Gwt, Twt, Fyd, and grain shape QTL were correlated with each other and QTL analysis revealed that QTL for these traits often mapped to the same genetic locations. The most significant QTL for the grain shape traits were located on chromosomes 4B and 4D, each accounting for up to 24.4% and 53.3% of the total phenotypic variation, respectively. In addition, the most significant QTL for Plht, Gwt, and Twt were all detected on chromosome 4D at the Rht-D1 locus. Rht-D1b decreased Plht, Gwt, Twt, and kernel width relative to the Rht-D1a allele. A narrow genetic interval on chromosome 4B contained significant QTL for grain shape, Gwt, and Plht. The ‘AC Domain’ allele reduced Plht, Gwt, kernel length and width traits, but had no detectable effect on Twt. The data indicated that this variation was inconsistent with segregation at Rht-B1 . Numerous QTL were identified that control these traits in this population. 5 Identification and Validation of a New Source of Low Grain Cadmium Accumulation in Durum Wheat Cadmium (Cd) is a heavy metal that has no known biological function and is toxic for many living organisms. The maximum level of Cd concentration allowed in the international market for wheat grain is 0.2 mg kg-1. Because phenotyping for Cd uptake is expensive and time consuming, molecular markers associated with genes conferring low Cd uptake would expedite selection and lead to the development of durum cultivars with reduced Cd concentrations. Here, we identified single nucleotide polymorphisms (SNPs) associated with a novel low Cd uptake locus in the durum experimental line D041735, which has hexaploid common wheat in its pedigree. Genetic analysis revealed a single major QTL for Cd uptake on chromosome arm 5BL within a 0.3 cM interval flanked by SNP markers. Analysis of the intervening sequence revealed a gene with homology to an aluminum-induced protein as a candidate gene. Validation and allelism tests revealed that the low Cd uptake gene identified in this study is different from the closely linked *Cdu1-B *gene, which also resides on 5BL. This study therefore confirmed that the durum experimental line D041735 contains a novel low Cd uptake gene that was likely acquired from hexaploid wheat. 6 Pleiotropic e ects of the wheat domestication gene Q on yield and grain morphology Mutation of the Q gene, well-known a ecting wheat spike structure, represents a key domestication step in the formation of today’s free-threshing, economically important wheats. In a previous study, multiple yield components and spike charac- teristics were associated with the Q gene interval in the bread wheat ‘Forno’ × European spelt ‘Oberkulmer’ recombinant inbred line population. Here, we reported that this interval was also associated with grain yield, grains m−2, grain morphol- ogy, and spike dry weight at anthesis. To clarify the roles of Q in agronomic trait performance, a functional marker for the Q gene was developed. Analysis of allelic e ects showed that the bread wheat Q allele conferred free-threshing habit, soft glumes, and short and compact spikes compared with q. In addition, the Q allele contributed to higher grain yield, more grains m−2, and higher thousand grain weight, whereas q contributed to more grains per spike/spikelet likely resulting from increased preanthesis spike growth. For grain morphology, the Q allele was associated with reduced ratio of grain length to height, indicating a rounder grain. These results are supported by analysis of four Q mutant lines in the Chinese Spring background. Therefore, the transition from q to Q during wheat domestication had profound e ects on grain yield and grain shape evolution as well, being a consequence of pleiotropy. 7 An Overexpressed Q Allele Leads to Increased Spike Density and Improved Processing Quality in Common Wheat (Triticum aestivum) Spike density and processing quality are important traits in the modern wheat production that is controlled by multiple gene loci. The associated genes have been intensively studied and new discoveries have been constantly reported during the past few decades. However, no gene playing significant roles in the development of these two traits was identified. In the current study, a common wheat mutant with extremely compact spikes and good processing quality was isolated and characterized. A new allele ( Qc1 ) of Q gene (an important domestication gene) responsible for the mutant phenotype was cloned and the molecular mechanism for the mutant phenotype was studied. Results revealed that Qc1 was originated from a point mutation that interferes with the miRNA172-directed cleavage of the Q transcripts, leading to its overexpression. It also reduces the longitudinal cell size of rachises, resulting in an increased spike density. Furthermore, Qc1 increases the number of vascular bundles, which suggests a higher efficiency in the transportation of assimilates in the spikes of the mutant than that of WT. This accounts for the improved processing quality. The effects of Qc1 on spike density and wheat processing quality were confirmed by analyzing nine common wheat mutants possessing four different Qc alleles. These results deepen our understanding of the key roles of Q gene and provide new insights for the potential application of Qc alleles in wheat quality breeding. 8 Transgenerationally precipitated meiotic chromosome instability fuels rapid karyotypic evolution and phenotypic diversity in an artificially constructed allotetraploid wheat Whereas a distinct karyotype with defined chromosome number and structure characterizes each biological species, it is intrinsically labile. Polyploidy or whole genome duplication (WGD) has played a pervasive and ongoing role in the evolution of all eukaryotes, and is the most dramatic force known to cause rapid karyotypic reconfiguration, especially at the initial stage. However, issues concerning transgenerational propagation of karyotypic heterogeneity and its translation to phenotypic diversity in nascent allopolyploidy, at the population level, have yet to be studied in detail. Here, we report a large-scale examination of transgenerationally propagated karyotypic heterogeneity and its phenotypic manifestation in an artificially constructed allotetraploid with a genome composition of AADD, i.e., involving two of the three progenitor genomes of polyploid wheat. Specifically, we show that ( i ) massive organismal karyotypic heterogeneity is precipitated after 12 consecutive generations of selfing from a single euploid founder individual; ( ii ) there exist dramatic differences in aptitudes between subgenomes and among chromosomes for whole-chromosome gain and/or loss and structural variations; ( iii ) majority of the numerical and structural chromosomal variations are concurrent due to mutual contingency and possible functional constraint; ( iv ) purposed and continuous selection and propagation for euploidy over generations did not result in enhanced karyotype stabilization; and ( v ) extent of karyotypic variation correlates with variability of phenotypic manifestation. Together, our results document that allopolyploidization catalyzes rampant and transgenerationally heritable organismal karyotypic heterogeneity that drives population-level phenotypic diversification, which lends fresh empirical support to the still contentious notion that WGD enhances organismal evolvability. 9 Genomic Imprinting was Evolutionarily Conserved during Wheat Polyploidization Genomic imprinting is an epigenetic phenomenon that causes genes to be differentially expressed depending on their parent-of-origin. To evaluate the evolutionary conservation of genomic imprinting and the effects of ploidy on this process, we investigated parent-of-origin-specific gene expression patterns in the endosperm of diploid (Aegilops spp.), tetraploid, and hexaploid wheat (Triticum spp.) at various stages of development via high-throughput transcriptome sequencing. We identified 91, 135, and 146 maternally or paternally expressed genes (MEGs or PEGs, respectively) in diploid, tetraploid, and hexaploid wheat, respectively, 52.7% of which exhibited dynamic expression patterns at different developmental stages. Gene ontology enrichment analysis suggested that MEGs and PEGs were involved in metabolic processes and DNA-dependent transcription, respectively. Nearly half of the imprinted genes exhibited conserved expression patterns during wheat hexaploidization. In addition, forty percent of the homeolog pairs originating from whole genome duplication were consistently maternally or paternally biased in the different subgenomes of hexaploid wheat. Furthermore, imprinted expression was found for 41.2% and 50.0% of homolog pairs that evolved by tandem duplication after genome duplication in tetraploid and hexaploid wheat, respectively. These results suggest that genomic imprinting was evolutionarily conserved between closely related Triticum and Aegilops species, and in the face of polyploid hybridization between species in these genera. 10 Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat(貌似去年这篇文章已经介绍过了) There is an urgent need to increase global crop production. Identifying and combining genes controlling indidviual yield components, such as grain weight, holds the potential to enhance crop yields. Transcriptomics is a powerful tool to gain insights into the complex gene regulatory networks that underlie such traits, but relies on the availability of a high-quality reference sequence and accurate gene models. Previously, we identified a grain weight QTL on wheat chromosome 5A (5A QTL) which acts during early grain development to increase grain length through cell expansion in the pericarp. In this study, we performed RNA-sequencing on near isogenic lines (NILs) segregating for the 5A QTL and used the latest gene models to identify differentially expressed (DE) genes and pathways that potentially influence pericarp cell size and grain weight in wheat. We sampled grains at four and eight days post anthesis and found genes associated with metabolism, biosynthesis, proteoloysis and defence response to be upregulated during this stage of grain development in both NILs. We identified a specific set of 112 transcripts DE between 5A NILs at either time point, including seven potential candidates for the causal gene underlying the 5A QTL. The 112 DE transcripts had functional annotations including non-coding RNA, transpon-associated, cell-cycle control, and ubiquitin-related processes. Many of the wheat genes identified belong to families that have been previously associated with seed/grain development in other species. However, few of these wheat genes are the direct orthologs and none have been previously characterised in wheat. Notably, we identified DE transcripts at almost all steps of the pathway associated with ubiquitin-mediated protein degradation. In the promoters of a subset of DE transcripts we identified enrichment of binding sites associated with C2H2, MYB/SANT, YABBY, AT-HOOK and Trihelix transcription factor families. In this study, we identified DE transcripts with a diverse range of predicted biological functions, reflecting the complex nature of the pathways that control early grain development. Further functional characterisation of these candidates and how they interact could provide new insights into the control of grain size in cereals, ultimately improving crop yield. 11 Defense Enzyme Responses in Dormant Wild Oat and Wheat Caryopses Challenged with a Seed Decay Pathogen Seeds have well-established passive physical and chemical defense mechanisms that protect their food reserves from decay-inducing organisms and herbivores. However, there are few studies evaluating potential biochemical defenses of dormant seeds against pathogens. Caryopsis decay by the pathogenic Fusarium avenaceum strain F.a .1 was relatively rapid in wild oat ( Avena fatua L.) isoline “M73,” with 50% decay after 8 days with almost no decay in wheat ( Triticum aestivum L.) var. RL4137. Thus, this fungal strain has potential for selective decay of wild oat relative to wheat. To study defense enzyme activities, wild oat and wheat caryopses were incubated with F.a .1 for 2–3 days. Whole caryopses were incubated in assay reagents to measure extrinsic defense enzyme activities. Polyphenol oxidase, exochitinase, and peroxidase were induced in whole caryopses, but oxalate oxidase was reduced, in response to F.a .1 in both species. To evaluate whether defense enzyme activities were released from the caryopsis surface, caryopses were washed with buffer and enzyme activity was measured in the leachate. Significant activities of polyphenol oxidase, exochitinase, and peroxidase, but not oxalate oxidase, were leached from caryopses. Defense enzyme responses were qualitatively similar in the wild oat and wheat genotypes evaluated. Although the absolute enzyme activities were generally greater in whole caryopses than in leachates, the relative degree of induction of polyphenol oxidase, exochitinase, and peroxidase by F.a .1 was greater in caryopsis leachates, indicating that a disproportionate quantity of the induced activity was released into the environment from the caryopsis surface, consistent with their assumed role in defense. It is unlikely that the specific defense enzymes studied here play a key role in the differential susceptibility to decay by F.a .1 in these two genotypes since defense enzyme activities were greater in the more susceptible wild oat, compared to wheat. Results are consistent with the hypotheses that (1) dormant seeds are capable of mounting complex responses to pathogens, (2) a diversity of defense enzymes are involved in responses in multiple plant species, and (3) it is possible to identify fungi capable of selective decay of weed seeds without damaging crop seeds, a concept that may be applicable to weed management in the field. While earlier work on seed defenses demonstrated the presence of passive defenses, this work shows that dormant seeds are also quite responsive and capable of activating and releasing defense enzymes in response to a pathogen. 12 Inter- and intraspecific variation in leaf economics traits in wheat and maize Leaf economics spectrum (LES) trait variation underpins multiple agroecological processes and many prominent crop yield models. While there are numerous independent studies assessing trait variation in crops, to date there have been no comprehensive assessments of intraspecific trait variation (ITV) in LES traits for wheat and maize: the world’s most widespread crops. Using trait databases and peer-reviewed literature, we compiled over 700 records of specific leaf area (SLA), maximum photosynthetic rates ( A max), and leaf nitrogen (N) concentrations, for wheat and maize. We evaluated intraspecific LES trait variation, and intraspecific trait-environment relationships. While wheat and maize occupy the upper 90th percentile of LES trait values observed across a global species pool, ITV ranged widely across the LES in wheat and maize. Fertilization treatments had strong impacts on leaf N, while plant developmental stage (here standardized as the number of days since planting) had strong impacts on A max; days since planting, N fertilization, and irrigation all influenced SLA. When controlling for these factors, intraspecific responses to temperature and precipitation explained 39.4 and 43.7% of the variation in A maxand SLA, respectively, but only 5.4% of the variation in leaf N. Despite a long history of domestication in these species, ITV in wheat and maize among and within cultivars remains large. ITV is a critical consideration to refine regional- to global models of agroecosystem structure, function, and food security. Considerable opportunities and benefits exist for consolidating a crop trait database for a wider range of domesticated plant species. 13 Cloning and characterization of a specific UDP-glycosyltransferase gene induced by DON and Fusarium graminearum TaUGT5: can reduce the proliferation and destruction of F. graminearum and enhance the ability of FHB resistance in wheat. Deoxynivalenol (DON) is one of the most important toxins produced by Fusarium species that enhances the spread of the pathogen in the host. As a defense, the UDP-glycosyltransferase (UGT) family has been deduced to transform DON into the less toxic form DON-3-O-glucoside (D3G), but the specific gene member in wheat that is responsible for Fusarium head blight (FHB) resistance has been little investigated and proved. In this study, a DON and Fusarium graminearum responsive gene TaUGT5, which is specific for resistant cultivars, was cloned with a 1431 bp open reading frame (ORF) encoding 476 amino acids in Sumai3. TaUGT5 is located on chromosome 2B, which has been confirmed in nulli-tetrasomic lines of Chinese Spring (CS) and is solely expressed among three homologs on the A, B and D genomes. Over-expression of this gene in Arabidopsis conferred enhanced tolerance when grown on agar plates that contain DON. Similarly, the coleoptiles of wheat over-expressing TaUGT5 showed more resistance to F. graminearum, evidencing reduced proliferation and destruction of plant tissue by the pathogen. However, the disease resistance in spikes was not as significant as that on coleoptile compared with wild-type plants. A subcellular localization analysis revealed that TaUGT5 was localized on the plasma membrane of tobacco leaf epidermal cells. It is possible that TaUGT5 could enhance tolerance to DON, protect the plant cell from the pathogen infection and result in better maintenance of the cell structure, which slows down pathogen proliferation in plant tissue. 14 Transcriptomic insights into phenological development and cold tolerance of wheat grown in the field Cold acclimation and winter survival in cereal species is determined by complicated environmentally regulated gene expression. However, studies investigating these complex cold responses are mostly conducted in controlled environments that only consider the responses to single environmental variables. In this study, we have comprehensively profiled global transcriptional responses in crowns of field grown spring and winter wheat genotypes and their near isogenic lines (NILs) with the VRN-A1 alleles swapped. This in-depth analysis revealed multiple signaling, interactive pathways that influence cold tolerance and phenological development to optimize plant growth and development in preparation for a wide range of over-winter stresses. Investigation of genetic differences at the VRN-A1 locus revealed that a vernalization requirement maintained a higher level of cold response pathways while VRN-A1 genetically promoted floral development. Our results also demonstrated the influence of genetic background on the expression of cold and flowering pathways. The link between delayed shoot apex development and the induction of cold tolerance was reflected by the gradual upregulation of ABA-dependent and CBF pathways. This was accompanied by the down regulation of key genes involved in meristem development as the autumn progressed. The chromosome location of differentially expressed genes between winter and spring wheat genetic backgrounds showed a striking pattern of biased gene expression on chromosome 6A and 6D indicating a transcriptional regulation at the genome level. This finding adds to the complexity of the genetic cascades and gene interactions that determine the evolutionary patterns of both phenological development and cold tolerance traits in wheat. 15 Association mapping for total polyphenol content, total flavonoid content and antioxidant activity in barley A genome-wide association study (GWAS) was conducted for total phenolic content (TPC), total flavonoid content (FLC) and antioxidant activity (AOA) in 67 cultivated and 156 Tibetan wild barley genotypes. Most markers associated with phenolic content were different in cultivated and wild barleys. The markers bPb-0572 and bPb-4531 were identified as the major QTLs controlling phenolic compounds in Tibetan wild barley. Moreover, the marker bPb-4531 was co-located with the UDP- glycosyltransferase gene ( HvUGT ), which is a homolog to Arabidopsis UGTs and involved in biosynthesis of flavonoid glycosides . 16 Mapping resistance to powdery mildew in barley reveals a large-effect nonhost resistance QTL The durability and effectiveness of nonhost resistance suggests promising practical applications for crop breeding, relying upon elucidation of key aspects of this type of resistance. We investigated which genetic factors determine the nonhost status of barley ( Hordeum vulgare L.) to powdery mildews ( Blumeria graminis ). We set out to verify whether genes involved in nonhost resistance have a wide effectiveness spectrum, and whether nonhost resistance genes confer resistance to the barley adapted powdery mildew. Two barley lines, SusBgtSC and SusBgtDC, with some susceptibility to the wheat powdery mildew B. graminis f.sp. tritici ( Bgt ) were crossed with cv Vada to generate two mapping populations. Each population was assessed for level of infection against four B. graminis ff.spp, and QTL mapping analyses were performed. Our results demonstrate polygenic inheritance for nonhost resistance, with some QTLs effective only to non-adapted mildews, while others play a role against adapted and non-adapted forms. Histology analyses of nonhost interaction show that most penetration attempts are stopped in association with papillae, and also suggest independent layers of defence at haustorium establishment and conidiophore formation. Nonhost resistance of barley to powdery mildew relies mostly on non-hypersensitive mechanisms. A large-effect nonhost resistance QTL mapped to a 1.4 cM interval is suitable for map-based cloning. 17 Expression of two barley proteinase inhibitors in tomato promotes endogenous defensive response and enhances resistance to Tuta absoluta The aim of this study was to investigate the in vivo effect of a serine proteinase inhibitor (BTI-CMe) and a cysteine proteinase inhibitor (Hv-CPI2) from barley on this insect and to examine the effect their expression has on tomato defensive responses. We found that larvae fed on tomato transgenic plants co-expressing both proteinase inhibitors showed a notable reduction in weight. Moreover, only 56% of these larvae reached the adult stage. The emerged adults showed wings deformities and reduced fertility. We also investigated the effect of proteinase inhibitors ingestion on the insect digestive enzymes. Our results showed a decrease in larval trypsin activity. Transgenes expression had no harmful effect on Nesidiocoris tenuis (Reuter) (Heteroptera: Miridae), a predator of Tuta absoluta, despite transgenic tomato plants attracted the mirid. We also found that barley cystatin expression promoted plant defense by inducing the expression of the tomato endogenous wound inducible Proteinase inhibitor 2 ( Pin2 ) gene, increasing the production of glandular trichomes and altering the emission of volatile organic compounds. 18 Genome-Wide Association Analysis of Grain Yield-Associated Traits in a Pan-European Barley Cultivar Collection A collection of 379 Hordeum vulgare cultivars, comprising all combinations of spring and winter growth habits with two and six row ear type, was screened by genome wide association analysis to discover alleles controlling traits related to grain yield. Genotypes were obtained at 6,810 segregating gene-based single nucleotide polymorphism (SNP) loci and corresponding field trial data were obtained for eight traits related to grain yield at four European sites in three countries over two growth years. The combined data were analyzed and statistically signi cant associations between the traits and regions of the barley genomes were obtained. Combining this information with the high resolution gene map for barley allowed the identi cation of candidate genes underlying all scored traits and superposition of this information with the known genomics of grain trait genes in rice resulted in the assignation of 13 putative barley genes controlling grain traits in European cultivated barley. Several of these genes are associated with grain traits in both winter and spring barley. 19 Alterations in wheat pollen lipidome during high day and night temperature stress Understanding the adaptive changes in wheat pollen lipidome during high temperature stress is critical to improving seed set and developing high temperature tolerant wheat varieties. We found that the most heat-responsive lipids in pollen were extraplastidic phospholipids, phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylinositol (PI), phosphatidic acid (PA), and phosphatidylserine (PS). Comparison of the present results on wheat pollen with results of our previous research on wheat leaves suggests that similar lipid changes contribute to high temperature adaptation in both leaves and pollen, though the lipidomes have inherently distinct compositions. 20 Drought Response in Wheat: Key Genes and Regulatory Mechanisms Controlling Root System Architecture and Transpiration Efficiency Abiotic stresses such as, drought, heat, salinity, and flooding threaten global food security. Crop genetic improvement with increased resilience to abiotic stresses is a critical component of crop breeding strategies. Wheat is an important cereal crop and a staple food source globally. Enhanced drought tolerance in wheat is critical for sustainable food production and global food security. Recent advances in drought tolerance research have uncovered many key genes and transcription regulators governing morpho-physiological traits. Genes controlling root architecture and stomatal development play an important role in soil moisture extraction and its retention, and therefore have been targets of molecular breeding strategies for improving drought tolerance. In this systematic review, we have summarized evidence of beneficial contributions of root and stomatal traits to plant adaptation to drought stress. Specifically, we discuss a few key genes such as, DRO1 in rice and ERECTA in Arabidopsis and rice that were identified to be the enhancers of drought tolerance via regulation of root traits and transpiration efficiency. Additionally, we highlight several transcription factor families, such as, ERF (ethylene response factors), DREB (dehydration responsive element binding), ZFP (zinc finger proteins), WRKY, and MYB that were identified to be both positive and negative regulators of drought responses in wheat, rice, maize, and/or Arabidopsis. The overall aim of this review is to provide an overview of candidate genes that have been identified as regulators of drought response in plants. The lack of a reference genome sequence for wheat and non-transgenic approaches for manipulation of gene functions in wheat in the past had impeded high-resolution interrogation of functional elements, including genes and QTLs, and their application in cultivar improvement. The recent developments in wheat genomics and reverse genetics, including the availability of a gold-standard reference genome sequence and advent of genome editing technologies, are expected to aid in deciphering of the functional roles of genes and regulatory networks underlying adaptive phenological traits, and utilizing the outcomes of such studies in developing drought tolerant cultivars. 21 Tissue-specific changes in apoplastic proteins and cell wall structure during cold acclimation of winter wheat crowns The wheat ( Triticum aestivum L.) crown is the critical organ of low temperature stress survival over winter. In cold-acclimated crowns, ice formation in the apoplast causes severe tissue disruption as it grows at the expense of intracellular water. While previous crown studies have shown the vascular transition zone (VTZ) to have a higher freezing sensitivity than the shoot apical meristem (SAM), the mechanism behind the differential freezing response is not fully understood. Cooling cold-acclimated crowns to –10 °C resulted in an absence of VTZ tetrazolium chloride staining, whereas the temperatures at which 50% of the SAM stained positive and 50% of plants recovered (LT50) were similar after cold acclimation for 21 (–16 °C) and 42 d (–20 °C) at 4 °C. Proteomic analysis of the apoplastic fluids identified dehydrins, vernalization-responsive proteins, and cold shock proteins preferentially accumulated in the SAM. In contrast, modifications to the VTZ centered on increases in pathogenesis-related proteins, anti-freeze proteins, and sugar hydrolyzing enzymes. Fourier transform infrared spectroscopy focal plane array analysis identified the biochemical modification of the cell wall to enhance methyl-esterified cross-linking of glucuronoarabinoxylans in the VTZ. These findings indicate that the SAM and VTZ express two distinct tissue-specific apoplastic responses during cold acclimation. 22 Quantitative trait loci (QTL) analysis of root traits under phosphorus deficiency at the seedling stage in wheat A segregating population of 136 recombinant inbred lines derived from a cross between the durum wheat cv. “Simeto” and the T. dicoccum accession “Molise Colli” was grown in soil and evaluated for a number of shoot and root morphological traits. A total of 17 quantitative trait loci (QTL) were identified for shoot dry weight, number of culms, and plant height and for root dry weight, volume, length, surface area, and number of forks and tips, on chromosomes 1B, 2A, 3A, 4B, 5B, 6A, 6B, and 7B. LODs were 2.1 to 21.6, with percent of explained phenotypic variability between 0.07 and 52. Three QTL were mapped to chromosome 4B, one of which corresponds to the Rht-B1 locus and has a large impact on both shoot and root traits (LOD 21.6). Other QTL that have specific effects on root morphological traits were also identified. Moreover, meta-QTL analysis was performed to compare the QTL identified in the “Simeto” × “Molise Colli” segregating population with those described in previous studies in wheat, with three novel QTL defined. Due to the complexity of phenotyping for root traits, further studies will be helpful to validate these regions as targets for breeding programs for optimization of root function for field performance. 今天的文献到此结束， 有没有你想要继续读的?如果有，欢迎分享给我们你的理解。
2018-01-22 Rui Wang 今天除了第一条推送以外，特地 为大家准备了一顿丰盛的小麦生信基础大餐 ， 主要就是介绍一下小麦基因组序列的各种数据库，其中就包括今天所介绍的IWGSC RefSeq 1.0 以及前段时间群里小伙伴聊到的在plants.ensembl上边的TGAC版本。当然，这其中最新最全的还是IWGSC RefSeq1.0，平常大家还是要首选这个数据库，但是当你的序列在这个版本上查不到或者你的genetic map跟RefSeq线性关系很差的时候，就必须要试一试其它的版本了。更重要的是，像一些小麦基因表达数据库或者小麦TILLING数据库并不是按照最新的IWGSC RefSeq 1.0来做annotation的，所以说掌握了小麦数据库的各种版本才能在以后的学习过程中游刃有余！ 内容一： Genome assemblies 介绍 来自： www.wheat-training.com 这份总结没有包括去年最新释放的 D genome 的数据库，不过大家读完了下面的总结肯定就能触类旁通了。 a) Introduction to the wheat genome Wheat is an allopolyploid of which there are two major types: hexaploid common wheat ( Triticum aestivum ssp. aestivum; 17 Gb genome size; AABBDD genomes), which is mainly used for bread and biscuit products tetraploid durum wheat ( Triticumturgidum ssp. durum ;12Gbgenomesize;AABB genomes), used mainly for pasta. Hexaploid wheat arose from a polyploidization event ~ 10,000 years ago, whereas tetraploids wheat arose ~ 400,000 years ago ( Figure 1 ). Figure 1: The evolutionary history of allopolyploid wheat. FromBorrill et al., 2015. DOI: 10.1111/nph.13533 Hexaploid wheat contains three closely related genomes (A, B and D) which contain homoeologous genes in a conserved order. Wheat homoeologues share over 95% sequence identity within coding regions and most wheat genes are expected to be present as three copies in the A, B, and D genome. Due to the high sequence conservation between homoeologues, genes may be functionally redundant or act in a dose-dependent manner. This means that often all three copies must be knocked out to cause a strong phenotype. However, in other cases, the homoeologous genes have developed specialized functions or become pseudogenized over time due to reduced selection pressure on duplicated genes. b) Multiple genome assemblies are available The large size of the wheat genome has made it very challenging to produce a reference genome. Different strategies have been used to create draft genome assemblies. Currently, several genome assemblies need to be used in a complementary fashion because no single reference is the best across all regions. A brief explanation about each genome assembly is given below alongside any caveats. c) Introduction to each assembly Chinese spring Survey Sequence (CSS) The International Wheat Genome Sequencing Consortium (IWGSC) has used flow-sorting to separate out individual chromosome arms. The landrace used (Chinese Spring) had aneuploid genetic stocks available, which have only one arm of each chromosome, e.g. the short arm of chromosome 1A is deleted so chromosome arm 1AL can be separated from the other chromosomes. This enabled the IWGSC to separate each individual chromosome arm by flow sorting, before sequencing each chromosome arm separately. Individual chromosome arms were sequenced to 30-240x coverage using Illumina NGS, generating a 10.2 Gb assembly of Chinese Spring (termed Chinese Spring survey sequence (CSS)). Gene models were created by mapping RNA-seq data and using gene models from related species. A total of 99,386 protein-coding genes were predicted, with 193,667 transcripts and splice variants. The gene models presented rely on the scaffolds assembled and in some cases, gene models are incomplete because of the underlying genomic scaffolds are not full-length assemblies. For example in some cases genes are split between two different genomic scaffolds (shown below), therefore one gene is given two different identifiers. Figure 2: CSS gene models are affected by truncated scaffolds. Chromosome 3B was assembled using a BAC by BAC approach and is currently considered the “gold standard” for the reference genome assembly. 3B gene models were created separately using RNA-seq data. CSS reference: IWGSC 2014, DOI:10.1126/science.1251788 CSS data access: http://archive.plants.ensembl.org/Triticum_aestivum/Info/Index W7984 A whole-genome sequencing approach was undertaken in the synthetic hexaploid wheat “Synthetic W7984”. This approached used large-insert sequencing libraries and enabled separate assemblies of the three homoeologues genomes, to a total assembly size of 9.1Gb. In some regions, the W7984 scaffolds are more continuous than the CSS, but for other regions, the CSS is more continuous than the W7984. Using both references will give the complete picture of genomic regions of interest. W7984 does not have any gene models associated with it. W7984 reference: Chapman et al.,2015 DOI: 10.1186/s13059-015-0582-8 W7984 data access: http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/blast_WGS.php TGAC A whole genome shotgun sequence assembly of Chinese Spring was carried out using nested long mate-pair libraries alongside a modified version of the DISCOVAR algorithm for assembly. This method created an assembly of total length 13.4 Gb, with approximately 10x N50 longer than the CSS and W7984 assemblies. Gene models from IWGSC were projected onto the TGAC assembly, with 99% of the total genes located on the TGAC assembly. De novo gene prediction has been carried out for the TGAC assembly resulting in a total of 273,739 transcripts (including non-coding and transcript variants). Of these, 104,305 are high confidence protein-coding genes. In general, these gene models are more complete than the CSS gene models due to the longer contig length within the TGAC assembly. These gene models are available from http://plants.ensembl.org TGAC reference: Clavijo et al., 2017 DOI:10.1101/gr.217117.116 TGAC data access: http://plants.ensembl.org/Triticum_aestivum/Info/Index?db=core https://wheatis.tgac.ac.uk/grassroots-portal/blast Triticum 3.1 A whole genome shotgun sequence assembly of Chinese Spring, which was assembled using short Illumina and long PacBio reads: the assembly was done in several steps using the MaSuRCA and Celera Assembler software. The combination of very long reads (average read length ~10 kb) coupled with deep sequencing of low error-rate short reads (65x coverage) produced an assembly with a total length of 15.3 Gb represented by 279,439 contigs with an N50 of 232,659 bp and average contig size of 54,912 bp. In contrast to other assemblies of the wheat genome, the Triticum 3.1 assembly is highly contiguous and does not contain unknown nucleotides (Ns). T he Triticum 3.1 assembly was aligned to an existing assembly of A egilops tauschii (the D-genome progenitor of hexaploidy wheat) to identify its D-genome portion; this data was saved into a separate assembly called Triticum D 1.0. There is currently no further annotation available for the Triticum 3.1 assembly. Triticum 3.1 reference: Zimin et al., 2017DOI: 10.1093/gigascience/gix097 Triticum 3.1 data access: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA392179 TriticumD 1.0 data access: ftp://ftp.ccb.jhu.edu/pub/data/Triticum_aestivum/Wheat_D_genome/ RefSeqv1.0 A whole genome assembly has been carried out by the IWGSC in collaboration with the company NRGene. Using a proprietary algorithm DeNovoMAGIC with Illumina sequencing data, a 14.5 Gbassembly was produced. This assembly has much larger contigs (N50 super-scaffold length 22.8 Mb) and represents a draft genome more similar in quality to rice and other model species. Sequences have been ordered using POPSEQ data and Hi-C (chromosome conformation capture) to generate 21 pseudomolecules representing the majority of the wheat genome. Gene models have been generated consisting of 107,891 high confidence genes (homology to genes in other species) and161,537 low confidence genes (e.g. truncated genes missing a start or stop codons and genes lacking transcriptional evidence or lacking homology to other species). WGA reference: unpublished WGA data access: available after registration with URGI. BLAST at https://urgi.versailles.inra.fr/blast_iwgsc/?dbgroup=wheat_whole_genome_assembliesprogram=bl astn All data downloadable at https://urgi.versailles.inra.fr/download/iwgsc/IWGSC-WGA/ d) Comparison between assemblies Currently, all 4reference genomes have their merits due to the differences in gene annotation, incorporation into other resources (e.g. expression browsers, SNP markers and TILLING mutants) and the variety which was sequenced. Table1. Comparison between different genome assemblies. 内容二： What is TGAC: 来自 https://www.wheatgenome.org/News/Latest-news/New-wheat-genome-assembly-available-at-TGAC The Genome Analysis Centre (TGAC) announced recently that it has made available a new assembly of the wheat genome. TheIWGSC welcomes the production of additional resources ahead of the completion of the full reference sequence, anticipated for 2018. This latest assembly provides an incremental improvement to the genic information currently available to breeders and researchers. Taking advantage of recent improvements in high throughput sequencing technologies, the new assembly from TGAC builds on the IWGSC chromosome survey sequence to assign improved gene sequences assembled from whole genome sequencing to individual wheat chromosomes. With this new resource, it will be easier to define the structures of genes and the sequences that surround them, which often have a role in their regulation. The challenge remains, however, to order all of this information along each of the chromosomes to support the identification and isolation of genes and regulatory elements underlying agronomically important traits in bread wheat. Towards this end, the IWGSC will continue to pursue the physical map-based sequencing of individual chromosomes, such as the recently completed 3B chromosome to (1) provide an efficient link between genetic maps and the draft sequences; and (2) achieve a reference sequence comparable in quality to that of the rice genome gold standard. The TGAC gene assemblies and all other future efforts that deliver genomic resources for bread wheat will be integrated by the IWGSC into the final gold standard wheat genome sequence.
2018年第三周小麦文献推荐（1.21）——2017年中国小麦领域高被引学者都有谁？ 最近有老师私下问我有没有认识优秀一点的学生，推荐读他的博士。我想了一圈没有，在我们公众号里比较活跃的人多数都是博士。后面我脑洞大开，如果有机会后面我们会针对我们公众号推送的一些内容出一些测试题，成绩优秀的奖励红包，择优向老师们推荐。也欢迎热爱小麦的小伙伴给我们投稿，分享实验和学习心得等。 还要说说今天看到的高被引学者榜单，我看了下我们小麦领域应该是4人，分别是：康振生院士、何中虎研究员、贾继增研究员、刘宝教授。这4位学者做小麦的应该都认识，我们前面也推送过很多他们研究组的文章，在公众号内搜索即可。如果名单有遗漏，欢迎留言补充。虽然我头发不是特别长，但是我见识特别短。 好了，继续我们今天的文献推荐。 1 Natural variation and genetic make‑up of leaf blade area in spring barley Despite long-standing studies in the morpho-physiological characters of leaf blade area (LA) in cereal crops, advanced genetic studies to explore its natural variation are lacking. The importance of modifying LA in improving cereal grain yield and the genes controlling leaf traits have been well studied in rice but not in temperate cereals. To better understand the natural genetic variation of LA at four developmental stages, main culm LA was measured from 215 worldwide spring barleys including 92 photoperiod-sensitive accessions and 123 accessions with reduced photoperiod sensitivity ( ppd - H1 ) locus under controlled greenhouse conditions (long-day; 16/8 h; ~ 20/~ 16 °C day/night). The LA of Ppd - H1 -carrying accessions was always smaller than in ppd - H1 -carrying accessions. We found that nine SNPs from the Ppd - H1 gene were present in the collection of which marker 9 (M9; G/T in the CCT-domain) showed the most significant and consistent effect on LA at all studied developmental stages. Genome-wide association scans (GWAS) showed that the accessions carrying the ppd - H1 allele T/M9 (late heading) possessed more genetic variation in LA than the Ppd - H1 group carrying G/M9 (early heading). Several QTL with major effects on LA variation were found close to plant stature-related heading time, phytohormone- and sugar-related genes. The results provide evidence that natural variation of LA is an important source for improving grain yield, adaptation and canopy architecture of temperate cereals. 2 A major QTL controlling the tolerance to manganese toxicity in barley (Hordeum vulgare L.) Waterlogging stress disturbs plant metabolism through increased ion (manganese and iron) toxicity resulting from the changes in the soil redox potential under hypoxic conditions. Our previous study found a significant correlation between the tolerance to Mn2+ toxicity and waterlogging stress tolerance in barley, suggesting that waterlogging tolerance could be increased by improving the tolerance to Mn2+ toxicity. In this study, a doubled-haploid (DH) population from the cross between barley varieties Yerong and Franklin (waterlogging-tolerant and -sensitive, respectively) was used to identify QTL controlling tolerance to Mn2+ toxicity based on chlorophyll content and plant survival as selection criteria. Four significant QTL for plant survival under Mn2+ stress ( QSur.yf.1H , QSur.yf.3H , QSur.yf.4H , and QSur.yf.6H ) were identified in this population at the seedling stage. Two significant QTL ( QLC.yf.3H and QLC.yf.6H ) controlling leaf chlorosis under Mn2+ stress were identified on chromosomes 3H and 6H close to QSur.yf.3H and QSur.yf.6H . The major QTL QSur.yf.3H , located near the marker Bmag0013, explained 21% of the phenotypic variation. The major QTL for plant survival on 3H was validated in a different DH population (TX9425/Naso Nijo). This major QTL could potentially be used in breeding programmes to enhance tolerance to both manganese toxicity and waterlogging. 3 Genome wide identification of wheat and Brachypodium type one protein phosphatases and functional characterization of durum wheat TdPP1a Reversible phosphorylation is an essential mechanism regulating signal transduction during development and environmental stress responses. An important number of dephosphorylation events in the cell are catalyzed by type one protein phosphatases (PP1), which catalytic activity is driven by the binding of regulatory proteins that control their substrate specificity or subcellular localization. Plants harbor several PP1 isoforms accounting for large functional redundancies. While animal PP1s were reported to play relevant roles in controlling multiple cellular processes, plant orthologs remain poorly studied. To decipher the role of plant PP1s, we compared PP1 genes from three monocot species, Brachypodium, common wheat and rice at the genomic and transcriptomic levels. To gain more insight into the wheat PP1 proteins, we identified and characterized TdPP1 a, the first wheat type one protein phosphatase from a Tunisian durum wheat variety Oum Rabiaa3. TdPP1a is highly conserved in sequence and structure when compared to mammalian, yeast and other plant PP1s. We demonstrate that TdPP1a is an active, metallo-dependent phosphatase in vitro and is able to interact with AtI2, a typical regulator of PP1 functions. Also, TdPP1a is capable to complement the heat stress sensitivity of the yeast mutant indicating that TdPP1a is functional also in vivo . Moreover, transient expression of TdPP1a::GFP in tobacco leaves revealed that it is ubiquitously distributed within the cell, with a strong accumulation in the nucleus. Finally, transcriptional analyses showed similar expression levels in roots and leaves of durum wheat seedlings. Interestingly, the expression in leaves is significantly induced following salinity stress, suggesting a potential role of TdPP1a in wheat salt stress response. 4 Estimating the responses of winter wheat yields to moisture variations in the past 35 years in Jiangsu Province of China Jiangsu is an important agricultural province in China. Winter wheat, as the second major grain crop in the province, is greatly affected by moisture variations. The objective of this study was to investigate whether there were significant trends in changes in the moisture conditions during wheat growing seasons over the past decades and how the wheat yields responded to different moisture levels by means of a popular drought index, the Standardized Precipitation Evapotranspiration Index (SPEI). The study started with a trend analysis and quantification of the moisture conditions with the Mann-Kendall test and Sen’s Slope method, respectively. Then, correlation analysis was carried out to determine the relationship between de-trended wheat yields and multi-scalar SPEI. Finally, a multivariate panel regression model was established to reveal the quantitative yield responses to moisture variations. The results showed that the moisture conditions in Jiangsu were generally at a normal level, but this century appeared slightly drier in because of the relatively high temperatures. There was a significant correlation between short time scale SPEI values and wheat yields. Among the three critical stages of wheat development, the SPEI values in the late growth stage (April-June) had a closer linkage to the yields than in the seedling stage (October-November) and the over-wintering stage (December-February). Moreover, the yield responses displayed an asymmetric characteristic, namely, moisture excess led to higher yield losses compared to moisture deficit in this region. The maximum yield increment could be obtained under the moisture level of slight drought according to the 3-month SPEI at the late growth stage, while extreme wetting resulted in the most severe yield losses. The moisture conditions in the first 15 years of the 21stcentury were more favorable than in the last 20 years of the 20th century for wheat production in Jiangsu. 5 Effect of Fusarium head blight management practices on mycotoxin contamination of wheat straw Management of Fusarium graminearum-associated mycotoxins in wheat grain has been extensively evaluated, but little is known about management of mycotoxins in straw. Two research trials were conducted at four locations from 2011 to 2014. The objective of the first trial was to determine the efficacy of fungicides, and the objective of the second trial was to evaluate the use of integrated disease management strategies, for the control of Fusarium head blight (FHB) and reducing the concentration of the Fusarium mycotoxins deoxynivalenol, 3-acetyl-deoxynivalenol, and 15-acetyl-deoxynivalenol in straw. In the first trial, it was determined that demethylation inhibitor (DMI) fungicides did not offer significant (P ≤ 0.05) reductions of mycotoxin concentrations in the straw compared to a no-fungicide control treatment, but significant (P ≤ 0.05) reductions in mycotoxin concentration were observed in the control when compared to treatments with the application of quinone outside inhibitor (QoI)-containing fungicides. In the second trial, mycotoxin concentrations in the straw were significantly (P ≤ 0.05) reduced in the moderately resistant cultivar compared to the susceptible cultivar, but were not effected by the use of a fungicide. The practices typically used to manage Fusarium mycotoxins in wheat grain, especially the selection of resistant cultivars and not using a QoI fungicide, may be an effective means to reduce mycotoxin concentrations in the straw. 6 Adult Plant Leaf Rust Resistance Derived from the Soft Red Winter Wheat Cultivar ‘Caldwell’ Maps to Chromosome 3BS ‘Caldwell’ is a US soft red winter wheat ( Triticum aestivum L.) that has partial, adult plant resistance to the leaf rust pathogen Puccinia triticina Eriks. A line of ‘Thatcher 2/Caldwell’ with adult plant resistance derived from Caldwell was crossed with ‘Thatcher’ to develop a population of recombinant inbred lines (RILs). The parents and RIL population were evaluated for segregation of leaf rust resistance in four field tests. A genetic map of the RIL population was constructed using 90K single-nucleotide polymorphism (SNP) markers with the Illumina Infinium iSelect 90K wheat bead array. Significant effects for reduction of leaf rust severity in all four tests were found for a quantitative trait locus on chromosome 3BS. Simple sequence repeat (SSR) markers linked to the adult plant resistance gene *Lr74 and kompetitive allele specific polymerase chain reaction (KASP) assay markers were added to the map on chromosome 3BS. Thatcher and the resistant Thatcher 2/Caldwell parent were negative for the presence of *Sr2 on chromosome 3BS based on the tightly linked marker csSr2 . The SSR marker cfb5006 linked closely to Lr74 mapped the closest to the logarithm of odds peak for leaf rust resistance on chromosome 3BS. The SNP and SSR markers on chromosome 3BS can be used to add Caldwell leaf rust resistance to wheat breeding germplasm. 7 Can spelt wheat be used as heterotic group for hybrid wheat breeding? The feasibility to switch from line to hybrid breeding is currently a hot topic in the wheat community. One limitation seems to be the lack of divergent heterotic groups within wheat adapted to a certain region. Spelt wheat is a hexaploid wheat that can easily be crossed with bread wheat and that forms a divergent genetic group when compared to elite bread wheat. The aim of this study was to investigate the potential of Central European spelt as a heterotic group for Central European bread wheat. We performed two large experimental field studies comprising in total 43 spelt lines, 14 wheat lines, and 273 wheat–spelt hybrids, and determined yield, heading time, plant height, resistance against yellow rust, leaf rust, and powdery mildew, as well as protein content and sedimentation volume. Heterosis of yield was found to be lower than that of hybrids made between elite wheat lines. Moreover, heterosis of the quality trait sedimentation volume was negative. Consequently, spelt wheat does not appear suited to be used as heterotic group in hybrid wheat breeding. Nevertheless, high combining abilities of a few spelt lines with elite bread wheat lines make them interesting resources for pre-breeding in bread wheat. Thereby, the low correlation between line per se performance and combining ability of these spelt lines shows the potential to unravel the breeding value of genetic resources by crossing them to an elite tester. 8 Genomic, Biochemical, and Modeling Analyses of Asparagine Synthetases from Wheat 9 Overexpression of a wheat (Triticum aestivum L.) bZIP transcription factor gene, TabZIP6 , decreased the freezing tolerance of transgenic Arabidopsis seedlings by down-regulating the expression of CBFs The basic leucine zipper (bZIP) proteins play important roles against abiotic stress in plants, including cold stress. However, most bZIPs involved in plant freezing tolerance are positive regulators. Only a few bZIPs function negatively in cold stress response. In this study, TabZIP6 , a Group C bZIP transcription factor gene from common wheat (Triticum aestivum L.), was cloned and characterized. The transcript of TabZIP6 *was strongly induced by cold treatment (4°C). TabZIP6 is a nuclear-localized protein with transcriptional activation activity. Arabidopsis plants overexpressing *TabZIP6 *showed decreased tolerance to freezing stress. Microarray as well as quantitative real-time PCR (qRT-PCR) analysis showed that CBFs and some key COR genes, including C OR47 and COR15B , were down-regulated by cold treatment in *TabZIP6- overexpressing Arabidopsis lines. TabZIP6 was capable of binding to the G-box motif and the CBF1 and CBF3 *promoters in yeast cells. A yeast two-hybrid assay revealed that TabZIP6, as well as the other two Group S bZIP proteins involved in cold stress tolerance in wheat, Wlip19 and TaOBF1, can form homodimers by themselves and heterodimers with each other. These results suggest that TabZIP6 may function negatively in the cold stress response by binding to the promoters of CBFs, and thereby decreasing the expression of downstream COR genes in TabZIP6 -overexpressing Arabidopsis seedlings. 10 Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome We constructed and analyzed the pangenome of Zymoseptoria tritici, a major pathogen of wheat that evolved host specialization by chromosomal rearrangements and gene deletions. We used single-molecule real-time sequencing and high-density genetic maps to assemble multiple genomes. We annotated the gene space based on transcriptomics data that covered the infection life cycle of each strain. Based on a total of five telomere-to-telomere genomes, we constructed a pangenome for the species and identified a core set of 9149 genes. However, an additional 6600 genes were exclusive to a subset of the isolates. The substantial accessory genome encoded on average fewer expressed genes but a larger fraction of the candidate effector genes that may interact with the host during infection. We expanded our analyses of the pangenome to a worldwide collection of 123 isolates of the same species. We confirmed that accessory genes were indeed more likely to show deletion polymorphisms and loss-of-function mutations compared to core genes. 11 2017年小麦基因编号 https://shigen.nig.ac.jp/wheat/komugi/genes/macgene/supplement2017.pdf 12 Genetic dissection of the relationships between grain yield components by genome-wide association mapping in a collection of tetraploid wheats Increasing grain yield potential in wheat has been a major target of most breeding programs. Genetic advance has been frequently hindered by negative correlations among yield components that have been often observed in segregant populations and germplasm collections. A tetraploid wheat collection was evaluated in seven environments and genotyped with a 90K SNP assay to identify major and stable quantitative trait loci (QTL) for grain yield per spike (GYS), kernel number per spike (KNS) and thousand-kernel weight (TKW), and to analyse the genetic relationships between the yield components at QTL level. The genome-wide association analysis detected eight, eleven and ten QTL for KNS, TKW and GYS, respectively, significant in at least three environments or two environments and the mean across environments. Most of the QTL for TKW and KNS were found located in different marker intervals, indicating that they are genetically controlled independently by each other. Out of eight KNS QTL, three were associated to significant increases of GYS, while the increased grain number of five additional QTL was completely or partially compensated by decreases in grain weight, thus producing no or reduced effects on GYS. Similarly, four consistent and five suggestive TKW QTL resulted in visible increase of GYS, while seven additional QTL were associated to reduced effects in grain number and no effects on GYS. Our results showed that QTL analysis for detecting TKW or KNS alleles useful for improving grain yield potential should consider the pleiotropic effects of the QTL or the association to other QTLs. 13 Molecular marker assisted breeding and genome composition analysis of Zhengmai 7698, an elite winter wheat cultivar Zhengmai 7698 is an elite winter wheat variety widely cultivated in the Southern regions of the Yellow-Huai River Valley of China. Here, we report the molecular markers used for breeding Zhengmai 7698 and the genome composition of this cultivar revealed using genome-wide SNPs. A total of 26 DNA markers derived from the genes controlling gluten protein quality, grain hardness, flour color, disease resistance, or pre-harvesting sprouting resistance were used during breeding. Consequently, Zhengmai 7698 had strong gluten, high grain hardness index, white flour color, and high levels of resistance to powdery mildew, stripe rust infections, and pre-harvesting sprouting. Using genome complexity reduction, 28,996 high-quality SNPs distributed on 21 wheat chromosomes were identified among Zhengmai 7698 and its three parental lines (4B269, Zhengmai 9405 and Zhoumai 16). Zhengmai 7698 shared 12,776, 14,411 and 16,085 SNPs with 4B269, Zhengmai 9405 and Zhoumai 16, respectively. Thus, the contributions of 4B269, Zhengmai 9405 and Zhoumai 16 to the genome of Zhengmai 7698 were comparable. Interestingly, Zhengmai 7698 had 307 unique SNPs that are absent in all three parents. We suggest that molecular markers facilitate selection of a wheat cultivar with multiple elite traits. Analysis of genome composition with SNPs may provide useful clues for further dissecting the genetic basis of improved wheat performance. 14 Characterization of a new Pm2 allele associated with broad-spectrum powdery mildew resistance in wheat line Subtil Wheat powdery mildew is a severe disease affecting yield and quality. Host resistance was proved to be effective and environment-friendly. Wheat line Subtil is an elite germplasm resource resistant to 28 of 30 tested Bgt isolates. Genetic analysis showed that the powdery mildew resistance in Subtil was conferred by a single dominant gene, temporarily designated PmSub. Using bulked segregant analysis, PmSub was mapped to chromosome arm 5DS, and flanked by the markers Bwm16 and Cfd81/Bwm21 at 5.0 and 0.9 cM, respectively. Allelism tests further confirmed PmSub was allelic with documented Pm2 alleles. Then, homologous sequences of Pm2a related sequence was cloned from Subtil and Chinese Spring. It was completely identical to the reported Pm2a sequence, but significantly different from that of Chinese Spring. A marker SWGI067 was developed based on the sequence divergence of homologous sequence in Subtil and Chinese Spring. SWGI067 was closely linked to PmSub, indicating that the gene PmSub itself was different from the cloned Pm2a related sequence. Meanwhile, Subtil produced significantly different reaction pattern compared with other genotypes with Pm genes at or near Pm2 locus. Therefore, PmSub was most likely a new allele of Pm2. PmSub has opportunities for marker-assisted selecting for high-efficiency wheat improvement. 15 Discovery of Consistent QTLs of Wheat Spike-Related Traits under Nitrogen Treatment at Different Development Stages Spike-related traits such as spike length (Sl), fertile spikelet number (Fsn), sterile spikelet number (Ssn), grain number per spike (Gns), and thousand-kernel weight (Tkw) are important factors influencing wheat yield. However, reliably stable markers that can be used for molecular breeding in different environments have not yet been identified. In this study, a double haploid (DH) population was used for quantitative trait locus (QTL) mapping of five spike-related traits under four different nitrogen (N) supply dates in two locations and years. Seventy additive QTLs with phenotypic variation ranging from 4.12 to 34.74% and 10 major epistatic QTLs were identified. Eight important chromosomal regions on five chromosomes (1B, 2B, 2D, 5D, and 6A) were found. Sixteen stable QTLs were detected for which N application had little effect. Among those stable QTLs, QSl.sdau-2D-1 , and QSl.sdau-2D-2 , with phenotypic variation explained (PVE) of 10.4 and 24.2%, respectively, were flanked by markers Xwmc112 and Xcfd53 in the same order. The QTLs QSsn.sdau-2B-1, QFsn.sdau-2B-1 , and QGns.sdau-2B , with PVE ranging from 4.37 to 28.43%, collocated in the Xwmc179 - Xbarc373 marker interval. The consistent kernel wheat QTL ( QTkw.sdau-6A ) on the long arm of chromosome 6A, flanked by SSR markers Xbarc1055 and Xwmc553 , showed PVE of 5.87–15.18%. Among these stable QTLs, the two flanking markers Xwmc112 and Xcfd53 have been validated using different varieties and populations for selecting Sl. Therefore, these results will be of great value for marker-assisted selection (MAS) in breeding programs and will accelerate the understanding of the genetic relationships among spike-related traits at the molecular level. 欢迎关注 小麦研究联盟
1 20 本期作者：胖丫 在大数据时代重新审视植物miRNA注释的标准 大家周末好! 我在吃饭的时候，听到隔壁桌说起学术造假的问题，武汉大学的长江学者被武汉大学的千人给举报了，一个什么机构的前主任举报了现主任。这件事先暂不论是非，造假这事还真可怕，特别是主观造假。在高校学术圈，没论文就如同没有子嗣，这句话出自那位北大的脱口秀博士，迫于发表的压力就有可能造假。有的人就调侃说，最怕接手前人的工作，指不定哪个地方存在定时炸弹。导师在这方面要做好教育，也要以身作则，基本的社会规范和学术道德一定要遵守。 言归正传，今天我们要谈的是主题small RNA中的miRNA。我们先前并没有过多的介绍small RNA, 主要因为这也是一个大坑，轻易不敢挖。后来我们了解到最近会有一篇小麦miRNA相关的文章将会发表在the plant cell上，我们也早已预约好作者届时和我们聊一聊。昨天凑巧在 the plant cell上看见一篇关于植物miRNA注释标准的文章发布，仍不住多看了两眼，既然看了索性就介绍一下这篇文章吧，权当抛砖引玉。文章的题目是“ Revisiting criteria for plant miRNA annotation in the era of big data ”，作者是Michael J. Axtell和Blake C. Meyers,文章的摘要如下。 MicroRNAs ( miRNAs ) are ~21 nucleotide-long regulatory RNAs that arise from endonucleolytic processing of hairpin precursors. Many function as essential post-transcriptional regulators of target mRNAs and long non-coding RNAs. Alongside miRNAs, plants also produce large numbers of short interfering RNAs ( siRNAs ), which are distinguished from miRNAs primarily by their biogenesis ( typically processed from long double-stranded RNA instead of single-stranded hairpins ) and functions (typically via roles in transcriptional regulation instead of posttranscriptional regulation). Next-generation DNA sequencing methods have yielded extensivedatasets of plant small RNAs, resulting in many miRNA annotations. However, it has become clear that many miRNA annotations are questionable. The sheer number of endogenous siRNAs compared to miRNAs has been a major factor in the erroneous annotation of siRNAs as miRNAs.Here, we provide updated criteria for the confident annotation of plant miRNAs, suitable for the era of “big data” from DNA sequencing. The updated criteria emphasize replication, the minimization of false positives, and they require next-generation sequencing of small RNAs. We argue that improved annotation systems are needed for miRNAs and all other classes of plant small RNAs. Finally, to illustrate the complexities of miRNA and siRNA annotation, we review the evolution and functions of miRNAs and siRNAs in plants. 人初到一个陌生的环境，由于离开了自己的地盘，离开了心里舒适区，往往会感到稍微心里恐慌。这其实是一种正常的动物生存本能。正是有这样一个本能，当我们对一个新领域不了解的时候，往往会感到很难。实际上，等你接触多了，真正了解了之后，也就觉得没什么了。面对一个下面会用到的新领域，just do it，做下去，其实没有你想象的难。如果之前没有接触过miRNA，不要害怕，英文不行，知网上也有很多优秀的中文博士论文，大家可以找来看看，多看一些，基本上就可以了解miRNA研究中一些常规套路，这样以后再看到类似的文章，在思想上就不会这么排斥了。所以说了这么多，关于miRNA的背景知识这里就不介绍了（找的理由好不好 ），如果你还不了解，网上能搜上万条结果。 本文主要关注MicroRNAs，Phased siRNAs (phasiRNAs)和Heterochromatic siRNAs (hc-siRNAs)。PhasiRNAs是一类特殊的小RNA，是在来自前体RNA的转录本的21或24-nt间隔产生的，而该前体往往是miRNA或者siRNA的靶基因，也即phasiRNAs是在其它小RNA的介导下产生的，下图展示的是拟南芥中phasiRNAs生成通路的一种模式。如果还是感到陌生，可以参见张启发院士2016年发表在PNAS上的文章“ PMS1T, producing phased small-interfering RNAs, regulates photoperiod-sensitive male sterility in rice ”，弄懂此文也就对phasiRNAs有个直观的认识了。 Heterochromatic siRNAs (hc-siRNAs)，其实我对hc-siRNAs这个名字是抵触的，能不能起个好点的名字，中文叫异染色质siRNAs。hc-siRNAs的产生过程和phasiRNAs有点类似，不过前体大概只有30-50nt，最后只产生一条长24nt的siRNA。hc-siRNAs往往靶向于新生的异染色质非编码RNA，在DNA的从头甲基化和异染色质组蛋白标记方面发挥着作用。除了这些小RNA还有很多其他类型的小RNA，比如最近发表在nature genetic上的一篇拟南芥的研究论文也是关于一种类型的小RNA的介绍，文章的题目是“ Transposon-derived small RNAs triggered by miR845 mediate genome dosage response in Arabidopsis ”，有兴趣的可以进一步关注下，我们小麦可遍地都是转座子啊 。 本文的作者在2008年的时候同样在the plant cell上发表了一篇关于植物miRNA注释标准的文章，文章题目是“Criteria for annotation of plant microRNAs”，鉴定过miRNA的小伙伴是不是很熟悉 。10年之后的2018年他们又发文说，2008年的那个标准已经落伍了，不适合时代的发展了，我和我们的小伙伴们有制定了一套新的标准。文中从多个方面阐述了新时期下为啥早先的标准不行了。下表列出了新旧版本标准的比较。文中有详细的解释，这里就不在一一说一些细枝末叶了，就文章一些细节方面的东西，欢迎进群交流。其实我们写了很多解读式的文章，群里却鲜有就这些文献的讨论，倒是我们主编群里会时不时就文献阅读方面的问题进行交流。看文献遇到不明白的地方可以去问问导师，师兄师姐，或者在群里或者留言询问，我们都会尽量解答，只有这样才会进步快。 同时，作者也给出了一个例子来说明为啥2008版落伍了。拟南芥的MIR399b和MIR405a，其中MIR399b基本都符合标准，而MIR405a却不合符大部分标准。 为什么要更新这样的一个标准，或者或为什么要避免错误的miRNA注释。做过miRNA鉴定的小伙伴一定了解，鉴定miRNA的软件很多很多，并且不同软件之间鉴定出来的miRNA差别很大。2014年专门有一篇文章使用一个数据集评价了这些软件。下图给出了几个评价指标，从这些指标来看miR-PREFeR和ShortStack这个款软件表现较好，但是要注意，这并不表示他们没有假阳性的结果出来，最好的那一款指不定在那个丈母娘的肚子里呢。最近不是流行人工智能嘛，说不定过些时候相关方面的软件就会出来了。最近的一款软件，Mirnovo tool，据说在动物里表现优秀，但在植物表现相对逊色，这个软件还有一个优点那就是不需要参考基因组。最近的 ShortStack 软件我使用了下，感觉还挺不错的，关键是还能鉴定phasiRNA。公司的小伙伴可以试着把你们的流程更新下。 作者还顺便吐槽了那些在一篇文章里发现了成百上千的新的miRNA的研究，并且还提醒审稿人要关切下这样的研究。因为即使在拟南芥里也才几百个miRNA。 下面谈到miRbase（ www.miRBase.org ）这个网站，该网站收录了很多物种中的miRNA，收录的miRNA主要来自于发表的文献。但是该网站收录的6942个植物miRNA位点中，只有8.5%的miRNA被认为是高可信的，这意味着miRbase里收录的miRNA可能很多都是有问题的。接着看下来，文章里有一大段是在吐糟miRbase的缺点和不作为，这里就不说了。 下面说到miRNA的保守性问题。这样个话题也是个坑，文中作者给出了自己的观点，下图列出了部分保守的miRNA的物种分布情况。 phasiRNAs有的时候会被认为是miRNA，比如水稻的miR5792，这其实是一个phasiRNA。造成这种局面的原因主要是因为miR5792只在某个特定的组织表达。而hc-siRNA在模式作物里研究的多一点。phasiRNA和hc-siRNA还需要更多的研究。 本文主要是对miRNA注释标准的更新，剩下的绝大部分都是在描述miRNA研究中存在的一些问题和难点。文章的解读就到此为止了，另外我还要介绍一个最近发表的miRNA靶基因的网站，该网站的靶基因数据是有降解组数据支持的，重要的是也支持我们小麦基因的查询。网站地址是 http://202.195.246.60/DPMIND/network.php?race_id=4565 ，发表的论文题目是“ DPMIND: Degradome-based Plant MiRNA-Target Interaction and Network Database ”。 欢迎关注 “ 小麦研究联盟 ”， 了解小麦新进展 投稿、转载、合作以及信息分布等请联系： wheatgenome
2018年第二周小麦文献推荐（1.14） 大家好！不知不觉今天是18年的第二周周末了。 昨天的推送收到很多反馈，胖丫让我感谢你们，她受益良多。有小伙伴问起Sentieon，昨天也没多说，今天多说两句，这个软件的功能和GATK功能类似，准确性上不输GATK，但是速度上要比它快N多倍。特别是当有大量样本需要做的时候，建议还是试一试Sentieon，毕竟时间就是金钱呢。这是一款商业软件，有兴趣的小伙伴可以邮件联系 support@sentieon.com ，可以获取试用版。也欢迎大家进群交流小麦方面的内容，可以加“wheatgenome”,老师或者博后也可以加“xiaoxuan8765”。 小麦组学研究在接来下2-3年一定是热点，除了中国春参考基因组，其它材料的基因组也会陆续发表。现在有各种组装技术加持，这些小麦族基因组不比参考基因组差，数据增多势必会促进我们的研究，但同时竞争也会更加激烈。作为传统的小麦研究者来讲，我们有材料，但是技术方面不成熟，而对于早期研究拟南芥、水稻等模式作物的研究者来讲，带着新技术新方法进入小麦也是顺其自然的过程。一个有技术，一个有材料或者数据，两者结合一定会有火花擦出来。回头看看最近2年的研究，这种合作方式越来越常见，最近黄三文小组和罗杰小组最近就联手在Cell上发表了一篇利用多组学数据研番茄果实的营养和风味的文章，这就是一个极好的合作共赢的例子。世界的发展也是这样的趋势，国家与国家之间联系越来越紧密，在这样一个信息和数据爆炸的时代，科研节奏会越来越快，专业的东西交给专业的人做，所以敞开胸怀合作一定不是坏选择。 又有点扯远了，下面让我们看看最近一周小麦方面又有哪些东西更新。 1 High throughput SNP discovery and genotyping in hexaploid wheat Because of their abundance and their amenability to high-throughput genotyping techniques, Single Nucleotide Polymorphisms (SNPs) are powerful tools for efficient genetics and genomics studies, including characterization of genetic resources, genome-wide association studies and genomic selection. In wheat, most of the previous SNP discovery initiatives targeted the coding fraction, leaving almost 98% of the wheat genome largely unexploited. Here we report on the use of whole-genome resequencing data from eight wheat lines to mine for SNPs in the genic, the repetitive and non-repetitive intergenic fractions of the wheat genome. Eventually, we identified 3.3 million SNPs, 49% being located on the B-genome, 41% on the A-genome and 10% on the D-genome. We also describe the development of the TaBW280K high-throughput genotyping array containing 280,226 SNPs. Performance of this chip was examined by genotyping a set of 96 wheat accessions representing the worldwide diversity. Sixty-nine percent of the SNPs can be efficiently scored, half of them showing a diploid-like clustering. The TaBW280K was proven to be a very efficient tool for diversity analyses, as well as for breeding as it can discriminate between closely related elite varieties. Finally, the TaBW280K array was used to genotype a population derived from a cross between Chinese Spring and Renan, leading to the construction a dense genetic map comprising 83,721 markers. The results described here will provide the wheat community with powerful tools for both basic and applied research 2 Mapping of quantitative trait loci for grain yield and its components in a US popular winter wheat TAM 111 using 90K SNPs Stable quantitative trait loci (QTL) are important for deployment in marker assisted selection in wheat (Triticum aestivum L.) and other crops. We reported QTL discovery in wheat using a population of 217 recombinant inbred lines and multiple statistical approach including multi-environment, multi-trait and epistatic interactions analysis. We detected nine consistent QTL linked to different traits on chromosomes 1A, 2A, 2B, 5A, 5B, 6A, 6B and 7A. Grain yield QTL were detected on chromosomes 2B.1 and 5B across three or four models of GenStat, MapQTL, and QTLNetwork while the QTL on chromosomes 5A.1, 6A.2, and 7A.1 were only significant with yield from one or two models. The phenotypic variation explained (PVE) by the QTL on 2B.1 ranged from 3.3-25.1% based on single and multi-environment models in GenStat and was pleiotropic or co-located with maturity (days to heading) and yield related traits (test weight, thousand kernel weight, harvest index). The QTL on 5B at 211 cM had PVE range of 1.8-9.3% and had no significant pleiotropic effects. Other consistent QTL detected in this study were linked to yield related traits and agronomic traits. The QTL on 1A was consistent for the number of spikes m-2 across environments and all the four analysis models with a PVE range of 5.8-8.6%. QTL for kernels spike-1 were found in chromosomes 1A, 2A.1, 2B.1, 6A.2, and 7A.1 with PVE ranged from 5.6-12.8% while QTL for thousand kernel weight were located on chromosomes 1A, 2B.1, 5A.1, 6A.2, 6B.1 and 7A.1 with PVEranged from 2.7-19.5%. Among the consistent QTL, five QTL had significant epistatic interactions (additive × additive) at least for one trait and none revealed significant additive × additive × environment interactions. Comparative analysis revealed that the region within the confidence interval of the QTL on 5B from 211.4-244.2 cM is also linked to genes for aspartate-semialdehyde dehydrogenase, splicing regulatory glutamine/lysine-rich protein 1 isoform X1, and UDP-glucose 6-dehydrogenase 1-like isoform X1. The stable QTL could be important for further validation, high throughput SNP development, and marker-assisted selection (MAS) in wheat. 3 Genotyping-by-Sequencing Derived High-Density Linkage Map and its Application to QTL Mapping of Flag Leaf Traits in Bread Wheat Winter wheat parents ‘Harry’ (drought tolerant) and ‘Wesley’ (drought susceptible) were used to develop a recombinant inbred population with future goals of identifying genomic regions associated with drought tolerance. To precisely map genomic regions, high-density linkage maps are a prerequisite. In this study genotyping-by- sequencing (GBS) was used to construct the high-density linkage map. The map contained 3,641 markers distributed on 21 chromosomes and spanned 1,959 cM with an average distance of 1.8 cM between markers. The constructed linkage map revealed strong collinearity in marker order across 21 chromosomes with POPSEQ-v2.0, which was based on a high-density linkage map. The reliability of the linkage map for QTL mapping was demonstrated by co-localizing the genes to previously mapped genomic regions for two highly heritable traits, chaff color, and leaf cuticular wax. Applicability of linkage map for QTL mapping of three quantitative traits, flag leaf length, width, and area, identified 21 QTLs in four environments, and QTL expression varied across the environments. Two major stable QTLs, one each for flag leaf length ( Qfll . hww-7A ) and flag leaf width ( Qflw . hww-5A ) were identified. The map constructed will facilitate QTL and fine mapping of quantitative traits, map-based cloning, comparative mapping, and in marker-assisted wheat breeding endeavors. 4 A genome-wide association study of wheat yield and quality-related traits in southwest China Wheat ( Triticum aestivum L.) is one of the most productive and important crops and its yield potential and quality characteristics are tightly linked with the global food security. In this study, genome-wide association study (GWAS) was conducted for yield and quality-related traits. Based on the high-density wheat 90K Illumina iSelect SNP Array, 192 bread wheat lines from southwest China, including 25 synthetic hexaploid wheat lines, 80 landraces, and 87 cultivars were analyzed. Association analysis results indicated that there were 57, 27, 30, and 34 SNPs associated with plant height (PH), grain protein content (GPC), thousand kernel weight (TKW), and SDS sedimentation volume (SSV) have been detected, respectively. Then, integrating RNA-Seq with bioinformatics analysis, 246 candidate genes (102 for GPC, 52 for TKW, and 92 for SSV) were found. Further analysis indicated that one up-regulated and two down-regulated expression genes affect GPC. Additionally, two haplotypes significantly affecting PH were detected in a 2.2-Mb genome region encompassing a gene which encoded an ubiquitin-specific protease, TaUBP24. The functional markers of TaUBP24 have been developed, which could be used for marker-assisted selection to improve wheat quality and yield. 5 Characterization of Novel Gene Yr79 and Four Additional QTL for All-stage and High-temperature Adult-plant Resistance to Stripe Rust in Spring Wheat PI 182103 Stripe rust, caused by Puccinia striiformis f. sp. tritici , is an important disease of wheat worldwide. Exploring new resistance genes is essential for breeding resistant wheat cultivars. PI 182103, a spring wheat landrace originally from Pakistan, has shown a high level of resistance to stripe rust in fields for many years, but genes for resistance to stripe rust in the variety have not been studied. To map the resistance gene(s) in PI 182103, 185 recombinant inbred lines (RILs) were developed from a cross with Avocet Susceptible (AvS). The RIL population was genotyped with SSR and SNP markers and tested with races PST-100 and PST-114 at the seedling stage under controlled greenhouse conditions and at the adult-plant stage in fields at Pullman and Mt. Vernon, Washington under natural infection by the stripe rust pathogen in 2011, 2012, and 2013. A total of five quantitative trait loci (QTL) were detected. QyrPI182103.wgp-2AS and QyrPI182103.wgp-3AL were detected at the seedling stage, QyrPI182103.wgp-4DL was detected only in Mt. Vernon field tests, and QyrPI182103.wgp-5BS was detected in both seedling and field tests. QyrPI182103.wgp-7BL was identified as a high-temperature adult-plant (HTAP) resistance gene and detected in all field tests. Interactions among the QTL were mostly additive, but some negative interactions were detected. The 7BL QTL was mapped in chromosomal bin 7BL 0.40-0.45 and identified as a new gene, permanently designated as Yr79 . SSR markers Xbarc72 and Xwmc335 flanking the Yr79 locus were highly polymorphic in various wheat genotypes, indicating that the molecular markers are useful for incorporating the new gene for potentially durable stripe rust resistance into new wheat cultivars. 6 Succession of Fungal and Oomycete Communities in Glyphosate-Killed Wheat Roots. The successional dynamics of root-colonizing microbes are hypothesized to be critical to displacing fungal pathogens that can proliferate after the use of some herbicides. Applications of glyphosate in particular, which compromises the plant defense system by interfering with the production of aromatic amino acids, is thought to promote a buildup of root pathogens and can result in a ‘greenbridge’ between weeds or volunteers and crop hosts. By planting two to three weeks after spraying, growers can avoid most negative impacts of the greenbridge by allowing pathogen populations to decline, but with the added cost of delayed planting dates. However, the specific changes in microbial communities during this period of root death and the microbial taxa likely to be involved in displacing pathogens are poorly characterized. Using high-throughput sequencing, we characterized fungal and oomycete communities in roots after applications of herbicides with different modes of action (glyphosate or clethodim) and tracked their dynamics over three weeks in both naturally infested soil and soil inoculated with Rhizoctonia solani *AG-8. We found that many unexpected taxa were present at high relative abundance (eg. *Pythium volutum and Myrmecridium species) in live and dying wheat roots and may play an under-recognized role in greenbridge dynamics. Moreover, communities were highly dynamic over time and had herbicide-specific successional patterns, but became relatively stable by two weeks after herbicide application. Network analysis of communities over time revealed patterns of interactions among taxa that were both common and unique to each herbicide treatment and identified two primary groups of taxa with many positive associations within-groups but negative associations between-groups, suggesting that these groups are antagonistic to one another in dying roots and may play a role in displacing pathogen populations during greenbridge dynamics. 7 Characterization of Adult Plant Resistance to Leaf Rust and Stripe Rust in Indian Wheat Cultivar ‘New Pusa 876’ Growing resistant varieties is the most effective and economical method for controlling rust of wheat ( Triticum aestivum L.). Resistance to leaf rust and stripe rust, caused by Puccinia triticina Erikss. and P. striiformis Westend. f. sp. tritici , respectively, was investigated in 148 F5recombinant inbred lines derived from a cross between ‘Avocet’ and ‘New Pusa 876’ (NP876). The parents and population were phenotyped for resistance in field trials for 3 and 2 yr for leaf rust and stripe rust, respectively, and genotyped with gene-linked molecular markers. The segregation analyses indicated that the adult plant resistance to leaf rust and stripe rust was conferred by five and four additive effect genes, respectively. Among them, the slow-rusting adult plant resistance gene Lr46/Yr29 reduced 14 and 16% of mean leaf rust and stripe rust severities, respectively, whereas a severity reduction of 26% occurred due to Lr67/Yr46 for both rusts. Both resistance genes were contributed by NP876. An additive effect between leaf rust resistance genes Lr46 and Lr67 was detected, with a reduction up to 11% when they were present together. The effect of combining Yr29 and Yr46 was additive but not significant, with a mean reduction of 5% in severity. New Pusa 876 can be used as a multiple rust resistance source to breed wheat varieties that may contribute towards durable resistance. 8 Temperature and Alternative Hosts Influence Aceria tosichella Infestation and Wheat Streak Mosaic Virus Infection Wheat streak mosaic, caused by Wheat streak mosaic virus (WSMV; family Potyviridae), is the most important and common viral disease of wheat (Triticum aestivum L.) in the Great Plains of North America. WSMV is transmitted by the wheat curl mite (WCM; Aceria tosichella). We evaluated how mean daily temperatures, cumulative growing degree-days, day of the year, and surrounding alternative host identity affected WCM infestation and WSMV infection of wheat from late summer through early autumn in Montana, United States. Cumulative growing degree-days, warm mean daily temperatures (i.e., 10°C), and surrounding alternative hosts interacted to alter risk of WCM infestation and WSMV infection. Wheat surrounded by Bromus tectorum L. and preharvest volunteer wheat had WCM infestation and WSMV infection rates of 88% in years when the mean daily temperature was 15°C in October, compared with 23% when surrounded by bare ground, and 1% when the temperature was 0°C regardless of surrounding alternative host. Mean daily temperatures in the cereal-growing regions of Montana during autumn are marginally conducive to WCM population growth and movement. As the region continues to warm, the period of WCM movement will become longer, potentially increasing the frequency of WSMV outbreaks. 9 Wheat resistances to Fusarium root rot and head blight are both associated with deoxynivalenol and jasmonate related gene expression Fusarium graminearum is a major pathogen of wheat causing Fusarium head blight (FHB). Its ability to colonize wheat via seedling root infection has been reported recently. Our previous study on Fusarium root rot (FRR) has disclosed histological characteristics of pathogenesis and pathogen defense that mirror processes of spike infection. Therefore, it would be interesting to understand whether genes relevant for FHB resistance are induced in roots. The concept of similar-acting defense mechanisms provides a basis for research at broad Fusarium resistance in crop plants. However, molecular defense responses involved in FRR as well as their relation to spike resistance are unknown. To test the hypothesis of a conserved defense response, a candidate gene expression study was conducted to test the activity of selected prominent FHB defense-related genes in seedling roots, adult plant roots, spikes and shoots. FRR was examined at seedling and adult plant stages to assess age-related pattern of disease and pathogen resistance. This study offers first evidence for a significant genetic overlap in root and spike defense responses, both in local and distant tissues. The results point to plant development-specific rather than organ-specific determinants of resistance, and suggest roots as an interesting model for studies on wheat-Fusarium interactions. 10 Three-Dimensional Analysis of Chloroplast Structures Associated with Virus Infection Chloroplasts are multifunctional organelles whose morphology is affected by environmental stresses. Although the three-dimensional (3D) architecture of thylakoid membranes has been reported previously, a 3D visualization of chloroplast under stress has not been explored. In this work, we used a positive-strand RNA ((+)RNA) virus, barley stripe mosaic virus (BSMV) to observe chloroplast structural changes during infection by electron tomography. The analyses revealed remodeling of the chloroplast membranes, characterized by the clustering of outer membrane-invaginated spherules in inner membrane-derived packets. Diverse morphologies of cytoplasmic invaginations ( CI s) were evident with spherules at the periphery and different sized openings connecting the CI s to the cytoplasm. Immunoelectron microscopy of these viral components verified that the aberrant membrane structures were sites for BSMV replication. The BSMV αa replication protein localized at the surface of the chloroplasts and played a prominent role in eliciting chloroplast membrane rearrangements. In sum, our results have revealed the 3D structure of the chloroplasts induced by BSMV infection. These findings contribute to our understanding of chloroplast morphological changes under stress conditions and during assembly of plant (+)RNA virus replication complexes. 11 No Time to Waste: Transcriptome Study Reveals that Drought Tolerance in Barley May Be Attributed to Stressed-Like Expression Patterns that Exist before the Occurrence of Stress Plant survival in adverse environmental conditions requires a substantial change in the metabolism, which is reflected by the extensive transcriptome rebuilding upon the occurrence of the stress. Therefore, transcriptomic studies offer an insight into the mechanisms of plant stress responses. Here, we present the results of global gene expression profiling of roots and leaves of two barley genotypes with contrasting ability to cope with drought stress. Our analysis suggests that drought tolerance results from a certain level of transcription of stress-influenced genes that is present even before the onset of drought. Genes that predispose the plant to better drought survival play a role in the regulatory network of gene expression, including several transcription factors, translation regulators and structural components of ribosomes. An important group of genes is involved in signaling mechanisms, with significant contribution of hormone signaling pathways and an interplay between ABA, auxin, ethylene and brassinosteroid homeostasis. Signal transduction in a drought tolerant genotype may be more efficient through the expression of genes required for environmental sensing that are active already during normal water availability and are related to actin filaments and LIM domain proteins, which may function as osmotic biosensors. Better survival of drought may also be attributed to more effective processes of energy generation and more efficient chloroplasts biogenesis. Interestingly, our data suggest that several genes involved in a photosynthesis process are required for the establishment of effective drought response not only in leaves, but also in roots of barley. Thus, we propose a hypothesis that root plastids may turn into the anti-oxidative centers protecting root macromolecules from oxidative damage during drought stress. Specific genes and their potential role in building up a drought-tolerant barley phenotype is extensively discussed with special emphasis on processes that take place in barley roots. When possible, the interconnections between particular factors are emphasized to draw a broader picture of the molecular mechanisms of drought tolerance in barley. 12 How exogenous nitric oxide regulates nitrogen assimilation in wheat seedlings under different nitrogen sources and levels Nitrogen (N) is one of the most important nutrients for plants and nitric oxide (NO) as a signaling plant growth regulator involved in nitrogen assimilation. Understanding the influence of exogenous NO on nitrogen metabolism at the gene expression and enzyme activity levels under different sources of nitrogen is vitally important for increasing nitrogen use efficiency (NUE). This study investigated the expression of key genes and enzymes in relation to nitrogen assimilation in two Australian wheat cultivars, a popular high NUE cv. Spitfire and a normal NUE cv. Westonia, under different combinations of nitrogen and sodium nitroprusside (SNP) as the NO donor. Application of NO increased the gene expressions and activities of nitrogen assimilation pathway enzymes in both cultivars at low levels of nitrogen. At high nitrogen supplies, the expressions and activities of N assimilation genes increased in response to exogenous NO only in cv. Spitfire but not in cv. Westonia. Exogenous NO caused an increase in leaf NO content at low N supplies in both cultivars, while under high nitrogen treatments, cv. Spitfire showed an increase under ammonium nitrate (NH4NO3) treatment but cv. Westonia was not affected. N assimilation gene expression and enzyme activity showed a clear relationship between exogenous NO, N concentration and N forms in primary plant nitrogen assimilation. Results reveal the possible role of NO and different nitrogen sources on nitrogen assimilation in Triticum aestivum plants. 13 Reference Quality Genome Assemblies of Three Parastagonospora nodorum Isolates Differing in Virulence on Wheat Parastagonospora nodorum , the causal agent of Septoria nodorum blotch of wheat, has emerged as a model necrotrophic fungal organism for the study of host-microbe interactions. To date, three necrotrophic effectors have been identified and characterized from this pathogen, including SnToxA, SnTox1, and SnTox3. Necrotrophic effector identification was greatly aided by the development of a draft genome of Australian isolate SN15 via Sanger sequencing, yet remained largely fragmented. This research presents the development of near-finished genomes of *P. nodorum *isolates Sn4, Sn2000, and Sn79-1087 using long-read sequencing technology. RNAseq analysis of isolate Sn4 consisting of eight time-points covering various developmental and infection stages mediated the annotation of 13,379 genes. Analysis of these genomes revealed large-scale polymorphism between the three isolates, including the complete absence of contig 23 from isolate Sn79-1087 and a region of genome expansion on contig 10 in isolates Sn4 and Sn2000. Additionally, these genomes exhibit the hallmark characteristics of a 'two-speed' genome, being partitioned into two distinct GC-equilibrated and AT-rich compartments. Interestingly, isolate Sn79-1087 contains a lower proportion of AT-rich segments, indicating a potential lack of evolutionary hot spots. These newly sequenced genomes, consisting of telomere to telomere assemblies of nearly all 23 *P. nodorum *chromosomes provides a robust foundation for the further examination of effector biology and genome evolution. 14 Exploration of Mechanisms for Internal Deterioration of Wheat Seeds in Postharvest Storage and Nitrogen Atmosphere Control for Properties Protection Wheat ( Triticum aestivum L.) seeds were stored in simulated conditions of four regions for 300 d. Changes of biochemical properties and electron microscope pictures demonstrated that unfavorable storage conditions caused serious internal deterioration and promoted the accumulation of unhealthy products in wheat seeds. Two hypotheses were proposed to explain the internal deterioration during storage. This work confirmed that the unfavorable storage conditions damaged enzymatic scavenging systems. As a result, without an effective scavenging system, serious internal deterioration occurred in wheat seeds. Atmospheric composition was adjusted to evaluate the potential of applying nitrogen atmosphere control in wheat storage. The results showed that 98% nitrogen gas in atmosphere effectively protected scavenging systems in wheat seeds and alleviate the internal deterioration. 15 Winter Wheat Yield Gaps and Patterns in China Wheat ( Triticum aestivum L.) yield stagnation has been reported in some regions of the world. China is the largest producer of wheat across the globe, but the pattern of its wheat yield stagnation remains poorly addressed. Here, our goal is to examine the temporal trends and spatial patterns of wheat yields along with possible causes based on a comprehensive assessment of winter wheat yield throughout China over the 31-yr period from 1980 to 2010. Combined with the Agricultural Production Systems Simulator (APSIM) wheat model, we assessed the winter wheat yield gaps and patterns in 1414 counties and at five physiogeographic regional scales across China to ascertain the driving factors of yield variations. Wheat yields increased in 53% of the 1414 counties, but the remaining counties experienced yields that never improved, stagnated, or collapsed from 1980 to 2010. The yield gap analysis showed that actual yields represented only 59% of the national average yield potential, indicating a substantial opportunity to improve winter wheat yields. Relatively larger yield gaps were observed in the northern China Plain (NC, 47%) and in southwestern China (SW, 45%). Although the yield gaps in these regions were accompanied by significantly progressive uptrends of actual yields, our results suggest that agronomic management could be further improved. Moreover, underperforming regions could potentially benefit from new investments and strategies to reliably increase actual yields and reverse trends in stagnation in winter wheat performance. 16 Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome We constructed and analyzed the pangenome of Zymoseptoria tritici , a major pathogen of wheat that evolved host specialization by chromosomal rearrangements and gene deletions. We used single-molecule real-time sequencing and high-density genetic maps to assemble multiple genomes. We annotated the gene space based on transcriptomics data that covered the infection life cycle of each strain. Based on a total of five telomere-to-telomere genomes, we constructed a pangenome for the species and identified a core set of 9149 genes. However, an additional 6600 genes were exclusive to a subset of the isolates. The substantial accessory genome encoded on average fewer expressed genes but a larger fraction of the candidate effector genes that may interact with the host during infection. We expanded our analyses of the pangenome to a worldwide collection of 123 isolates of the same species. We confirmed that accessory genes were indeed more likely to show deletion polymorphisms and loss-of-function mutations compared to core genes. 17 Expressed Ay HMW glutenin subunit in Australian wheat cultivars indicates a positive effect on wheat quality Out of the six HMW-GS genes, 1Ay is usually not expressed in bread wheat cultivars . In the current study, an active 1Ay gene has been integrated into two Australian wheat cultivars, Livingston and Bonnie Rock, through conventional backcross approach. Three sister lines at BC4F4 generation for each cross were obtained and underwent a series of quality testing. Results show that the active 1Ay subunit increased the amount total protein, Glutenin/Gliadin ratio and unextractable polymeric protein. The expressed 1 Ay also resulted in up to 10% increase of gluten content, 5% increase of glutenin, and hence increased the HMW- to LMW-GS ratio without affecting the relative amount of other subunits. Milling yield and Flour swelling were decreased in the Livingston lines and remained mostly unchanged for Bonnie Rock. Alveograph result showed that Ay improved dough strength in Livingston and dough extensibility in Bonnie Rock. Zeleny sedimentation value was found to be higher in all three lines of Bonnie Rock but only in one of Livingston derivatives. The dough development time and peak resistance, determined on the micro Z-arm mixer were increased in most cases. Overall, the integration of Ay subunit showed significant positive effects in bread making quality.
131 Genetic Analysis of Grain Shape, Grain Weight, Test Weight, Milling Yield, and Plant Height in a Spring Wheat Cross Curt McCartney Agriculture and Agri-Food Canada Wheat grain shape affects traits under selection by breeders (e.g. grain weight, test weight, and milling yield). A doubled haploid (DH) population of the cross RL4452/‘AC Domain’ was used to study the genetic basis of seed shape. Quantitative trait loci (QTL) analyses were conducted on a total of 18 traits: 14 grain shape traits, plant height, 1000-grain weight, test weight, and milling yield. Grain samples were harvested from trials grown at Glenlea, Brandon and Morden in Manitoba, Canada, between 1999 and 2004. Kernel shape was studied through digital image analysis with an Acurum® grain analyzer. Plant height, grain weight, test weight, flour yield, and grain shape were correlated with each other and QTL analysis revealed that QTL for these traits often mapped to the same genetic locations. The most significant QTL for grain shape traits were located on chromosomes 4B and 4D coincident with QTL for plant height. The most significant QTL for plant height, grain weight, and test weight mapped to the Rht-D1 locus on chromosome 4D. Rht-D1b *decreased plant height, grain weight, test weight, and kernel width relative to the *Rht-D1a allele. A narrow genetic interval on chromosome 4B contained significant QTL for grain shape, grain weight, and plant height. The ‘AC Domain’ allele reduced plant height, grain weight, kernel length and width traits, but had no detectable effect on test weight. The cumulative data indicated that this variation was inconsistent with segregation at Rht-B1 . Numerous additional QTL were also identified that control these traits in this population. 132 Genome-Wide Association Study of Winter Bread Wheat ( Triticum aestivum L.) in Response to Drought in a Multi-Environment European Network. Gaëtan Touzy ARVALIS Institut du Végétal Drought is one of the main abiotic stresses limiting wheat ( Triticum aestivum L. ) growth and productivity around the world. Many climate-based simulations have predicted an increase in the frequency and intensity of this abiotic stress. The delivery of new high yielding and stress-tolerant cultivars is now necessary and requires an improved understanding of the basis of the physiological and genetic response to drought. A panel of 220 European elite cultivars was evaluated in 32 field experiments. Grain yield and yield components were scored for each trial. A crop model was run with detailed climatic data and soil water status, to identify the timing, intensity and history of stress for each combination of genotype/trial. Cultivars were genotyped with the TaBW420K chip. This dataset gives us the opportunity for a detailed study of genetic by environmental interactions. Three scenarios of water deficit have been identified in this trial network. The grain yield loss in the two stressed scenarios was between 7 to 12% when compared to the non-stressed scenarios. A large genetic variability of grain yield was identified, with a genotypic variation affecting the mean by ± 15%. In the same way, GxE interactions affected the grain yield mean by 12.5%. GWAS were performed using multi-environment mixed models. Several QTLs were identified in the different stress scenarios, the allelic effects of these QTLs have been related to the environmental co-variables. Methods and results will be discussed especially those regarding the impacts of QTLxE interactions on grain yield and components and grain yield. 133 Getting to the Finishing Line: Integrating Optical and Physical Mapping for Megabase-Scale Resolution and Correct Annotation of Wheat Chromosome 7A Rudi Appels Murdoch University Recent advances in whole-genome sequence assembly algorithms and chromosome conformation capture (Hi-C) have enabled the production of the first full-scale pseudomolecules in hexaploid wheat (IWGSC RefSeq v1.0). Resources developed by the IWGSC over the last decade, including BAC libraries and physical maps were critical in validating the sequence and extending scaffolds into super-scaffolds, tripling the assembly N50 from 7Mb to 21Mb in IWGSC RefSeq v1.0. An independent assembly of chromosome 7A based on integrating a variety of datasets, including a BAC-based physical map, mate-pair sequencing, and optical mapping, resulted in the chromosome being assembled into 129 scaffold islands covering 735.1Mb. This assembly combined with the IWGSC RefSeq v1.0 enabled extensive validation as well as the elevation of regions of the chromosome from its existing high-quality draft status to finished status (less than one error per 100,000 base pairs). Integrating all available assembly resources, provided a complete classification of the chromosome into 17 contiguous regions with an N50 of 120Mb, the linear order of which could be independently validated using an 8-way MAGIC molecular genetic map. The value of fully validated sequence at long- and short-range is demonstrated using a number of regions of agronomic importance, including manual curation of the gene space. 134 RNA-Seq Analysis Reveals Jasmonates Related Pathways Associate with Salinity Tolerance in Wheat Qiaoling Luo Institute of Genetics and Developmental Biology, Chinese Academy of Sciences To explore the salt tolerance mechanism of wheat, we carried out RNA sequencing with 12 samples from three seedling tissues of salt-tolerant variety Xiaoyan 60 and high-yielding variety Zhongmai 175 under the salt treatment and the control. After analysis of different expression, 703, 979, 1197 differentially expressed genes (DEGs) were found respectively in new leaves, old leaves and root in Xiaoyan 60 when compared the salt treatment and the control, while the corresponding DEGs number in Zhongmai 175 were 613, 1401 and 1301. Further analysis demonstrated many DEGs were related with salt tolerance. Gene Ontology (GO) analysis showed the term “fatty acid biosynthesis process” was significantly enriched in new and old leaves of Xiaoyan 60, concurrently, the KEGG pathways “linoleic acid metabolism” and “alpha-linolenic acid metabolism” were also enriched. And most DEGs in these processes were up regulated, which indicated the level of jasmonate could be improved because the synthesis of jasmonate (JA) was through “alpha-linolenic acid metabolism”. In root tissue of Xiaoyan 60, the most significantly enriched KEGG pathway was “glucosinolate biosynthesis”, which could be induced by JAs. Differently, the most significantly enriched GO terms in the new and old leaves of Zhongmai 175 were “response to red or far red light” and “cellular response to starvation”. And similarly, the KEGG pathway “photosynthesis – antenna proteins” was also significantly enriched. Further analysis demonstrated that almost all the DEGs in these terms or pathways in Zhongmai 175 were down regulated, which manifested that the photosynthesis system may be damaged in Zhongmai 175, especially in the old leaves.These results indicate the jasmonates (JAs) related signal pathways may play a vital role in the salt tolerance of Xiaoyan 60. Inversely, the effects of JAs related pathways may be weaker in Zhongmai 175, and the photosynthesis system is destroyed due to the salinity stress. 135 GrainGenes: New Content, New Tools, New Tutorials Victoria Carollo Blake USDA ARS WRRC GrainGenes (https:// graingenes.org ; https://wheat.pw.usda.gov ) is the USDA-ARS database for wheat, barley, oat, and rye genetics and genomics. The GrainGenes project is moving toward a genome-centric resource to accommodate the ‘big data’ now available for the Triticeae and Avena. In this demo, we will 1) demonstrate the use of the new genome browsers on GrainGenes; 2) describe the variety-specific BLAST databases; 3) review the wealth of new content; and 4) share the collection of recently created topic-specific tutorials. Collaborations with The Triticeae Toolbox (T3), WheatIS, and Agriculture and Agri-Food Canada (AAFC) will assure that GrainGenes remains an important resource for the small grains research community. Mutual projects with our collaborators and future directions for the GrainGenes project will be discussed. 136 Multiplex Restriction Amplicon Sequencing (MRASeq), a New Next Generation Sequencing-Based Marker Platform for Genotyping Amy N. Bernardo Kansas State University Marker-assisted breeding enables the indirect selection of traits that are difficult and/or costly to phenotype thereby saving time and money, and increasing selection efficiency. To be useful in breeding programs, markers for genome-wide genotyping must be low cost, randomly distributed throughout the genome, high-throughput, and technically simple. We developed a PCR and NGS-based, low cost, high-throughput genotyping technology for genome-wide marker assays. This technology, designated as Multiplex Restriction Amplicon Sequencing (MRASeq), reduces genome complexity by PCR-amplification of selected portions of genomic regions flanked by restriction sites and is achieved using tailed and semi-degenerate PCR primers with restriction enzyme sequence at the 3’-end. MRASeq is flexible because the restriction enzyme sequence and the adjacent degenerate base sequence in the primers can be altered to suit the species of interest. MRASeq uses restriction sites as primer sites and does not make use of restriction enzymes. The incorporation of unique barcodes during a second PCR allows hundreds of samples to be multiplexed in one sequencing run. Linkage mapping of polymorphic MRASeq SNP markers in an allohexaploid wheat biparental population showed random distribution of SNPs across genomes. MRASeq on wheat and barley natural populations generated thousands of SNPs suitable for genomic selection. Therefore, this marker platform can be used for linkage mapping, background selection, or any other purpose in which large numbers of markers are needed. This simple, flexible and high-throughput genotyping method should be useful in genotyping laboratories, plant breeding programs, and genetic research. 137 Complete Chloroplast Genomes of *Aegilops tauschii *coss. and *Ae.Cylindrica *Host Sheds Light on Plasmon D Evolution Mari Gogniashvili Institute of Molecular Genetics, Agricultural University of Georgia Hexaploid wheat (Triticum aestivum L., genomes AABBDD) originated in South Caucasus by allopolyploidization of the cultivated Emmer wheat T. dicoccum (genomes AABB) with the Caucasian Ae. tauschii ssp strangulata (genomes DD). Genetic variation of Ae. tauschii is an important natural resource, that is why it is of particular importance to investigate how this variation was formed during Ae. tauschii evolutionary history and how it is presented through the species area. The D genome is also found in tetraploid Ae. cylindrica Host (2n = 28, CCDD). The plasmon diversity that exists in Triticum and Aegilops species is of great significance for understanding the evolution of these genera. In the present investigation the complete nucleotide sequence of plasmon D (chloroplast DNA) of nine accessions of Ae. tauschii and two accessions of Ae. cylindrica are presented. Twenty-eight SNPs are characteristic for both TauL1 and TauL2 accessions of Ae. tauschii using TauL3 as a reference. Four SNPs are additionally observed for TauL2 lineage. The longest (27 bp) indel is located in the intergenic spacer Rps15-ndhF of SSC. This indel can be used for simple determination of TauL3 lineage among Ae. tauschii accessions. In the case of Ae. cylindrica additionally 7 SNPs were observed. The phylogeny tree shows that chloroplast DNA of TauL1 and TauL2 diverged from the TauL3 lineage. TauL1 lineage is relatively older then TauL2. The position of Ae. cylindrica accessions on Ae. tauschii phylogeny tree constructed on chloroplast DNA variation data is intermediate between TauL1 and TauL2. The complete nucleotide sequence of chloroplast DNA of Ae. tauschii and Ae. cylindrica allows to refine the origin and evolution of D plasmon of genus Aegilops. 138 Can We Apply Lessons Learned from Manual Gene Annotation in Human and Mouse to Wheat? Jane Loveland EMBL-EBI The Ensembl-HAVANA team have significant expertise in manual genome annotation and over the last 15 years have been providing reference gene annotation for whole genomes (human, mouse and zebrafish), individual chromosomes (Pig chr X and Y), genes (Rat, Pig) and regions (MHC of Gorilla, Pig, Dog, Wallaby, Tasmanian devil) of community interest. Comprehensive manual annotation of high quality genomes is labour intensive and as such is not practical for very many genomes, however, automated gene annotation methods such as the Ensembl genebuild pipeline, can do a good job of a capturing the geneset, particularly protein coding genes. It is clear that experts in individual communities will want to improve the baseline automated annotation, for example to adequately capture their knowledge of functionally important genes or resolve annotation errors in complex regions such as gene clusters that present particular challenges for automated pipelines. We have a history of successful annotation workshops that have been co-ordinated by our team, namely for cow, pig and rat, where we provided training and annotation expertise to particular communities. As individual groups and communities create their own gene annotation, there is a danger that any divergence in their approach could hinder accurate downstream analysis both within and between species. For example, the CCDS collaboration between ourselves and RefSeq was established to agree common annotation for at least one CDS in every protein-coding gene in the already well annotated human and mouse genomes. Despite the technical expertise in both groups and the wealth of available experimental data in these species, small differences in starting annotation guidelines led to significant differences in the annotated genes, requiring the resolution of many hundreds of annotation differences. We will present our guidelines and practices for annotation, based on our accumulated knowledge from producing reference gene annotation as framework that could be used to inform the approach of a community towards manual annotation, for example, by providing guidelines that can be used in a platform agnostic way to help inform decisions on annotating structural and functional information for genes and transcripts. 139 The Hexaploid Oat Genome Nick Sirijovski Lund University Relative to other cereals such as rice, barley and wheat, very little is know about the genetics of oat. Cultivated oat ( Avena sativa ) is a hexaploid comprised of three diploid genomes (AACCDD). It has a 1C genome of 21 chromosomes with a total size estimated to 13Gb. The large genome size and polyploidy has meant that deciphering the genetics of cultivated oat has lagged behind other cereals. Recently, oat has received much attention due to well documented health benefits of consuming this ‘super food’, which in turn has lead to increased production of oat-based novel foods and ingredients e.g. dairy alternatives, beta-glucan extracts, and even meat substitutes. With the fast paced development of next generation sequencing technologies, it has now become possible and affordable to undertake genome sequencing of hexaploid oat using short read technology. Herein we report on the status of the Swedish oat genome sequencing project, which is part of the newly inaugurated ScanOats research center in Lund, Sweden. 140 Cloning of the Zero-Rowed Spike 1 in Barley Shun Sakuma Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Inflorescence architecture is a major determinant of the components of final grain yield in the cereals. The inflorescence can take the form of a panicle (rice, sorghum, and maize) or a spike (wheat, barley and rye). Barley’s spike is composed of three spikelets (one central spikelet and two lateral spikelets) per rachis node that is a unique character of Hordeum species among Triticeae. Cultivated barley ( Hordeum vulgare ssp. vulgare L.) produces either two-rowed (central spikelet fertile; lateral spikelets sterile) or six-rowed (complete fertility of the three spikelets) spikes. The six-rowed spike or lateral spikelet fertility is under the control of Six-rowed spike 1 ( vrs1) , vrs2 , vrs3, vrs4 and Intermedium spike-c ( int-c ). However, the genetic basis of three-spikelet structure in a distichous manner was not fully elucidated yet. To address this, we identified the zero-rowed spike 1 ( zrs1 ) mutant derived from mutagenesis of wild barley ( Hordeum vulgare ssp. spontaneum L.). The zrs1 mutant shows severe spikelet initiation defects and its distichous pattern is lost. At the vegetative growth the phylotaxis is normal as wildtype, however, after reproductive stage some tillers show onion-like leaf structure. We conducted genetic analysis using whole genome sequencing and RNA sequencing approach to reveal the genetic basis of the zrs1 mutant. 141 Gene Flow between Rye and its Wild Relatives Mona Schreiber IPK Gatersleben Rye ( Secale cereale L.) is a cereal grass that is an important food crop in Central and Eastern Europe. In contrast to its close relatives wheat and barley, it was not a founder crop of Neolithic agriculture, but is considered a secondary domesticate that may have become a crop plant only after a transitory phase as a weed. As a minor crop of only local importance, genomic resources in rye are underdeveloped, and few population genetic studies using genome-wide markers have been published to date. We collected genotyping-by-sequencing data for 603 individuals from 101 genebank accessions of domesticated rye and its wild progenitor S. cereale *subsp. vavilovii* and related species in the genus Secale . Variant detection in the context of a recently published draft sequence assembly of cultivated rye yielded 55,744 single-nucleotide polymorphisms with present genotype calls in 90 % of samples. Analysis of population structure recapitulated the taxonomy of the genus Secale . We found only weak genetic differentiation between wild and domesticated rye with likely gene flow between the two groups. Moreover, incomplete lineage sorting was frequent between Secale *species either because of on-going gene flow or recent speciation. Our study highlights the necessity of gauging the representativeness of *ex situ germplasm collections for domestication studies and motivates a more in-depth analysis of the interplay between sequence divergence and reproductive isolation in the genus Secale . 142 Challenges and Opportunities of Connecting Phenotype with Genotype; Perspectives from Seeds of Discovery and Excellence in Breeding. Sarah Hearne CIMMYT International Maize and Wheat Improvement Center Management of data along complex and logistically challenged crop research and breeding processes is often the last thing to be considered in planning processes and is consequently an Achilles heel, limiting the impact of many projects and initiatives. Here we present a review of some of the challenges, interventions and opportunities in data management from the perspectives of an established initiative and a new cross commodity platform. The Seeds of Discovery initiative (SeeD) aims to explore and leverage high value novel diversity for maize and wheat breeding application. In the 6.5 years since inception, SeeD has generated vast quantities of genotypic and phenotypic data from extensive evaluation of germplasm bank accessions. The effective management of this data along the collection, curation, analysis and dissemination continuum has evolved, resulting in multidisciplinary and multi-institutional development of systems, standard operating procedures and business rules. We present some of the experiences of SeeD in developing effective practices to connect genotype with phenotype. The CGIAR Excellence in Breeding Platform (EiB), established in 2017, is developing a resource and support structure to modernize breeding programs targeting the developing world. EiB draws from innovations in the public and private sector to provide access to cutting-edge tools, services and best practices, training and practical advice for breeding programs. Data accuracy, integrity and interconnectivity are fundamental to breeding gain and EiB is placing strong emphasis on the sharing of best practices and resources in this area. Current plans and initial platform activities in this area will be presented. 143 Advanced Genomics Tools for Deep Insights into Complex Genome Systems Jayson Talag Arizona Genomics Institute The Arizona Genomics Institute (AGI) has played significant roles in numerous genome projects over the past 15 years, including Asian and African rice and its 20 wild relatives, maize, wheat, Brachypodium, date palm, sugarcane, citrus, cacao, soybean and its wild relatives, brassicas, tomato, tree nuts, etc. AGI’s expertise is not limited to plants, and includes model species like Drosophila (19 genomes), zebra finch, Biomphalaria and nurse shark, dingo, as examples. AGI’s philosophy is that the first genome sequence of any species should be as high a quality as possible. To achieve this standard, AGI is currently employing long-read sequencing platform – e.g. PacBio’s SEQUEL. Using this instrument, our read lengths Sub read N50 average 20KB, with 23KB on some projects. The average output is ~5Gb/cell, with some over 9Gb/cell. Using this technology to sequence BAC-pool we published two of the highest quality indica rice genomes August of 2016. Theses genome have now been upgraded with the addition of whole genome shotgun PacBio data resulting in near gap free assemblies with less than 20 gaps/genome. A critical key to our success lies in our ability to isolate high-quality high-molecular weight DNA as initial substrates for library construction. We have found that specific considerations must be addressed to achieve access to genomic substrates (HMW DNA and RNA) for downstream high quality performance. These include defined tissue types and collection protocols, careful extraction procedures and chemistry modifications, advanced purification steps using both chemical and electrophoretic methods, and very stringent quality control measures to assure substrate performance. Our methods have been used to produce high quality substrates for a variety of different applications such as Pacbio, Illumina, RNAseq, 10x Genomics, Dovetail, BAC library construction, etc. 144 Integrating and Displaying Plant Gene Expression in Expression Atlas Laura Huerta European Bioinformatics Institute (EMBL-EBI) Expression Atlas ( https://www.ebi.ac.uk/gxa ) is a database and web-service at EMBL-EBI that selects, curates, re-analyses and displays gene expression data in a baseline context, e.g. to find genes expressed in different tissues in potato, and in a differential context, e.g. to find up-regulated genes in response to stripe rust and powdery mildew in wheat. Plant experiments from ArrayExpress, GEO and SRA/ENA/DDBJ are selected for curation and analysis. Data curation involves enriching sample annotation with additional metadata, annotating metadata with Experimental Factor Ontology (EFO) terms and deciding comparisons for differential expression analysis based on associated publications and correspondence with the original researchers. Data analysis is performed using open source tools for microarray data and our standardized pipeline iRAP ( https://github.com/nunofonseca/irap ) for RNA-seq data. Currently, we provide gene expression analysis results for more than 700 plant experiments across 20 different plant species. Expression Atlas can be searched by gene, gene set and biological condition queries. The use of EFO annotations allows efficient search via ontology-driven query expansion and facilitates data integration across multiple experiments. We offer downstream analysis and visualization such as gene co-expression, biological variation among replicates, transcript quantification, visualization of gene expression in Gramene genome browser and enrichment of Gene Ontology terms and Reactome pathways. Finally, we have developed an automatic pipeline that discovers new plant RNA-seq data at ENA for 45 different species, performs quality control, alignment to the genome reference in Ensembl plants and quantification of gene and exon expression. The analysis results are available via our RNASeq-er API ( https://www.ebi.ac.uk/fg/rnaseq/api/ ). 145 Mining DNA Methylation Variations in Alleles and Homeologs using CGmapTools Weilong Guo China Agricultural University DNA methylation is important for gene silencing and imprinting in both plants and animals. We developed software CGmapTools (freely available at https://cgmaptools.github.io/ ) as a toolset for mining DNA methylation information in BS-seq data, by integrating ~40 command-lines applications into one package. This package uses CGmap and ATCGmap as the format interfaces, and designed binary formats to reduce the file sizes and support fast data retrieval, and can be applied for context-wise, gene-wise, bin-wise, region-wise, and sample-wise analyses and visualizations. To accurately identifying heterozygous SNVs from partially C-to-T converted, we designed two methods, BayesWC and BinomWC, that substantially improved the precision of heterozygous SNV calls from ~80% to 99% while retaining comparable recalls. With these SNV calls, we provided functions for allele-specific DNA methylation (ASM) analysis and visualizing the methylation status on reads. Applying ASM analysis to a previous dataset, we found that an average of 1.5% of investigated regions showed allelic methylation, which were significantly enriched in transposon elements and likely to be shared by the same cell-type. A dynamic fragment strategy was utilized for DMR analysis in low-coverage data. Recently, we develop new method for mining differential DNA methylations among homeologs, suitable for allopolyploid genomes, such as bread wheat. The new method also support visualising DNA methylomes variations and genomic variations among homeologs. 146 New Genotyping Technology, GRAS-Di, Using Next Generation Sequencer Hiroyuki Enoki Toyota Motor Corporation We developed new genotyping technology, Genotyping by Random Amplicon Sequencing-Direct (GRAS-Di). This technology consisted of sample preparation using high concentration random primer, NGS and data analysis. The sample preparation was very simple. It was not necessary to do primer design, enzyme digestion, fragmentation, size selection, adaptor ligation, and sample normalization. It was only two steps PCR for NGS library without specialized equipment. Rice BIL population was used for evaluation of genotyping by GRAS-Di (96 samples / lane of HiSeq2500). The number of reads for each amplicon was highly reproducibility, r 0.99, with repetition. Over ten thousand SNPs were detected among the BIL population and the SNPs were distributed uniformly rice genome. The ratio of missing value was very low, 1.5%. The reproducibility of SNP was 99.9% with repetition. If there was no reference sequence, genotype data could be detected by GRAS-Di using original algorism based on amplicon analysis. Theoretically, the technology is also applicable to other creatures, including highly polyploidy creatures. We performed the applicability test for several creatures. The result shown that the technology was applicable for over fifty creatures, including wheat, soybean, tomato, potato, sugarcane, cow, pig, chicken, tuna and human. The technology could be provided over 30,000 multiplex sequencing at once. We think that GRAS-Di would be very easy and very powerful technology for genome wide genotyping in many creatures. We signed licensing agreement with Kazusa DNA Research Institute, Eurofins Genomics, and GeneBay for GRAS-Di. 147、Stacking Multiple Stem Rust Resistance Genes at a Single Locus for Durable Resistance in Wheat Ming Luo Commonwealth Scientific and Industrial Research Organisation Stem rust disease caused by the fungal pathogen Puccinia graminis f.sp tritici is a significant threat to global wheat production. The most cost effective way to control this disease is by genetic resistance. However major gene resistance is often readily overcome by pathogen evolution when resistance genes are deployed singularly. Combining major resistance genes is believed to extend their durability as multiple mutations are required in the pathogen to overcome this polygenic resistance. Major resistance genes can be combined by conventional breeding however this is a labour intensive process and resistance gene combinations are difficult to maintain in segregating families. In this study, we have used cloned stem rust resistance genes Sr22, Sr35, Sr45, Sr46 and Sr50 and the multi-pathogen adult plant rust resistance gene Sr55/Lr67/Yr46/Pm46/Ltn3 to produce binary vectors containing combinations of these genes. Constructs containing either 3, 4, 5 or 6 rust resistance genes were produced and transformed into bread wheat by Agrobacterium transformation. Molecular/genetic analysis demonstrated that some transgenic wheat lines contain all the resistance genes present in the binary vector used for transformation (ie. up to six) and these genes are inherited as a single locus in progeny plants. Transgenic plants are resistant to wheat stem rust disease with resistance co-segregating with the multigene transgenic locus. 148 MAGIC Yield: Using an Eight Founder Population for the Genetic Dissection of Yield and Yield Components in UK Winter Wheat Benedetta Saccomanno NIAB Multiparent advanced generation inter-cross (MAGIC) populations are a powerful mapping resource in crop genetics for the dissection of complex traits, previously hindered by relatively low genetic recombination and allelic diversity of traditional bi-parental populations. Wheat (*Triticum aestivum *L.) is a major arable crop of global importance, covering 1.6 million hectares in the UK alone (AHDB survey, 2017). Breeders and farmers must continue to improve wheat grain yield and yield stability to help meet demand from an increasing population, and to ensure food security in the face of the effects of climate change. The Magic Yield project helps address these problems by using an eight-founder MAGIC population (Mackay *et al. *2014), consisting of 1,000 lines created by inter-crossing eight elite UK winter wheat varieties over three generations, to study the genetic basis of yield and yield components. With the participation of five wheat breeding companies, we conducted field trials at five UK sites for two consecutive years, phenotyping yield and a suite of pre- and post-harvest yield components. Phenotypic data coupled with Illumina iSelect 90k SNP genotype data (Gardner *et al. *2016) allowed the detection of a total of 76 quantitative trait loci (QTL) across all year, trait and site combinations. Flanking markers for selected QTL were converted to Kompetitive Allele Specific PCR (KASP) markers to aid fine-mapping and consequent characterization of genes controlling yield. Ultimately, the resources generated will aid the selection of wheat lines with improved performance within breeding programs, for the downstream benefit to growers and end-users.
118 Genome-Specific Amplicon Sequencing Strategy Provides Robust Markers across D Genome in Allohexaploid Wheat Goro Ishikawa Institute of Crop Science, National Agriculture and Food Research Organization (NARO)Tohoku Agricultural Research Center, National Agriculture and Food Research Organization (NARO) In allohexaploid wheat, array-based genotyping platforms have been widely used for genetic analyses. However, when commercially available arrays were applied for Japanese varieties, there was a low rate of polymorphism and biased distribution of markers across the genomes, especially the D genome. These results indicate that our materials are genetically distant from those used to design the arrays. To increase genome-wide mapping markers suitable for our materials, we have established an efficient procedure to detect nucleotide polymorphisms, and a robust method for genotyping by sequencing genome and site-specific amplicons. Here we present the procedure focusing on the D genome. By sequence capture and next-generation sequencing, 12,551 polymorphisms between wheat varieties ‘Hatsumochi’ and ‘Kitahonami’ were detected across the three genomes. The flanking sequences of target polymorphisms were blasted against the International Wheat Genome Sequencing Consortium survey sequences, and three homoeologous sequences were identified. Based on the polymorphisms among the genomes, 396 D genome-specific primer pairs were designed using an in-house Java pipeline. Approximately 80% of the designed primers successfully amplified genome-specific products, indicating that they could be genotyped as easily as a diploid species. Linkage maps of recombinant inbred lines between the two varieties revealed that the newly developed markers were uniformly distributed across the D genome and greatly extended the total coverage. This result proved that the strategy described here can be useful to increase the number of markers at target sites. This work was supported by grants from the Ministry of Agriculture, Forestry and Fisheries of Japan (NGB1002, NGB1007). 119 Breeding Strategies using Genomic Selection Increase Genetic Gain in Wheat Breeding Programs Biructawit B. Tessema Molecular Biology and Genetics, Aarhus University The traditional wheat breeding programs have been running for several years yet the genetic gain has been very limited. However, the use of genomic information for a selection criterion can increase genetic gain. This study was set to see how much genetic gain can be increased by implementing genomic selection on traditional wheat breeding program. In addition, we investigated the effect of genetic correlation between different traits on genetic gain. A series of wheat breeding programs that run simultaneously for 30 years was simulated using stochastic simulation, meaning each year a new breeding program starts with a cross of 60 parental lines followed by six generations of selfing. Selection was performed on three different generations. At F2, phenotypic selection was performed on breeder’s visual preference. At F5 and F6, either phenotype or Genomic Estimated Breeding Value (GEBV) was used to select on yield. Yield at F5 and F6 was considered as different traits because they differ in plot size, population density, and number of plot replications. Plot heritability of these traits were 0.1, 0.2, and 0.3 while the economic values were 0, 0, and 1. In addition, we simulated different levels (0.3, 0.5, 0.7, 0.9) of genetic correlation between F2 and F5 as well as between F5 and F6. The varied selection criterion and varied genetic correlations make a total of 16 scenarios. GEBV as a selection criterion significantly increased genetic gain by 10% compared to phenotype. Besides, the genetic gain was higher with the higher genetic correlation between traits. 120 Genomic Selection for End-Use Quality Traits in Soft White Wheat (Triticum aestivum L.) Jayfred Gaham Godoy Washington State University End-use quality traits in soft white wheat are complex traits that are controlled by multiple genetic factors with minor effects. A previous genome-wide association study (GWAS) identified 105 SNP markers for end-use quality traits but these markers only explained 5 – 30% of the phenotypic variation leaving a larger portion of unaccounted heritability. Genomic selection (GS) is a breeding method to predict breeding values using genome-wide markers. GS can simultaneously model all additive genetic variance that is unaccounted for in GWAS. We assessed the application of GS for 21 end-use quality traits using a panel of 469 elite soft white winter wheat from Pacific Northwest breeding programs that were genotyped with 15,229 SNP markers. Genomic prediction using single and multi-trait models were evaluated using the R packages rrBLUP and PHENIX, respectively. Single trait prediction estimates were calculated using the gBLUP model. The multi-trait model used genetic information from the kinship matrix and trait correlation to estimate genomic estimated breeding values (GEBVs). Prediction accuracies following a 10-fold cross validation were 30 – 87% for the single trait model and 69 – 99% for the multi-trait model. Prediction accuracies were significantly higher (up to a 100% increase) in the multi-trait model especially for low heritability traits. Our results suggest that genomic selection can be an efficient tool to develop soft white wheat with superior end-use quality traits. We are currently validating the multi-trait GS model to predict end-use quality performance in different breeding populations (e.g. F5 single plots and double haploids) using genotype-by-sequencing data. 121 Fine Mapping a Major QTL Controlled Tiller Number and Plant Height Using a Wheat660K SNP Array Tao Xu Nanjing Agricultural University Tiller number and plant height are two major agronomic traits in cereal crops affecting plant architecture and grain yield. NAUH167, a mutant of common wheat landrace Wangshuibai induced by ethylmethyl sulfide (EMS) treatment, exhibits higher tiller number and reduced plant height. A stable major QTL designated QHt.nau-2D controlling plant height and tiller number, was mapped to the short arm of chromosome 2D flanked by markers QHT239 and QHT187 covering a predicted physical distance of 6.77 Mb. To further map the QHt.nau-2D loci, a population consisted of 6009 F2 progeny from a cross 2011I-78 /NAUH167 was constructed. At the same time, additional molecular markers were developed to saturate the QHt.nau -2D region based on the Wheat660K SNP array. On the basis of Chinese Spring sequences, 53 ARMS-PCR and 18 CAPS/dCAPS markers were designed to detect the polymorphism between 2011I-78 and NAUH167. Finally, QHt.nau-2D was located within a genetic region of 0.5 cM between markers QHT239 and SNP17 spanning a 1.22 Mb physical genomic region of Ae. tauschii chromosome 2DS. The genetic and physical maps of *QHt.nau-2D *provide a framework for map-based cloning and this research would facilitate the characterization of plant height and tiller number in wheat. 122 Survey Sequencing of Flow-Sorted H**aynaldia villosa Chromosome 6VS Wentao Wan Nanjing Agricultural University Haynaldia villosa has been recognized as a useful germplasm for wheat breeding and improvement and the availability of genomic sequence would accelerate its research and application. In the present work, the short arm of H.** **villosa chromosome 6V in which powdery mildew resistant gene Pm21 have been mapped was flow-sorted by flow cytometry from a telocentric chromosome addition line of 6VS and sequenced using Illumina platform. We obtained a total of 47.7Gb raw sequencing reads and by de novo assembly 230.39Mb assembled sequence. Repetitive elements account for about 74.91% of the genome. 3,276 genes were annotated in the coding fraction of the genome which account for about 2.1%. The syntenic regions of 6VS genes were searched and identified on wheat group 6 chromosomes 6AS, 6BS, 6DS, rice chromosome 2, Brachypodium chromosome 3, and sorghum chromosome 4. Based on the size difference of intron for the synteny genes among 6VS genome and wheat group 6 chromosomes, we designed 222 IT markers, in which 120 markers had specific amplification on 6VS genome.The preliminary genomic sequence of 6VS provides genetic information for cloning genes on this chromosome and developing IT markers for molecular marker assisted breeding and physical map construction. 123 Speed Breeding with Genomic Selection to Accelerate Wheat Variety Development Amy Watson The University of Queensland Genomic selection (GS) in wheat could accelerate yield gain principally through a reduction in breeding cycle duration. A method for rapid generation advance called ‘speed breeding’ (SB) enables up to six generations of spring wheat per year, and could be used to accelerate breeding population development and be combined with GS in various breeding schemes to enable even further gains. To improve the accuracy of selection for improved yields, many heritable traits that are genetically correlated with yield could be measured in the field and used in multi-trait models to improve genetic gain (over that of traditional single-trait models only containing yield data of the training population). To test these hypotheses, a 260 multi-parent spring wheat population, genotyped with 8,000 DArT polymorphic markers, underwent yield trials over three years. Trial plots were also phenotyped for height and normalized difference vegetation index (NDVI) using a hand-held GreenSeeker sensor. Yield prediction accuracy was accessed using five-fold cross validation and predicting into different years. Results indicate multi-trait GS prediction including field proxy traits improved selection for field-based yield over that of single-trait models. These traits could be phenotyped in the field following rapid line development under SB and used with training population yield data to advance genetic gain and wheat variety development. 124 High Level of Structural and Sequence Divergence between Homologous Regions of Bread Wheat and T. militinae within the Powdery Mildew Resistance Locus Qpm.Tut-4A Eva Janáková Institute of Experimental Botany Introgression of QPm.tut-4A locus from Triticum militinae into the distal end of bread wheat chromosome 4AL confers improved resistance against powdery mildew. The locus was high-density mapped and delimited to 0.024 cM using 8327 individuals and 75 markers. Using additional 2052 ph1 *lines seven new recombinations were identified. After chromosome walking, final flanking markers *owm169 *and *owm228 were mapped and the region was found 640.8 kbp and 480.2 kbp long in cv. Chinese Spring (CS) and *T. militinae *(TM), respectively. The cM/Mb ratio is much smaller compared to these commonly found at the end of wheat chromosomes. The sequenced region was annotated and 16 and 12 protein coding genes were identified in CS and TM, respectively. Out of them, seven CS and six TM genes were not syntenic. Furthermore, intergenic regions do not show a significant similarity between CS and TM. The TM region containing the remaining six genes has a syntenic counterpart in CS, but that region was duplicated and one of the duplications was inverted. The duplication and inversion were accompanied by gene loss and four of the TM genes have their counterparts in both duplicated regions in CS. Finally, three genes from the CS region do not have their homologs in the TM region. These structural and sequence differences are major reasons for the discrepancy between the expected and observed cM/Mb ratio. This work was supported by award LO1204 from the National Program of Sustainability I and by the Estonian Ministry of Agriculture. 125 Technologies to Increase Genetic Potential Productivity Under Abiotic Stress for Winter Wheat and Barley Crops, in Climatic Condition from Braila Plain, Romania Daniela Trifan BRAICOOP Agricultural Cooperative - Research DepartmentAgricultural Research and Development Station Each agricultural crop has a theoretical genetic potential, which is represented by the production quantity and quality obtained by the variety of culture, in perfect condition. But perfect conditions for culture there are in few places, especially lately, when seen increasingly accelerated phenomenon of climate change. Increasing theoretical genetic potential for productivity was achieved for each species grown in many years of genetic research, both in the laboratory and in the field experiences. Every year is putting out more and more performing varieties with increased resistance to drought, heat, pests and diseases etc. But genetic potential to the maximum occurs when growing conditions are as close genetically programmed requirements. The abiotic stress can significantly reduces the genetic productivity potential from the very early stages of germination and the vegetation, if the conditions are not fulfilled optimum microclimate (humidity, temperature, nutrients, absence of pests and diseases, etc.). On the other hand, even if the plant grew and developed normally, but is attacked by diseases or pests in a phase of vegetation close to reproduction, this can significantly reduce production unless corrective measures and effective protection of agricultural crops. This paper presents the results about monitoring of genetic potential at some winter wheat and barley varieties, and the results of agrophytotechnical methods to increase genetic potential on production and product quality. The experiments during in the period 2012 - 2017, at Agricultural Research and Development Station of Braila, Romania, by comparing the genetic production potential of some varieties of wheat and barley under different densities and dates of sowing, different fertilization (chemical and biological), and the application of plant biostimulators, also. 126 Structural Organization and Gene Duplication in the Chromosomal Region Harboring the Alpha-Gliadin Gene Family in Aegilops tauschii Yong Q. Gu USDA ARS, Western Regional Research Center Among the wheat prolamins important for its end-use traits, α-gliadins are the most abundant and also a major cause of food-related allergies and intolerances. Previous studies of various wheat species estimated between 25 to 150 α-gliadin genes reside in the Gli-2 locus regions. To better understand the evolution of this complex gene family, the DNA sequence of a 1.75-Mb genomic region spanning the Gli-2 locus was analyzed in the diploid grass, Aegilops tauschii , the ancestral source of D genome in hexaploid bread wheat. Comparison with orthologous regions from rice, sorghum, and Brachypodium revealed rapid and dynamic changes only occurring to the Ae. tauschii Gli-2 region, including insertions of high numbers of non-syntenic genes and a high rate of tandem gene duplications, the latter of which have given rise to 12 copies of α-gliadin genes clustered within a 550-kb region. Among them, five copies have undergone pseudogenization by various mutation events. Insights into the evolutionary relationship of the duplicated α-gliadin genes were obtained from their genomic organization, transcription patterns, transposable element insertions, and phylogenetic analyses. An ancestral GLR gene encoding putative amino acid sensor in all four grass species has duplicated only in Ae. tauschii and generated three more copies that are interspersed with the α-gliadin genes. Phylogenetic inference and different gene expression patterns support functional divergence of the Ae. tauschii GLR copies after duplication. Our results suggest that the duplicates of α-gliadin and GLR genes have likely taken different evolutionary paths; conservation for the former and neofunctionalization for the latter. 127 Comparison of Durum Landraces with Northern Great Plains Adapted Cultivars and Identification of Selection Sweeps Jason Fiedler North Dakota State University Durum wheat ( T. turgidum ssp. Durum, AABB ) is a key crop for high-value food production. Modern breeding programs over the last century have developed a number of elite cultivars that are adapted for growth in the Northern Great Plains. To investigate the genomics underlying this adaptation, we compare 449 global durum lines from the Wheat Coordinated Agricultural Project with 34 advanced lines from the North Dakota State University (NDSU) Durum Breeding Program. We used genotype-by-sequencing (GBS) to identify 21,030 single nucleotide polymorphisms (SNP)s in the populations and measured genetic diversity on several scales. We find that population sub-structure designations largely agree with regional adaptation, and lines adapted to the Northern Great Plains show relatively low genetic diversity and high allelic fixation. We identified 23 genetic intervals that display differential allelic fixation between un-adapted and improved lines, suggesting that these linkage blocks are important for durum improvement. Screening potential lines for these linkage blocks could accelerate breeding efforts, and understanding the genes in these regions could shed light on the molecular characteristics of elite lines. 128 PolySNP: An R Package for Calling Polyploid SNP Array Data using Gaussian Mixture Models Matthew T. McGowan Washington State University The genomic complexity in polyploid plant species makes genotype calling difficult when processing data generated from a high-density SNP array. We present a novel computational method and a software package for calling genotypes from raw hexaploid wheat data generated using the 9k iSelect® assay previously developed for wheat. This method involves fitting an indeterminatenumber of Gaussian mixture components and identifying the optimal number of clusters using an EM-like algorithm implemented in the 'Rmixmod' package. Then markers with bi-allelic patterns are further analyzed by merging outlier clusters and identifying heterozygous clusters. Genotypes are then called based on cluster assignment. Furthermore, models generated with a diverse population can be later used to call genotypes for smaller populations, drastically reducing computational complexity for subsequent calls. This method was tested using a diverse wheat population (n = 1654) and resulting genotypes were compared to previously called genotypes using the current standard method of manual curation. Genomic predictions were generated for both genotype sets using the gBLUP method implemented in the 'rrBLUP' package in R for five different phenotypes. Regression coefficients for predicted vs observed values were improved by 1.38% when using genotypes generated with this new method. Despite an increased computational cost of using Gaussian mixture models, a reduced supervision requirement and increased ability to resolve complex signal patterns allow it to generate more predictive genotypes with less manual manipulation. 129 Genotypic and Phenotypic Evaluation of Preharvest Sprouting in Two and Six Row Barley Jason Walling USDA, ARS, MWA, Cereal Crops Research Unit, Madison, WI Preharvest Sprouting (PHS) is a problem negatively affecting both yields and quality of cereal crops grown world-wide. Preharvest Sprouting can be generalized as the propensity of a seed to begin germination while still on the parent plant and is most widely observed in regions with high humidity and/or excessive periods of rain. Barley with signs of PHS is rejected for malt and can only be sold as feed, results in a loss to the grower of about half the value. Preharvest sprouting is a complex trait involving contributions from both multi-genic and environmental factors. Recently, a gene ( TaPHS1 ), was described in Triticum aestivum *(wheat) whose variable genotype and specific gene expression were associated with wheat lines that show either resistance or susceptibility to PHS. Here we present the exonic sequencing and genotypic characterization of the barley ( Hordeum vulgare ) homolog *HvPHS1 in over 120 barley lines. Additionally, we evaluated each of these lines for dormancy using standard germination tests and also for PHS by challenging intact heads to sprout in an artificial rain chamber. 130 Mining Natural Variation in Triticeae to Improve Plant Immunity Burkhard Steuernagel John Innes Centre It is widely acknowledged that during domestication many crops went through a genetic bottleneck leading to loss of large parts of intraspecific diversity. Modern agriculture therefore seeks to recruit genetic diversity from wild relatives to improve crops. One important area of crop improvement is breeding for resilience to biotic stress. Mining resistance genes from crop wild relatives, however, is a laborious endeavour due to their poor agronomy, ploidy differences, and limited genomic resources. Gene cloning projects are usually long procedures involving the creation of populations dedicated to only a single gene. Here we report Association Genetics using Resistance gene ENrichment SEQuencing (AgRenSeq) to rapidly clone resistance genes from a wild diversity panel through association genomics of selectively captured and sequenced resistance gene analogues. We demonstrate our concept by mining a panel of 151 accessions of Aegilops tauschii , a wild relative of wheat, for resistance genes against the wheat stem rust causing fungus Puccinia graminis f. sp. tritici .
91 Genetic Dissection of Morphological and Phenological Traits Associated with Domestication Syndrome in Durum × Wild Emmer Wheat RIL Population Andrii Fatiukha Institute of Evolution and the Department of Evolutionary and Environmental Biology, Faculty of Science and Science Education, University of Haifa Domestication and subsequent evolution under domestication of wheat caused substantial genetic changes, which affected plant morphology, physiology and phenology. Morphological characters, such as compactness of spikes, the number of side shoots, can be mentioned as domestication related traits in cereals. We suggest to consider the angle of side shoots (Ash) as a novel trait associated with the domestication syndrome. The objective of this study is to provide a better understanding of the antagonism between natural and man-made selection of the traits under domestication in order to identify the significant changes in phenology and morphology of wheat during domestication. We used a recombinant inbred line (RIL) population derived from a cross between Triticum durum (cv. Langdon) and *Triticum dicoccoides *(acc. G18-16) for mapping of quantitative trait loci (QTL) of five morphological and three phenological traits. A total of 36 QTL effects were identified that were co-located in 21 loci. Eight of these loci showed pleiotropic effects on the studied traits (including phenology). A major QTL effect of Ash, co-located with strong phenological effect, was identified on chromosome 2BL. We found that phenological loci affected the duration of flowering and development of wheat in different manners. The duration of the reproductive stage in cereals affects the development of apical meristem and many other morphological traits, such as the number of spikelets per spike and the number of side shoots. These results shed more light on shaping of wheat plant architecture and development during its evolution under domestication. 92 Molecular Dissection of AGPase Enzyme and its Genes in Wheat and Ten Other Species Ritu Batra Ch. Charan Singh University ADP-glucose pyrophosphorylase (AGPase) is a heterotetramer with two large subunits (LS) and two small subunits (SS). It plays a critical role in starch biosynthesis. Using the well characterized Sh2 (LS: large subunit) and Bt2 *(SS: small subunit) genes of maize AGPase as references, true orthologs were identified in seven other monocots ( Triticum urartu , *Aegilops tauschii , wheat, rice, barley, sorghum and Brachypodium ) and three dicots ( Arabidopsis , chickpea and potato). The detailed structure, function and evolution of the genes encoding the LS and the SS among monocots and dicots were studied. The results of the present study suggested that: (i) at the DNA level, the genes controlling the SS are more conserved than those controlling the LS; the variation in both is mainly due to intron number, intron length and intron phase distribution; (ii) at protein level, the SS genes are more conserved relative to those for LS; (iii) “QTCL” motif (providing thermostability to AGPase ) present in SS showed evolutionary differences in AGPase belonging to wheat 7BS, T. urartu , rice and sorghum, while “LGGG” motif in LS was present in all species except T. urartu and chickpea; (iv) expression analysis revealed downregulation of both subunits under conditions of heat and drought stress. The wheat sequences identified in the present study will be utilized to design genome specific primers. These primers will be used to amplify the three copies each of AGPase LS and SS genes located on homoeologous group 1 and 7 chromosomes, respectively in a set of wheat genotypes (20 heat tolerant, 20 heat sensitive and 8 moderately heat tolerant/sensitive) to identify alleles of AGPase LS and SS genes that may impart thermotolerance. 93 NAC Transcription Factor and Laccase Gene: Key Players in Deciphering FHB Resistance Mechanism in Wheat QTL-Fhb1 Nancy Soni McGill University Fusarium head blight (FHB) is one of the most devastating and alarming diseases of wheat around the globe. In addition to causing a loss in wheat crop yield, it also reduces grain quality with mycotoxin contamination. Among 121 quantitative trait loci (QTLs) associated with FHB resistance, QTL-Fhb1 is considered to have major resistance effects. Wheat near isogenic lines (NILs), derived from Sumai 3 and Thatcher cross, were sequenced using Illumina HiSeq technology to capture the genes localized within the fine mapped QTL-Fhb1 region located within a 1.27cM interval. A total of 26 genes were putatively identified, of which, wheat NAC transcription factor ( TaNAC ), which is also known as a master regulator of plant secondary cell wall biosynthesis, was found polymorphic. Also, a laccase gene ( TaLAC ) which catalyzes cell wall lignification was also found polymorphic. Associated semi-comprehensive metabolomics study revealed a few important metabolites related to phenylpropanoid and flavonoid pathway with high fold change in pathogen inoculated samples. When the TaNAC or TaLAC silenced, the fungal biomass and the disease severity increased. However, no significant change in RR metabolites observed. In-silico analysis revealed secondary wall NAC binding element (SNBE) site in the promoter region of TaLAC , which suggest the regulation of laccase gene by NAC transcription factor, thus, unveiling the mechanism of FHB resistance associated with QTL-Fhb1 . 94 Mapping QTL for Fusarium Head Blight Resistance in Canadian Spring Wheat AC Barrie Dinushika Thambugala Agriculture and Agri-Food Canada Breeding for resistance to Fusarium head blight (FHB) in Canadian spring wheat is hampered by a poor understanding of genetics of resistance, particularly native FHB resistance. Here we dissected the genetic basis of FHB resistance in the Canadian spring wheat variety, AC Barrie which possesses an intermediate level of FHB resistance. A recombinant inbred line (RIL) population from the cross Cutler/AC Barrie and a doubled haploid (DH) population of the cross AC Barrie/Reeder were evaluated for FHB resistance in multiple field nurseries. Genotyping was performed with the Illumina Infinium 90K wheat SNP beadchip. IM and ICIM analyses identified numerous QTL controlling FHB resistance in the AC Barrie/Cutler RIL population on chromosomes 1B, 2A, 2B, 2D, 3B, 4D, 5A, and 6B and Barrie contributed most of these QTL. Major QTL for FHB resistance from AC Barrie were mapped on chromosomes 3B and 6B at the expected locations of Fhb1 and Fhb2 . Plant height locus Rht-D1 was identified on 4D, and Ppd-D1 locus was mapped on chromosome 2D. An additional FHB resistance QTL from AC Barrie mapped to the same region as a QTL from Nyubai on 3BS, near the centromere (3BSc). AC Barrie has a unique haplotype at Fhb1 , Fhb2 , and 3BSc relative to known resistance sources such as Sumai-3, Wuhan-1, and Nyubai. The DH population of the cross AC Barrie/Reeder is also being studied and results will be presented at the meeting. This study provides insight into the genetic basis of FHB resistance in Canadian spring wheat variety AC Barrie. 95 A Major Tan Spot Race-Nonspecific Resistance Gene in Tetraploid and Hexaploid Wheat Justin D. Faris USDA-ARS Tan spot, caused by the necrotrophic fungus Pyrenophora tritici-repentis *( Ptr ), is a major foliar disease of both common and durum wheat. Over the past few decades, research has revealed that wheat- Ptr* interactions are based on an inverse gene-for-gene system, where pathogen-secreted necrotrophic effectors (also known as host-selective toxins) induce susceptibility when recognized by dominant sensitivity genes in the host. However, a few race-nonspecific resistance QTLs have also been reported. In 2005, Faris and Friesen reported a race-nonspecific QTL with major effects on chromosome 3B in the Brazilian hard red spring wheat line BR34, and Kariyawasam et al. (2016) reported a QTL in the same region in the soft white spring wheat cultivar ‘Penawawa’. Here, we evaluated the Langdon durum– Triticum dicoccoides accession Israel-A chromosome substitution lines (LDN-DIC) for reaction to all races. With the exception of LDN-DIC 3B being highly resistant, LDN and all the LDN-DIC lines were moderately to highly susceptible. A recombinant inbred chromosome line population derived from LDN x LDN-DIC 3B was used to map the location of a single dominant resistance gene using SSR markers. In addition, chromosome 3B linkage maps in the BR34- and Penawawa-derived mapping populations were reconstructed using the Illumina 90K SNP array and SSRs, and the disease data was reanalyzed. Comparative mapping indicated that BR34, Penawawa, and T. dicoccoides accession Israel-A all likely possess the same chromosome 3B tan spot resistance gene. Current progress on marker development and deployment of the gene will be presented. 96 Development of Diagnostic Markers for the Detection of Functional and Non-Functional Alleles of Yr15 Tzion Fahima Institute of Evolution and the Department of Evolutionary and Environmental Biology, Faculty of Science and Science Education, University of Haifa Stripe rust, caused by the fungus Puccinia striiformis f.s. tritici ( Pst ), is a destructive disease of wheat globally. Depletion of effective resistance to Pst in cultivated wheat has led to search for new resistance genes in the wild relatives of wheat. One of the most promising genes conferring broad-spectrum resistance to stripe rust is Yr15 , derived from wild emmer wheat ( Triticum dicoccoides ) accession G25. Yr15 , mapped on chromosome arm 1BS, has recently been cloned by our consortium and designated as Wheat Tandem Kinase 1 ( WTK1 ). We found wtk1 susceptible alleles in most 274 tested durum, bread, and wild emmer wheat lines. Out of 69 tested durum and bread wheat cultivars and lines, only 33 Yr15 introgression lines contained the functional allele ( Wtk1 ) from G25 and were resistant to Pst . The remaining 36 susceptible lines carried non-functional alleles ( wtk1 ), which included insertions of large transposable elements that resulted in changes in reading frame. Development of reliable molecular markers can facilitate the introgression of Yr15 into new varieties via marker-assisted selection. Diagnostic markers designed based on the polymorphism between the WTK1 *alleles are preferred in order to avoid negative linkage drag. Therefore, we have designed highthroughput co-dominant KASP markers that can differentiate between the functional ( Wtk1 ) and all known non-functional ( wtk1)* alleles, and can be used in breeding programs for development of modern cultivars with high resistance to stripe rust. 97 A Novel Approach of Rapid and Targeted Gene Transfer from Wild Relatives into Crop Plants Kanwardeep Singh Washington State University The focus of the USAID funded innovation lab is to develop heat tolerant wheat varieties while understanding the heat tolerance trait at molecular, genetic, physiological and biochemical level. Since wild relatives of crop plants are known for their biotic and abiotic stress tolerance, one aspect of the project is to develop a fast, accurate, targeted and efficient method of transferring value added genes such as those controlling heat stress tolerance from wild relatives into cultivated wheat. But so far targeted transfer of such genes has been difficult because of Ph1 gene imposed restriction on chromosome pairing and recombination between wheat and wild relative chromosomes. With more than 300 useful genes transferred from the wild relatives into wheat, most have not been used in breeding because the transfers were either complete chromosome/arm or large segments which often carried undesirable traits along with the useful genes. We cloned a candidate for the Ph1 gene, silencing of which resulted in a phenotype characteristic of Ph1 gene mutants. Complementation of a Ph1 gene mutant ( ph1b ) with the candidate gene under its native promoter restored the chromosome pairing function. In this study, we transiently silenced the gene via VIGS to induce chromosome pairing and recombination between chromosome 1BS of wheat with 1RS of rye. Out of 250 plants that were analyzed, 66 plants showed recombination between wheat and rye chromosome arm. With an average of 5, the number of rye segments in each recombinant plant ranged from 1 to 6. The size of the rye segment transferred to wheat background ranged from 2 to 100 Mb. Although recombination hot-spots were obvious, recombination events were distributed on the entire chromosome arm. 98 The Cloned Yr15 Gene (WTK1) Encodes Two Kinase-like Protein Domains, Both Required for Conferring Broad-Spectrum Resistance to Stripe Rust Tzion Fahima Institute of Evolution and the Department of Evolutionary and Environmental Biology, Faculty of Science and Science Education, University of Haifa Stripe rust, caused by Puccinia striiformis f. sp. tritici ( Pst ), is a devastating fungal disease that threatens global wheat production. The wild emmer wheat gene Yr15, *located on chromosome 1BS ,* confers resistance to a broad spectrum of Pst races. Comparative genomics, chromosome walking, BAC libraries (wild emmer and bread wheat), whole genome assemblies, EMS mutagenesis and transgenic approaches enabled us to clone Yr15 and validate its function. The Yr15 protein has a novel structure for R-genes in wheat with two kinase-like domains in tandem, designated here Wheat Tandem Kinase 1 (WTK1). We have shown that both kinase domains are essential for conferring Pst resistance. Macro- and microscopic observations of development and accumulation of fungal biomass suggest that the hypersensitive response plays a central role in the resistance mechanism, limiting the development of fungal feeding structures. Non-functional alleles of Yr15 in T. dicoccoides , T. durum and T. aestivum differ from the functional allele of DIC G25 by indels, creating truncated proteins. Therefore, we designed diagnostic markers that differentiate between functional and non-functional Yr15 alleles. Our results suggest that Yr15* has the potential to improve stripe rust resistance in a wide range of tetraploid and hexaploid wheat germplasm. The absence of the functional Yr15 in tested durum and common wheat varieties highlights the value of DIC germplasm as a reservoir of resistance genes for wheat. 99 Exploring Genetic Diversity in Bread Wheat Using Nested Association Mapping Melissa Garcia School of Agriculture, Food and Wine, University of Adelaide The rate of genetic gain in breeding programs can be increased by extending the amount of variation available for selection using land races and exotic germplasm. However, exotic germplasm carries a range of undesirable traits that limits their suitability for modern agriculture. Backcrossing to locally adapted varieties and pre-selection for traits is therefore required to ensure meaningful data are generated in field trials. Multi-parental schemes such as Nested Association Mapping (NAM) populations improve the use of exotic germplasm as a resource for the discovery of novel traits and QTL/genes. NAM combines the power of linkage analysis and the precision of association mapping. When jointly analysed, NAM populations can provide higher power to detect QTL than any of the constituent biparental families separately. We selected 75 highly diverse hexaploid spring-type wheat accessions from regions of the world that are affected by heat and drought stress. These accessions were crossed with two Australian elite varieties as founder parents, and BC1F6 populations were generated. Twenty individuals from each of 28 NAM sub-populations were genotyped at BC1F4 using a targeted genotype by sequencing assay. These lines are being grown in a completely randomised field trial with two replications. Plots were phenotyped for NDVI, relative maturity and presence of awns. Plant height, yield, thousand grain weight and harvest index will be obtained at harvest. Genome wide association analysis is underway. Selected populations which maximize diversity and power will be phenotyped in multiple field trials across Australia next year. 100 New Genotyping Technology, GRAS-Di, Using Next Generation Sequencer Hiroyuki Enoki Toyota Motor Corporation We developed new genotyping technology, Genotyping by Random Amplicon Sequencing-Direct (GRAS-Di). This technology consisted of sample preparation using high concentration random primer, NGS and data analysis. The sample preparation was very simple. It was not necessary to do primer design, enzyme digestion, fragmentation, size selection, adaptor ligation, and sample normalization. It was only two steps PCR for NGS library without specialized equipment. Rice BIL population was used for evaluation of genotyping by GRAS-Di (96 samples / lane of HiSeq2500). The number of reads for each amplicon was highly reproducibility, r 0.99, with repetition. Over ten thousand SNPs were detected among the BIL population and the SNPs were distributed uniformly rice genome. The ratio of missing value was very low, 1.5%. The reproducibility of SNP was 99.9% with repetition. If there was no reference sequence, genotype data could be detected by GRAS-Di using original algorism based on amplicon analysis. Theoretically, the technology is also applicable to other creatures, including highly polyploidy creatures. We performed the applicability test for several creatures. The result shown that the technology was applicable for over fifty creatures, including wheat, soybean, tomato, potato, sugarcane, cow, pig, chicken, tuna and human. The technology could be provided over 30,000 multiplex sequencing at once. We think that GRAS-Di would be very easy and very powerful technology for genome wide genotyping in many creatures. We signed licensing agreement with Kazusa DNA Research Institute, Eurofins Genomics, and GeneBay for GRAS-Di. 101、Stacking Multiple Stem Rust Resistance Genes at a Single Locus for Durable Resistance in Wheat Ming Luo Commonwealth Scientific and Industrial Research Organisation Stem rust disease caused by the fungal pathogen Puccinia graminis f.sp tritici is a significant threat to global wheat production. The most cost effective way to control this disease is by genetic resistance. However major gene resistance is often readily overcome by pathogen evolution when resistance genes are deployed singularly. Combining major resistance genes is believed to extend their durability as multiple mutations are required in the pathogen to overcome this polygenic resistance. Major resistance genes can be combined by conventional breeding however this is a labour intensive process and resistance gene combinations are difficult to maintain in segregating families. In this study, we have used cloned stem rust resistance genes Sr22, Sr35, Sr45, Sr46 and Sr50 and the multi-pathogen adult plant rust resistance gene Sr55/Lr67/Yr46/Pm46/Ltn3 to produce binary vectors containing combinations of these genes. Constructs containing either 3, 4, 5 or 6 rust resistance genes were produced and transformed into bread wheat by Agrobacterium transformation. Molecular/genetic analysis demonstrated that some transgenic wheat lines contain all the resistance genes present in the binary vector used for transformation (ie. up to six) and these genes are inherited as a single locus in progeny plants. Transgenic plants are resistant to wheat stem rust disease with resistance co-segregating with the multigene transgenic locus. 102 MAGIC Yield: Using an Eight Founder Population for the Genetic Dissection of Yield and Yield Components in UK Winter Wheat Benedetta Saccomanno NIAB Multiparent advanced generation inter-cross (MAGIC) populations are a powerful mapping resource in crop genetics for the dissection of complex traits, previously hindered by relatively low genetic recombination and allelic diversity of traditional bi-parental populations. Wheat (*Triticum aestivum *L.) is a major arable crop of global importance, covering 1.6 million hectares in the UK alone (AHDB survey, 2017). Breeders and farmers must continue to improve wheat grain yield and yield stability to help meet demand from an increasing population, and to ensure food security in the face of the effects of climate change. The Magic Yield project helps address these problems by using an eight-founder MAGIC population (Mackay *et al. *2014), consisting of 1,000 lines created by inter-crossing eight elite UK winter wheat varieties over three generations, to study the genetic basis of yield and yield components. With the participation of five wheat breeding companies, we conducted field trials at five UK sites for two consecutive years, phenotyping yield and a suite of pre- and post-harvest yield components. Phenotypic data coupled with Illumina iSelect 90k SNP genotype data (Gardner *et al. *2016) allowed the detection of a total of 76 quantitative trait loci (QTL) across all year, trait and site combinations. Flanking markers for selected QTL were converted to Kompetitive Allele Specific PCR (KASP) markers to aid fine-mapping and consequent characterization of genes controlling yield. Ultimately, the resources generated will aid the selection of wheat lines with improved performance within breeding programs, for the downstream benefit to growers and end-users. 103 “Am Hidden, Feeling Hot! Do Something!” – Heat Stress on Wheat Roots Sundaravelpandian Kalaipandian CSIRO (Agriculture and Food) High temperature is a major threat to plant productivity due to climate change. Often the hidden-half of the plant is more sensitive to heat stress than the above ground parts. Heat stress affects the roots by limiting water and nutrient uptake, which in turn affect shoot water demand and photosynthesis. However, the molecular mechanism of root responses to heat stress is poorly understood. Recently, we have studied the role of TaHsfC2a gene in wheat. Overexpression of TaHsfC2a-B in transgenic wheat plants increased survival rate to about 90% while only 15% of wild-type plants survived after heat treatment at 43°C. Interestingly, we observed that the shoots were drying but the roots were intact after heat treatment in the transgenic plants, which contributed to recovery of the shoots, however all parts of the wild-type plants died after heat treatment. Reactive oxygen species (ROS) was shown to have a major role in abiotic stresses including heat stress. We found that the transgenic plant roots accumulate very low hydrogen peroxide (H2O2) when compared with wild-type plant roots. To understand the molecular mechanisms underlying the heat stress and ROS in the roots, the transcriptome of TaHsfC2a transgenic and wild-type roots are being studied by using RNA-sequencing. In addition, we found that TaHsfC2a was markedly up-regulated under drought and abscisic acid treatment, and we have also identified the potential targets of this gene (TaHSP70d and TaGalSyn) and confirmed through transactivation studies. Our study will identify candidate genes to develop heat resistant varieties in wheat. 104 Leveraging the Root Angle QTLome to Enhance Climate Resilience in Wheat Marco Maccaferri DipSA, Department of Agricultural Science, University of Bologna Optimisation of root system architecture (RSA) is an important objective for the sustainability of durum wheat grown under drought-stressed conditions. In the present study, linkage and association mapping (AM) for RSA evaluated at the seedling stage evidenced 20 clusters of quantitative trait loci (QTLs) for root length and number as well as 30 QTLs for root growth angle (RGA). The most divergent RGA phenotypes observed by seminal root screening were validated by root phenotyping of field-grown adult plants. QTL analysis of RSA and grain yield data indicates RGA as a valuable target to enhance grain yield and yield stability across different soil moisture regimes (Maccaferri et al. 2016). Based on their relative additive effects, allelic distribution in the AM panel and co-location with QTLs for yield, eight RGA QTLs have been prioritised in terms of breeding interest and value. These QTLs were investigated for gene content based on the chromosomal pseudomolecules of Chinese Spring T. aestivum and the TriAnnot v4.3 gene prediction and annotation pipeline and the Zavitan T. dicoccoides genome assembly (Avni et al. 2017). The chromosome regions contained 25 to 242 predicted genes (123 on average). In six RGA QTLs, from one to four gene annotations were involved in auxin pathways. The comparison between the T . aestivum and T . dicoccoides gene content indicates the high quality of the T . *dicoccoides *assembly and its usefulness to identify candidates to explore the polymorphism and the structural variation of drought-related genes present in the A and B wheat genomes. 105 A TRIM Insertion led to a Gene Resurrection Event that causes Male Sterility in Wheat Jizeng Jia Chinese Academy of Agricultural Sciences The male sterile ms2 mutant has been known for 40 years1 and has become extremely important in the commercial production of wheat. However, the gene responsible for this phenotype has remained unknown. We here report the map-based-cloning of the Ms2 gene. The Ms2 *locus is remarkable in several ways that have implications in basic biology. Beyond having no functional annotation and clearly having undergone pseudogenization, we found that the *Ms2 allele in the ms2 mutant acquired a terminal-repeat retrotransposon in miniature (TRIM) element in its promoter. This TRIM element is responsible for the anther-specific Ms2 *activation that confers male sterility. The identification of *Ms2 not only unravels the genetic basis of a historically-important breeding gene, but also illustrates pseudogenization at the population level and shows that resurrection of an unfixed pseudogene in the population can contribute to genetic novelty and phenotypic plasticity. 106 Fine Mapping of D-Genome Yield QTLs in Hexaploid Wheat Increasing crop yields is an ever more crucial endeavor as the global human population continues its near exponential growth. One strategy to meeting future food demands is identifying and incorporating yield-enhancing genes into elite crop lines. Wheat ( Triticum aestivum , 2n=6x=42 AABBDD), which supplies a fifth of humans’ calories worldwide, can reap the benefits of the genetic variation from the D-genome progenitor, Aegilops tauschii *(2n=2x=14 DD), which may supply yield-boosting alleles. A nested association mapping population of the D-genome (DNAM) was created from direct hybridization of the hard white winter variety, KS05HW14, and seven *Ae. tauschii *accessions and backcrossing the F1 progeny twice to KS05HW14 to regain euploidy. BC2F4 derived lines from the DNAM population were phenotyped for grain yield in Manhattan, KS; Hays, KS; and Richville, MI in 2015 and 2016, and Marianna, AR; Champaign, IL; Brookings, SD; and Pullman, WA in 2016. A genome-wide association analysis identified QTL conferring higher grain yield. Large-effect QTL identified on chromosomes 2DS and 6DL were contributed by the recurrent parent. QTL on chromosomes 2DL and 7DS were derived from the Ae . tauschii *accessions, TA1615 and TA1718. KASP markers designed for significant SNPs on the QTL identified the following segregating regions: 25.4Mb to 29.5Mb on 2DS, 430.4Mb to 575.9Mb on 2DL, 463.5Mb to 473.3Mb on 6DL, and 517.0Kb to 12.5Mb on 7DS. These data were used to create heterozygous inbred families that will be used in QTL fine-mapping and identifying yield-enhancing genes. 107 Integrating Genomic Selection in Breeding for Resistance to Rusts and Foliar Diseases in Wheat Fnu Philomin Juliana CIMMYT Genomic selection is a promising technology that could increase genetic gains for quantitative disease resistance and help eliminate susceptible lines, before costly disease screening. To evaluate the potential integration of GS as a breeding tool, we tested genomic prediction for several diseases in CIMMYT’s 1st year yield trials (YT) and 2nd year elite yield trials (EYT), from 2015-2016 and 2016-2017. While the YTs comprised about 9,000 lines, the EYTs were a subset comprising 1,092 lines. All lines were genotyped using genotyping-by-sequencing and the YTs were phenotyped for response to Ug99 stem rust (SR) race in Njoro, Kenya. The EYTs were phenotyped for SR in Njoro; yellow rust (YR) in Ludhiana, India; Fusarium head blight (FHB) in El Batan, Mexico; Septoria tritici blotch (STB) in Toluca, Mexico and spot blotch (SB) in Agua Fria, Mexico. The maximum within-nursery and across-nursery prediction accuracies were 0.74 and 0.60 for SR, 0.59 and 0.50 for YR, 0.42 and 0.21 for FHB, 0.50 and 0.18 for STB and 0.56 and 0.37 for SB, respectively. We also observed that at different selection intensities, GS could discard upto a maximum of 92% of the susceptible lines discarded by PS and select upto 61% of the resistant lines selected by PS, within nurseries. However, when selections were made across-nurseries, GS could discard 73.8-90.2% of the susceptible lines and select 24.5-61.6% of the resistant lines. While these results are promising, further efforts to improve prediction accuracies are crucial for the successful integration of GS in wheat disease resistance breeding. 108 Spatio-Temporal Asymmetry of the Meiotic Pathway in Hexaploid Bread Wheat Kim Osman University of Birmingham During meiosis homologous recombination (HR) generates genetic variation and provides the physical links (crossovers - COs) necessary for accurate segregation of chromosomes. In most eukaryotes the distribution of COs along chromosomes is non-random due to the influence of multiple levels of control which ensure each chromosome pair receives at least one CO and which discourage additional COs forming in adjacent chromosomal regions. Further complexity is evident in the tendency of chiasmata (the cytological manifestation of COs) to form in favourable regions of the chromosome. In some species this has led to the restriction of COs/chiasmata to particular chromosomal locations. In hexaploid wheat and other cereals the predominantly distal location of COs creates a problem of linkage-drag in the recombinationally ‘cold’ centromere/proximal and interstitial regions where agronomically important traits cannot be readily separated from undesirable ones. As partners in a collaborative project involving five UK research groups and two wheat-breeding companies, our aim is to understand the factors influencing CO formation in hexaploid wheat in order to manipulate the process and unlock genetic diversity for crop improvement. Building on research in Arabidopsis meiosis, we are employing molecular cytogenetic techniques to perform a detailed analysis of key stages in the recombination pathway during the progression of prophase I. Here we present data showing that early recombination events in Cadenza are spatio-temporally asynchronous, initiating in the distal chromosomal regions and later spreading throughout the chromatin. This pattern reflects the distribution of euchromatin within the nucleus as revealed by immunolocalisation of various histone modifications. 109 Accelerated Cloning and Characterization of the Wheat Adult Plant Resistance Gene Lr68 Sreya Ghosh John Innes Centre Adult Plant Resistance (APR) genes are broad-spectrum, partial resistance genes that can contribute to sustainable control of wheat rust diseases. However, a lack of precise molecular markers complicates their characterization and practical use in breeding programmes. At the same time, the long generation time of wheat has become a limiting factor for breeders to respond quickly to an outbreak. As the APRs cloned so far do not belong to any common gene family, it is not possible to use general features of these identified APRs to conduct biased searches for novel APRs. This project aims to rapidly clone the recently discovered APR gene Lr68 (Leaf Rust 68) using an unbiased gene isolation technique called MutChromSeq, which combines chromosome flow-sorting and mutational genomics, and is independent of fine mapping. It also aims to combine marker-assisted selection with accelerated generation advancement (“speed breeding”) for rapid germplasm structuring and field performance evaluation. Cloning APRs allows breeders to trace genes cheaply and quickly using gene-specific markers, enabling them to build effective and durable resistance gene pyramids. It also allows us to elucidate any common mechanism of action they have, helping researchers and breeders understand better the basis of their durable resistance. 110 Functional Study of TabZIP15 in Regulation of Wheat Abiotic Stress Tolerances Lichao Zhang Institute of Crop Sciences bZIP transcription factors are one of the most important transcription factor families which play important roles in response to biotic and abiotic stresses. However, few studies of the functions of bZIP transcription factors in regulation of abiotic stresses tolerance have been done in wheat. TabZIP15 encoded a bZIP transcription factor of C subfamily, which was mapped on the wheat chromosome 7DL. TabZIP15 was induced by salt, PEG, cold stresses and exogenous ABA treatment. The protein encoded by TabZIP15 was localized in the nucleus through transient expressed in tobacco epidermal cells, and possessed transcription activation activity in yeast with an N-terminal transcriptional activation domain. Overexpression of TabZIP15 improved the drought and freeze tolerance of transgenic Arabidopsis plants. Yeast one-hybrid experiments showed that TabZIP15 transcription factor can bind to ABRE cis-acting elements. Yeast library screening experiments and luciferase complementation assay (LCI) showed that TabZIP15 can interact with enolase TaENO-b, indicating that TabZIP15 may regulate abiotic stress tolerance through glycolysis and gluconeogenesis pathway. 111 Gene Regulatory Networks Reveal Novel Genes Controlling Senescence in Wheat Philippa Borrill John Innes Centre Monocarpic senescence in crops is essential to enable nutrient remobilisation from photosynthetic tissues to the grain. This process must be tightly regulated to prevent premature senescence adversely affecting yields, however few genes controlling senescence have been identified in wheat. We are using a combination of approaches to identify novel regulatory genes affecting the early processes controlling senescence. We have generated a high-resolution RNA-Seq time-course of ten time-points from anthesis until the first visible signs of flag leaf senescence. To understand the key genes driving transcriptional changes, we used a combination of gene regulatory network analyses to identify modules of co-expressed genes and hub genes regulating the transcriptional processes across this time-course. From these networks, we selected ten transcription factors as candidate genes for further characterisation. We have generated double knock-out mutants of these candidate genes using the sequenced tetraploid TILLING population. Preliminary results show that two out of five candidate genes tested to date have roles in monocarpic senescence. Further studies are in progress to characterise the effects of these novel senescence regulators on nutrient remobilisation. The availability of new genomic resources, such as high-quality genome sequences and TILLING knock-out mutants, has enabled the study of genes regulating senescence at an unprecedented resolution. These genes may represent new breeding targets to adapt senescence to the environment and to modulate grain nutrient content which is influenced by the rate of senescence. 112 Identification of a Candidate Gene for* Sr9h*-Mediated Wheat Stem Rust Resistance by MutRenSeq Matthew N. Rouse USDA-ARS Cereal Disease Lab The wheat stem rust resistance gene Sr9h confers major-effect resistance to stem rust pathogen race TTKSK (Ug99) and maps to chromosome arm 2BL in the cultivar ‘Gabo 56’. Sr9h is one of seven phenotypic Sr9 *alleles and the only *Sr9 *allele effective to TTKSK. We report here the identification of a candidate *Sr9h gene, by the rapid MutRenSeq approach. A total of 1603 EMS-mutagenized M2 families were screened with race TTKSK. We identified eight TTKSK-susceptible mutants that shared greater than 99% genome identity with Gabo 56 based on the 90K SNP chip. Nonsense or missense mutations were identified in the same NB-LRR candidate gene for seven of the eight mutants. A KASP marker derived from the candidate NB-LRR gene co-segregated with TTKSK resistance in two populations but appears to be a part of an NB-LRR gene family with multiple copies and pseudo genes based on the syntenic 2BL region of Chinese Spring and wild emmer wheat. Therefore we are currently sequencing chromosome 2B from Gabo56 and CM664, a second line with Sr9h , to fully characterize the Sr9h locus. Cloning the Sr9h gene and understanding the variation and unique phenotypic diversity underlying this complex locus will greatly enhance our understanding of the molecular mechanisms of resistance and race specificity and could provide extensive knowledge for long-term projects including the development of new resistance alleles and for the deployment of durable resistance. 113 Association Mapping of Stem Rust in Minnesota Spring Wheat Lines Cyrus Kimani Ndung'u University of Minnesota Stem rust caused by Puccinia graminis f. sp. tritici, especially the Ug99 (TTKSK) race, is a serious threat to wheat production around the world and can cause up to 100% yield loss in susceptible cultivars. However, there are some Minnesota cultivars that have shown resistance to stem rust, including that caused by Ug99. It is therefore important to identify the QTLs for stem rust resistance in this germplasm. Association mapping is one of the most common method used to detect QTLs and genetically characterize germplasm. Our objective was to identify QTLs for resistance to the Ug99 family of stem rust pathogen races in a collection of 384 spring wheat breeding lines from the University of Minnesota. The germplasm was screened for stem rust both in the field and as seedlings in a greenhouse. Field screening in Kenya and Ethiopia (2016 and 2017) facilitated data collection on the germplasm response to virulent races of the Ug99 race group. The seedling screening was done at the USDA-ARS CDL BSL3 greenhouse using TTKSK and TRTTF races. The germplasm was genotyped using the wheat 90K SNP Chip. The data was then analyzed using the GAPIT package in R using the Q+K model. Significant QTLs were detected in both field seasons in Kenya but none were detected in Ethiopia. Additionally, significant QTLs for resistance to TTKSK and TRTTF races were detected in the greenhouse. Resistance to TTKSK in the greenhouse seemed to be temperature sensitive, with different QTLs being detected at different temperatures. 114 Resource Optimization with Multi-Trait Genomic Prediction for Bread Wheat Quality Bettina Lado Universidad de la Republica Multi-trait genomic prediction models are a useful strategy to predict traits that otherwise are challenging due to labor intensity, difficulty, and cost. This is particularly important in the context of resource allocation in plant breeding programs. However, is not well known the amount of phenotyping that could be replaced by including phenotypic information on correlated traits. The objective of this work was to compare the predictive ability of multi-trait models, 1) by using different training population sizes for different quality traits, and 2) by testing different proportions of lines with phenotypic information for correlated traits. A group of 495 wheat lines were genotyped using genotyping by sequencing and phenotyped for eight bread quality traits. Cross-validation was used to evaluate the predictive ability of different multi-trait models using 10 to 80% of lines as training population and 50, 75 or 100% information on correlated traits. The results showed that predictive ability for all traits did not change when using more than 30% of lines as training population and 100% of the information on correlated traits. Moreover, the predictive ability of multi-trait models decreased when information on correlated traits was reduced to 50%. Overall, our results indicate that inclusion of information on correlated traits in training and testing wheat lines is a useful approach to replace phenotyping of expensive traits, allowing to reduce costs and better allocate resources in breeding programs. 115 Evidence for the Lr46 Leaf Rust Resistance Gene in the Wheat Cultivar Carberry Ron E. Knox Agriculture and Agri-Food Canada, SCRDC Stacking and deployment of pleiotropic genes for resistance to multiple fungal diseases in wheat variety development is expected to increase the durability of resistance. To achieve this gene stacking objective through molecular breeding, an understanding of which genes currently exist in adapted germplasm is necessary. The cultivar Carberry is a popular hard red spring wheat variety in Canada with good rust resistance. Pedigree, phenotype, and DNA marker evidence suggested Carberry possesses the leaf rust resistance gene Lr46 . Lr46 is a slow rusting adult plant resistance gene located on chromosome 1B that provides resistance against leaf rust and other diseases such as stripe rust, stem rust, and powdery mildew. We undertook an investigation to test the hypothesis that Carberry possesses Lr46 . A doubled haploid population comprising 297 lines was developed from the F1 of a cross of Carberry with the universally leaf rust susceptible cultivar Thatcher. The population was evaluated for leaf rust reaction in four field nursery environments: near Swift Current SK from 2014 to 2016, and Morden MB in 2016. The population was also assessed for stem rust response in 2014 and 2016 near Swift Current. The population was genotyped using the 90K Infinium iSelect assay and following linkage map construction with JoinMap 4.1, 5457 markers were used for quantitative trait locus (QTL) analysis using MapQTL 6. Two QTL for leaf rust resistance were identified from Carberry on chromosome 1B, one of which was coincident with a stem rust resistance QTL that mapped to the location of Lr46 . 116 Starp: A User-Friendly and Broadly Applicable Technique for SNP Genotyping in Wheat and Other Crops Yunming Long North Dakota State University Single nucleotide polymorphisms (SNPs) are widely distributed in the genome of every organism. Recent advances in DNA sequencing technology have accelerated the discovery of variations in DNA sequences. Multiplex chip-based technology for genome-scale SNP genotyping has made great progress in the past two decades. However, PCR-based genotyping of individual SNPs remains a challenge task. Here, we report a novel SNP genotyping method designated semi-thermal asymmetric reverse PCR (STARP), which combines all of the advantages in accuracy, throughput, simplicity, and operational costs as well as compatibility with multiple platforms. STARP assays employ two universal priming element-adjustable primers (PEA-primers) and one group of three locus-specific primers: two asymmetrically modified allele-specific primers (AMAS-primers) and their common reverse primer. The two AMAS-primers are used to specifically amplify target alleles and generate PEA-primer binding sites. The two PEA-primers are common for all genotyping assays to stringently target AMAS-primer amplicons with similar PCR efficiencies and for flexible detection using either gel-free fluorescence signals or gel-based size separation. STARP is a broadly applicable and more user-friendly alternative to KASP. We developed numerous STARP markers associated with important agronomic genes for low cadmium accumulation and resistance to Hessian fly, Fusarium head blight, and stem rust in wheat. These STARP markers have being employed in wheat breeding. In addition, STARP technique has been successfully extended to analyze the differential expression of the homologous genes and specifically amplify target DNA fragments in highly repetitive regions. STARP will facilitate genomic research in wheat and other species with large and complex genomes. 117 Molecular Genetic Characterisation of Triple Rust Resistance in Aegilops tauschii Naveenkumar Athiyannan Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, University of QueenslandCommonwealth Scientific and Industrial Research Organisation Bread wheat (Triticum aestivum) is the third most cultivated crop worldwide, and a major caloric source for the human population. Global wheat production is under constant threat due to the constant evolution of highly virulent fungal pathogens such as Puccinia sp that cause rust disease. Losses due to rust disease are routinely minimised through the deployment of host plant-mediated genetic resistance in commercial cultivars. However, pathogens evolve virulence to overcome this resistance. Therefore continuous supply of new sources of resistance is essential for sustainable rust management. Resistance from the wild relatives of hexaploid wheat is a valuable resource as they broaden the gene pool of available resistance genes. In this study, CPI110672, an accession of the D genome progenitor Aegilops tauschii, *was chosen for in-depth analysis as it resists the three wheat rust diseases namely leaf, stem and stripe rust. To characterise this triple rust resistance, we conducted genetic analysis using a mapping population derived from the cross between CPI110672 and a susceptible accession CPI110717. Through rust infection screening and 90K SNP marker analysis, the chromosome position and closely linked markers were identified. Physical maps for the chromosome region carrying these rust resistance genes were generated using the new reference genome sequences of hexaploid wheat Chinese Spring IWGSC Ref Seq v1.01 and the diploid Ae. tauschii accession, AL8/782,3. Comparative genomics of these reference sequences together with contigs assembled from the sequenced genome of CPI110672 facilitated the identification of candidate genes. Functional analysis will be conducted through transformation into the rust-susceptible wheat cultivar fielder.
61、Introgression of a Newly Discovered Xanthophyll Acyl Transferase into Durum Wheat Diane Mather The University of Adelaide The carotenoid lutein is the main yellow pigment in the grain of both bread wheat (AABBDD) and durum wheat (AABB). Lutein confers health benefits and is important in determining the colour of wheat-based food products. During postharvest storage of bread wheat grain, lutein can be converted into lutein esters, which are more stable than free lutein. This esterification does not occur in durum wheat. Recently, we mapped the esterification trait to a locus on chromosome 7D. We have now confirmed that a gene at that locus encodes a xanthophyll acyl transferase (XAT). This is the first such enzyme to be functionally confirmed in any plant species. Given the importance of stable yellow pigment for pasta and other durum-based products, we wanted to transfer the Xat1 gene into durum wheat. We crossed a 7D(7A) disomic chromosome substitution line of Langdon durum with DBA-Aurora, an Australian durum cultivar. This provided opportunities for 7D-7A pairing and recombination in the F1 generation. Using marker assays designed for 7D-7A SNPs, we screened F2 progeny for evidence of spontaneous 7D-7A recombination. Plants with recombinant chromosomes were discovered, including one with only a short distal 7D segment that includes the *Xat1 *gene. Homozygous recombinant progeny were developed and are being backcrossed to DBA-Aurora to develop a high-performing durum with improved lutein stability. This work demonstrates that with the use of appropriate crosses and markers, plants with intergenomic recombinations can be discovered for use in breeding. 62、Evaluation of Winter-Survival of Winter Wheat By Drone-Generated Multi-Spectral Imagery Identified Two Quantitative Trait Loci on Chromosome 5A Yi Chen University of Guelph The harsh and unpredictable winters in the high latitude regions of the northern hemisphere often leads to high risk of winterkill for winter wheat ( Triticum aestivum *L.). One of the key traits that influence winter-survival is the timing of the transition from vegetative to reproductive stage, as wheat loses cold tolerance after the transition. The goal of this research is to investigate the genetic basis of winter-survival in Canadian winter wheat and to identify the combination of key candidate gene alleles that is optimal for high-latitude winter wheat. The Canadian Winter Wheat Diversity Panel (CWWDP), which includes 450 winter wheat genotypes with various levels of winter-hardiness, was phenotyped under field conditions in Ontario, Canada. Normalized difference vegetation index (NDVI) was extracted from multi-spectral imagery captured by unmanned aerial vehicle (UAV) as a measure of winter-survival. The diversity panel was genotyped with the 90K Illumina SNP chip and additionally for allelic variation at the candidate gene loci that have demonstrated significant effect on flowering time and cold tolerance. This included the major vernalization gene loci on group 5 chromosomes ( VRN-A1, VRN-B1, and *Vrn-D1 ), C-Repeat Binding Factor ( CBF ) -12 *and *-15 on chromosome 5A and photoperiod response loci on chromosome 5D ( PPD-D1 ) and 5A ( PPD-A1 ). Genome-wide association studies identified two major quantitative trait loci on chromosome 5A, which correspond to the frost resistance loci Fr-A1 *and *Fr-A2 . This result is consistent with previous reports on the role of chromosome 5A in winter-survival and showcased the potential of UAV-based phenotyping in genetics research. 63、Completion of the ‘Jagger’ Winter Wheat Genome Leads to Identification of Aegilops Ventricosa 2NS Translocation and Impact in Kansas Wheat Breeding Liangliang Gao Kansas State University Since its release 23 years ago, the winter wheat cultivar Jagger has had a huge impact on wheat production in the US and around the globe and became a parental germplasm in many of the current cultivars of the central U.S. Importantly, Jagger also possesses the Aegilops ventricosa 2NS translocation fragment, which is associated with disease resistance against multiple wheat pathogens including the devastating wheat blast fungus. Here we present the first de novo assembly and anchoring of the Jagger genome based on the NRGene DeNovoMAGIC 3.0 pipeline and chromosome conformation capture technology (Hi-C). We were able to successfully anchor ~3000 scaffolds with a cumulative length of 14.2 Gb and an N50 of 10.5 Mb to build 21 draft pseudomolecules. Overall, these draft pseudomolecules showed high collinearity with the reference Chinese Spring genome (IWGSC RefSeq v1). The Jagger genome will be a powerful tool in the analysis of the wheat pan genome and the dissection of important agronomic traits. To illustrate its utility, we delineated the Aegilops**ventricosa 2NS translocation fragment in Jagger, consisting of a ~30 Mb fragment identified through alignment of Jagger chromosome 2A to ‘Chinese Spring’ chromosome 2A. We also developed a pipeline for identification of 2NS translocations in wheat breeding lines using genotyping by sequencing (GBS) data and reference genomes. Our results suggest that the 2NS translocation segment is widely present in KS breeding lines, and is potentially providing a yield benefit over the span of 11 years of the breeding program. 64、A Megabase-Scale Comparative Analysis of Wheat Chromosome 2D from Two Wheat Cultivars Unravels Molecular Mechanisms of Genome Evolution Simon Krattinger King Abdullah University of Science and Technology (KAUST) Recent improvements in DNA sequencing technologies and assembly algorithms have paved the way to generated high-quality genome assemblies of the large and complex genomes of wheat and its wild relatives. These genome assemblies form the basis to study the evolutionary dynamics of wheat genomes on a megabase-size scale. Here, we provide a comparative analysis of two high-quality assemblies of the 729-megabase-sized chromosomes 2D of wheat landrace Chinese Spring (IWGSC RefSeq v1.0) and the modern Swiss spring wheat line ‘CH Campala Lr22a ’. In general, there was a high degree of sequence conservation along the chromosome. Analysis of large insertions and deletions (InDels) revealed four large InDels of a total size of 2.2 Mb. The molecular signatures at their breakpoints enabled to identify unequal crossing over and double-strand break repair as the molecular causes of these InDels. In addition, the gene content of the two chromosomes were compared. This comparison revealed that 99% of the genes were present and collinear in both the cultivars. The fraction of unique single-copy genes observed was 0.44% for Chinese Spring and 0.71% for ‘CH Campala Lr22a’ . Hence, our analysis provides evidence that the number of genotype-specific genes is considerably smaller than previously estimated. 65 Identification of Quantitative Trait Loci (QTL) Associated with Fusarium Head Blight and Septoria Resistance in a Maxine/ Redeemer Winter Wheat Population Ljiljana Tamburic-Ilincic University of Guelph Fusarium head blight (FHB) and Septoria tritici blotch (STB) are important wheat diseases in North America. The objective of this study was to map loci associated with FHB traits, STB and plant height in a Maxine/Redeemer winter wheat population. Evaluation of FHB and STB resistance was performed using spray inoculation of a mixture of F. graminearum *and Septoria tritici blotch *isolates, respectively and under natural infections in replicated trials across three environments in Ontario, Canada. FHB disease incidence and severity were recorded and FHB index was calculated. For both diseases, the population showed a continuous distribution pattern and transgressive segregation of progeny. DArT markers were used to generate a genetic map and quantitative trait loci (QTL) analysis were performed by evaluating 105 doubled-haploid lines. FHB resistance QTL were identified on chromosome 2A, 4A, 6A, 3B, 4B, 2D and 3D, while QTL for STB were identified on chromosome 4B and 7A. Plant height QTL were identified on chromosome 4A, 6A, 4B and 2D. QTL identified in this study will be used in winter wheat breeding programs using marker assisted selection (MAS). 66 Activation of Seminal Root Primordia during Wheat Domestication Reveals Underlying Mechanisms of Plant Resilience Guy Golan Hebrew University of Jerusalem Seminal roots constitute the early root system of major crops of the Poaceae family. Although variation in seminal root number was described in several crops, mechanisms through which seminal root number (SRN) are controlled and in turn contribute to environmental adaptation are poorly understood. Here, we show that SRN increased upon wheat domestication due to the activation of root primordia which are suppressed in wild wheat, a trait controlled by factors expressed in the germinating embryo. We used variation in seminal root number (SRN) between wild and domesticated wheat to investigate its bearing on water uptake and seedling resilience. The persistence of wild roots at their primordial state promoted seedling recovery from episodic water-stress through re-activation of root primordia following rehydration. In spite of their lower root number, wild seedlings transpired more than domesticated seedlings. Additionally, transpiration rate was associated with higher shoot:root ratio in wild wheat, indicating contrasting strategies of resource allocation between wild and domesticated wheat. Our findings suggest that under well-watered conditions, lower root number enables direction of resources to aboveground without limiting water uptake. Furthermore, the maintenance of roots at their primordial state and their re-activation following rehydration maybe regarded as seedling protective mechanism against episodic water-stress. The results underscore SRN as an adaptive trait that was reshaped upon domestication. Identification of factors associated with the plasticity of the SRN phenotype expands our understanding on the evolutionary dynamics of wheat and may serve to optimize root number in future breeding efforts. 67 IWGSC Phase II: What's Next for the IWGSC Kellye Eversole IWGSC In 2017, the International Wheat Genome Sequencing Consortium (IWGSC) achieved the first high quality, annotated reference sequence of bread wheat, IWGSC RefSeq v1.0. In phase II, the consortium will continue to deliver valuable tools and resources for wheat scientists and breeders through the functional annotation of the reference sequence and the generation of a pan genome that represents the breadth of diversity for bread wheat. An overview of the future activities of the IWGSC will be presented. 68 Genome-Wide Association Mapping for Seedling Heat Tolerance in Winter Wheat Frank Maulana Noble Research Institute, LLC Heat stress at seedling stage is one of the most common issues of winter wheat in a dual-purpose management system in the southern Plains. However, the genetic mechanism underlying seedling heat tolerance in wheat is not well studied. To dissect the genetic basis of this trait, we conducted a genome-wide association mapping study (GWAS) using 200 hard red winter wheat lines from the Triticeae Coordinated Agricultural Project (TCAP), genotyped using the wheat i select 90K SNP genotyping array. The plants were initially planted under optimal temperature in growth chambers. At three leaf stage, plants were subjected to two temperature regimes, high temperature (40/35oC day/night) as heat stress treatment, and optimal growth temperature (25/20oC day/night) as control for 14 days. Data were collected on leaf chlorophyll content (LCC), shoot length (SL), number of leaves (LN), and percent of seedling recovery (PSR) under optimal growth temperature following the heat stress treatment. GWAS was performed using mixed linear model (MLM). Significant marker-trait associations were found on all the traits under both optimal and heat-stressed growth conditions. In addition, heat stress responding marker-trait associations were also detected. Once validated, these SNPs will be used in marker-assisted selection of seedling heat tolerance in wheat. 69 Indo-UK Research Collaboration to Improve Nitrogen Use Efficiency in Wheat Soma Marla ICAR.NBPGR Nitrogen is the major agronomic input that determines the performance and productivity of wheat crop in both India and UK. With nitrogen being the major production cost for farmers, it has a huge environmental footprint, in terms of pollution of ground waters and generation of greenhouse gases. To minimize the use of applied Nitrogen fertilizers a cross-Institute pre-breeding programme (INEW virtual centre) under India-UK partnership is being executed to identify sources of traits and developing markers for use in academic research and transfer to commercial breeding programmes and responsibility for delivering improved wheat varieties to Indian farmers. The Virtual Joint Centre is bringing together major wheat researchers from ICAR.IARI in New Delhi, Indian Institute of Wheat and Barley Research, Karnal, Bourlag Institute for South Asia, Punjab, National Bureau of Plant Genetic resources, New Delhi and National Research Centre for Plant Biotechnology, New Delhi,Punjab Agricultural University. UK partner institutions are Rothamsted research, University of Nottingham, University of Bristol, John Inns Centre and National Institute of Agricultural Botany. The core of the project is precision field trials being conducted in India and UK using germplasm from both countries, in which the fate of nitrogen in the plant will be followed from root uptake to seed maturity, at limiting and adequate levels of fertilisation. Its impact on grain yield and grain quality in these lines will be studied in detail using the platform technologies (Fig.1) providing information on the relationship between performance and phenology. Major mandate includes integrated study of the genetic, biochemical and molecular basis for improved N use efficiency from mechanisms of nitrogen uptake to partitioning in the grain and effects on processing quality. Candidate genes that control key processes limiting N use efficiency will be identified. The study will be supported by genotyping of germplasm and identification of key genes, enzymes involved, their variation employing high density SNP arrays and transcriptome analysis. Molecular markers developed for key traits will be transferred to wheat breeders in UK and India. 70 Genome-Wide Analysis of MIKC-Type MADS-Box Genes in Wheat: A Primer for Crop Improvement Alice Kennedy University College Dublin MIKC-type MADS-box genes encode transcription factors with prominent roles in plant development. They constitute key regulators of flowering time, floral organ identity, seed and fruit development. MADS-box genes have also been the target of domestication processes in numerous plant species. Understanding the function and evolution of MADS-box genes in crops is therefore of considerable interest for future crop improvement programs. Here, we present a genome-wide analysis of the MIKC-type MADS-box gene family from wheat. We identified more than 200 MIKC-type MADS-box genes, considerably more than in other monocots, partly due to the hexaploid nature of wheat. MIKC* genes as well as representatives from 15 distinct MIKCc subfamilies were identified. Our preliminary analyses indicate that some MADS-box gene subfamilies (e.g. AGL17-like genes) expanded considerably in wheat whereas others (e.g. AGL6-like genes) have relatively few members as compared to other moncots. Using in silico analyses we deduced a relatively strong conservation of expression pattern within each subfamily, indicating functional similarity among closely related homologs. We will use the identified MADS-box genes to screen for sequence variation among different wheat lines. This will provide a starting point to reveal how allelic variation in MADS-box genes may affect agronomically important traits in wheat. 71 Classification of Wheat Varieties in Satellite Images to Perform GWAS Samuel R. Revolinski Dept. of Crop and Soil Science, Washington State University With dramatic reduction of sequencing cost, field trials have become the major burden of plant breeding to improve grain yield, quality and resistance to biotic and abiotic stress, especially on large scale. Abundant available satellite images have the potential to provide valuable data in regards to infection from disease, responses to drought and heat, as well as grain yield and quality. Most of these are due to the improvement of sensing resolution and shorter time intervals between pictures taken. The Satellite WorlView-2, launched in 2009, provides sensing at resolution within a meter on a near daily base. We review the satellite imagery resources and usages, including disease detection, crop discrimination, drought tolerance, nitrogen efficiency. Our objective was to inspire the joint usage of remote imagery data and genomic data for the genetic improvement in crops. 72 A Transcriptome Analysis of Genes Involved in the Production of Reactive Oxygen Species By P. triticina during Its Infection on Wheat Xiben Wang Agriculture and Agri-Food Canada Reactive oxygen species (ROS) play an important role during host and pathogen interactions and are often an indication of induced host defense responses. The importance of these radicals for pathogenesis of the obligate biotrophic fungus, Puccinia triticina *( Pt ), has not been investigated. In this study, we demonstrate that *Pt *generates ROS, including superoxide, H202 and hydroxyl radicals, during its infection of wheat. Through pharmacological inhibition, we show that ROS are critical for both *Pt urediniospore germination and intercellular growth. A Pt *genome-wide screening identified 291 putative genes associated with general redox homeostasis and the search in RNA-seq data sets representing *Pt urediniospore germination, early and late infection stages on susceptible wheat cultivar Thatcher, found 37 genes annotated to encode known products related to oxidative stress responses. We identified two canonical Pt genes encoding NADPH oxidases ( PtnoxA and PtnoxB ), as well as a regulatory gene, *PtnoxR. *Real time qPCR analysis showed that all three genes were differentially regulated during urediniospore germination and infection on wheat. 73 Detoxification of Mycotoxins as a Source of Resistance to Fusarium Head Blight: From Brachypodium distachyon to Triticum aestivum Miriam Gatti Institute of Plant Sciences Paris-Saclay Fusarium head blight (FHB) caused by fungi of the Fusarium genus is a widespread disease of wheat ( Triticum aestivum ) and other small-grain cereal crops. The main causal agent of FHB, Fusarium graminearum , can produce mycotoxins mainly belonging to type B trichothecenes, such as deoxynivalenol (DON) that can negatively affect humans, animals and plants. Several quantitative trait loci (QTLs) for resistance to FHB have been identified some of which have been correlated with efficient DON detoxification, mainly through the conjugation of DON into DON-3- O -glucose (D3G), a reaction catalyzed by UDP-glucosyltransferases (UGTs). Nevertheless, only few studies have conducted functional analyses to directly correlate DON glucosylation and resistance in planta and none were performed on wheat UGT gene(s). Our team, using the model cereal species Brachypodium distachyon , has recently demonstrated that the Bradi5g03300 UGT is able to confer tolerance to DON following glucosylation of DON into DON 3- O -glucose and is involved in the early establishment of quantitative resistance to FHB. In the present work, we transferred the functional analyses conducted on the model species Brachypodium distachyon to bread wheat. In a first approach the B. distachyon Bradi5g03300 gene has been introduced through biolistic-mediated transformation in the wheat variety Apogee, susceptible to FHB. The phenotypic analyses conducted on homozygous transgenic wheat constitutively expressing the Bradi5g03300 gene showed that they exhibit higher resistance to FHB as well as increased root tolerance to DON compared to the control line. In parallel, using a synteny approach between B. distachyon and bread wheat genomes we identified a wheat candidate gene orthologous to the B. distachyon Bradi5g03300 gene. This wheat gene after validation through gene expression pattern during wheat infection, was introduced by transformation into B. distachyon to rapidly determine its ability to conjugate DON into D3G *in planta *and its involvement in FHB resistance. In conclusion, this project contributes to increase the knowledge concerning the functional relationship between DON glucosylation and FHB resistance in wheat and provide candidate genes to include in selection processes. 74 Genetic Architecture of Recombination Rate and Its Effects in Allopolyploid Wheat Katherine Jordan Kansas State University Recombination is a natural process that shapes the landscape of natural alleles within a population. Understanding the genetic basis of how variation in recombination rate is maintained and its effects are important to manipulate the recombination process in crops in order to improve them. We dissected naturally occurring variation in recombination rate present in a spring wheat NAM population and found it is mostly defined by rare alleles with small effects that explain up to 48.3% of the variation in our population. Specifically we identified 66 regions within the genome that contribute to the observed natural variation. Our regions are enriched for meiotic functioning genes, and encompass many conserved recombination genes. Further dissection suggests that the genetic architecture of recombination is predominantly additive and controlled by trans-acting features. In addition, we observed evidence of additive genetic factors that contribute to pericentromeric crossover (CO) frequency without affecting the frequency of telomeric COs. We have also observed a negative effect of linkage drag on deleterious mutation load resulting in excess strong-effect mutations in the pericentromeric genomic regions with constrained recombination. This information suggests manipulation of wheat is possible by influencing CO distribution and frequency, thus unlocking the whole genome without the consequences for linkage drag in wheat improvement. 75 Genomic Prediction and Genome-Wide Association Study of Grain Yield, Kernel Weight, and Kernel Number in a Durum Wheat Breeding Population Evan Salsman North Dakota State University North Dakota leads the United States in acreage and production of durum wheat . Improvements in durum grain yield can result in substantial increases in profit for both farmers and the state. To date, all cultivar yield improvement in the North Dakota State University Durum (NDSU) Wheat Breeding Program has been achieved with phenotypic selection on replicated-plot yield trials in late generations. Applying genomic selection (GS) in earlier generations prior to replicated-plot testing could potentially increase genetic gain if the prediction model has merit. To understand the prospect of GS in the NDSU durum germplasm, unbalanced yield trials including approximately 1,000 breeding lines were used to generate GS models and predict breeding values of lines from the 2015 and 2016 generations. Generally, forward prediction accuracies increased as lines from additional breeding generations were added to the model. Forward prediction accuracies for the 2016 generation were 0.44, 0.42, and 0.35 for grain yield, kernel weight, and kernel number, respectively. Additionally, genome-wide association mapping revealed quantitative trait loci (QTL) for kernel weight. This information can further our understanding of genetic gain plant breeders can expect when applying GS to complex traits in an active wheat breeding program. 76 Application of CRISPR/Cpf1-Based Genome Editing in Polyploid Wheat Wei Wang Kansas State University, Department of Plant Pathology CRISPR/Cas9 has been widely applied in many organisms as a powerful genome editing tool. However, its target sites amenable to editing are limited by the 3’-end NGG proto-spacer adjacent motif (PAM). The CRISPR/Cpf1 requires 5’-end TTV or TTTV PAMs providing opportunities for targeting the AT-rich regions. The genome editing ability of FnCpf1 and LbCpf1 were assessed in wheat by combining transient expression in the wheat protoplasts and next generation sequencing (NGS) of the target regions. While no genome editing events were found for FnCpf1, about 1/3 of the designed targets for LbCpf1 showed the evidence of genome editing. The efficiency of editing was up to 10%, comparable to that of SpCas9 in the wheat protoplasts. We are also testing the editing efficiency of the mutated LbCpf1 (G532R/K538V/Y542R, henceforth LbCpf1m), which in mammalian cells was shown can induce mutations with the 5’-end of the TATV PAM. Multiplex gene editing using Cas9 is somewhat limited by the size of the transgenic constructs. The ability of Cpf1 to process its own CRISPR RNA (crRNA) and the shorter length (43 nucleotides) of crRNA make it a promising multiplex genome editing tool. Multiplex gene editing constructs with different numbers of crRNAs under the control of a single promoter were constructed. All multiplex genome editing constructs generated indels/insertions at the targets sites with the efficiency comparable to that of a single crRNA construct. Our results show that the LbCpf1 can further expand the set of tools available for engineering the wheat genome. 77 Identification of Quantitative Trait Loci (QTL) Associated with Fusarium Head Blight Resistance in a D8006W/ Superior Winter Wheat Population Anjan Neupane Department of Plant Science, University of Manitoba Fusarium head blight (FHB) caused by Fusarium graminearum is a major disease of wheat in North America. FHB infection reduces grain yield, affects end-use quality, and accumulates mycotoxins such as deoxynivalenol (DON) in the grain. The objective of this research was to identify QTL associated with FHB resistance. A doubled haploid soft white winter wheat population consisting of 107 lines from the cross D8006W/Superior was used. Evaluation for FHB reaction was performed using spray inoculation of a macroconidia mixture of four *F. graminearum *isolates representing two chemotypes in replicated field disease nurseries in three locations in Canada in 2016 and 2017. Disease incidence and severity were recorded 21 days post inoculation and FHB index was calculated. Percentage Fusarium damaged kernels and DON content were measured from collected grain samples. Both parental lines showed moderate reaction across all environments for FHB traits. However, the population showed transgressive segregation for FHB reaction with a wide continuous distribution. Genotyping of the population was performed using the 90K Illumina Infinium iSelect single nucleotide polymorphism array and 5194 high quality SNP were selected for analysis. Linkage mapping and QTL analysis is under processing. This experiment will be repeated in field nurseries in 2018. Significant FHB resistance QTL identified from this project will be used in winter wheat breeding programs using marker assisted selection. 78 Widening the Genepool and Identifying Genes Controlling Key Traits in Rice and Wheat Robert J. Henry University of Queensland/QAAFI Food security can be advanced by capturing more useful diversity in crop improvement and by better understanding the molecular basis of key traits that limit the rate of genetic gain in breeding. Recent genome sequencing research has identified wild populations representing significant new diversity in the primary gene pool of rice. This provides new sources of resistance to pests and disease, diversity to allow adaptation to climate change and novel grain qualities with potential consumer appeal and health benefits. Analysis of the transcriptome of the developing grain of diverse wheat germplasm has identified the genetic control of traits such as milling performance, hardness, and end-use quality (bread and chapatti). Genetic improvements can generate more grain per hectare more flour per tonne of wheat and more end-product per tonne of flour. These studies have demonstrated the great diversity of response to heat stress in the wheat gene pool. When combined these developments offer large improvements in food security. 79 A Near-Finished Reference Genome for the Wheat Blast Fungus Provides Insight on Pathogenicity and Adaptation Zhao Peng Kansas State University University of Florida Wheat blast, a devastating new fungal disease caused by the haploid fungus Magnaporthe oryzae pathotype Triticum *(MoT), has been spreading in South America since it was first reported in Brazil in 1985. This disease jumped to Bangladesh in 2016 and now poses a major threat to wheat production in South Asia and beyond. To produce a MoT reference genome, the highly aggressive MoT isolate B71, collected in Bolivia in 2012, was sequenced and assembled with long PacBio reads, Illumina sequences, and a novel scaffold technology using Long-Insert-End-Pair (LIEP) sequences, resulting in a near telomere-to-telomere assembly. The availability of the near-finished assembly facilitated the dissection of genomic structural variation (SV) between B71 and a less aggressive MoT strain isolated in Brazil in 1988, as well as among multiple *M . oryzae isolates adapted for infecting wheat or other crop species. A dispensable mini-chromosome in the B71 genome was identified through the SV analysis and verified, while none or two mini-chromosomes were found in two other MoT isolates. Two effector genes first characterized in the rice blast pathogen, M. oryzae pathotype Oryza , occur together in the MoT mini-chromosome, where both genes maintain characteristic in planta specific expression. The results imply the potential role of the mini-chromosome in the pathogenicity and adaptation of MoT. 80 Identification of Consistent Loci for Fusarium Head Blight Resistance in Northern European Spring Wheat through Genome-Wide Association Mapping Susanne Windju Graminor Fusarium head blight resistance is quantitative, highly complex and divided into several different resistance types. QTL that are effective against several of the resistance types would be a valuable contribution for resistance breeding against this devastating wheat disease. A panel of 299 spring wheat lines with different geographical origin was tested in spawn-inoculated field trials and subjected to visual FHB assessment. In addition, DON level was analysed in the harvested seed. Anther extrusion (AE) was also assessed, in separate field trials. The panel was genotyped with the Affymetrix 35K SNP chip. Eight QTL, significant in three or more testing environments, were detected associated with both FHB and DON. These QTL were detected on chromosomes 1AS, 1AL, 2BL, 3B, 4AL, 5AL, 7AS and 7BS. AE was negatively correlated with FHB and DON, and association mapping could reveal seven AE QTL that coincided with the QTL detected for FHB and DON. The lines tested in the wheat panel harboured from zero to all the detected QTL, and the results show that resistance can be significantly increased by combining several of these resistance alleles. This information enhances the possibility to select crossing parents to obtain varieties more resistant to FHB and DON. 81 Harnessing ‘Left behind’ Drought-Adaptive Alleles for Modern Wheat Improvement Yehoshua Saranga R. H. Smith Institute of Plant Science Genetics in Agriculture, The Hebrew University of Jerusalem The genetic diversity in wild ancestors of crop plants has been considerably eroded throughout plant domestication, evolution under cultivation and recent plant breeding, thereby making modern crop germplasm vulnerable to various biotic and abiotic stresses. Therefore, an important task of modern breeding is to identify and reintroduce valuable ‘left behind’ alleles into the modern domesticated gene pool. Introduction of such alleles has been mostly employed for improving biotic stress resistances, while abiotic stress adaptations received only minor attention. Water deficit is the major environmental factor limiting crop productivity, hence developing drought-resistant crop cultivars is essential to ensure a sustainable agricultural production under the ongoing climatic change. Wild emmer wheat ( Triticum turgidum ssp. dicoccoides Thell.), the progenitor of the domesticated durum ( T. turgidum *spp. durum* (Desf.) MacKey) and bread ( T. aestivum L.) wheats, harbors a rich allelic diversity that is valuable for future improvement. Selected drought-adaptive QTL alleles were introgressed from wild emmer wheat into modern durum and bread wheat cultivars and the resultant near isogenic lines (NILs) were tested for their drought responses. NILs introgressed with wild emmer QTL on chromosome 7A, exhibited under water-limited conditions greater grain yield, osmotic adjustment, photosynthetic capacity and root development compared with their recurrent parent. Selected NILs, carrying the 7A QTL in two genetic backgrounds, tested across 3 years under commercial field conditions, exhibited a significant advantage over their parental cultivars, particularly under drought, thus confirming the potential of this left behind QTL allele for improving drought resistance in modern wheat. 82 Development of Genetic and Genomic Resources to Evaluate Wheat Organellar Genome Variants and their Functional Implications Katie L. Liberatore Department of Plant Pathology, University of MinnesotaCereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service Organellar genome diversity represents a potential untapped source for improving agronomic traits. Due to the nature of hybridization and domestication events that led to modern cultivated wheat, organellar (mitochondria and chloroplast) genome diversity was dramatically reduced. However, wheat has the largest known collection of alloplasmic (alien cytoplasm) lines. In these lines, the cytoplasms, and therefore the organelles, of wild relatives have been mismatched with the nuclear genome of domesticated wheat through extensive backcrossing. Disruption of native nuclear-cytoplasmic interactions (NCI) impacts a number of agronomic traits including fertility, biomass, grain yield, and stress response. To understand the functional implications of organellar genome variants and genetic mechanisms underlying NCI, we generated organellar genomic resources. We developed a method to couple organellar DNA enrichment from total gDNA utilizing a pull-down approach and ultra-low input library preparations for long-read sequencing. We sequenced 20 organellar-enriched samples with PacBio, including 13 diverse wild species, T. durum , T. aestivum cv. Chinese Spring, and three alloplasmic lines. We also generated Illumina short-read sequences for 75 cultivars, wild species, and alloplasmics. Comparative analyses are investigating organellar diversity across the Triticum-Aegilops complex and how sequences change in the alloplasmic condition. In parallel, we are generating additional genetic and genomic resources in wheat and the model system Brachypodium distachyon for functional genomics studies. These resources will be useful to the broader community for furthering our understanding of the molecular mechanisms involved in NCI and their affects on plant phenotype as well as for breeding efforts to improve agronomic traits. 83 POTAGE: A Visualisation Tool for Speeding up Gene Discovery in Wheat Radosław Suchecki The University of Adelaide POPSEQ Ordered Triticum aestivum *Gene Expression (POTAGE) is a web application which accelerates the process of identifying candidate genes for quantitative trait loci (QTL) in hexaploid wheat. This is achieved by leveraging several of the most commonly used data sets in wheat research. These include the Chromosome Survey Sequences, their order along the chromosomes determined by the population sequencing (POPSEQ) approach, the gene predictions and RNA-Seq expression data. POTAGE aggregates those data sets and provides an intuitive interface for biologists to explore the expression of the predicted genes and their functional annotation in a chromosomal context. The interface accelerates some of the laborious and repetitive tasks commonly undertaken in the process of identifying and prioritising genes which may underlie QTL. We illustrate the utility of POTAGE by showing how a short-list of candidate genes can quickly be identified for a QTL linked to pre-harvest sprouting - a major cause of quality and yield loss in wheat production. The candidate genes identified using POTAGE included *TaMKK3 , which was recently reported as a causal gene for seed dormancy in wheat, and a mutation in its barley ortholog has been shown to reduce pre-harvest sprouting. In addition to the public version of POTAGE , we have also developed a Docker image for quickly deploying POTAGE locally and work-flows showing how to add your own expression data sets to a local installation. This is of particular relevance to those who work with unpublished data sets or would like to deploy POTAGE on their own hardware. 84 Evaluation of the Effect of an Alien Chromosome Segment Translocated from Aegilops sharonensis on Recombination Frequency in Wheat Motohiro Yoshioka Graduate School of Agriculture, Kyoto University Background: The resolution of genetic map depends on meiotic crossover frequency between homologous chromosomes. Due to a low crossover frequency in the wheat genome (Triticum aestivumL.), a large population is needed to obtain informative recombinants. Moreover, it has been demonstrated that artificial allotriploids in the Brassica species exhibit genome-wide elevation in recombination frequency. However, the effect of alien chromosomes on meiotic recombination still remains poorly understood in crop species. Thus, the purpose of this study is to demonstrate if the alien chromatin (segments) can increase recombination/crossover frequency in wheat. Methods : We developed an F2 population derived from an accession DT4B-4Ssh. The terminal segment of the chromosome 4Ssh of Aegilops sharonensis was translocated to chromosome 4B of Chinese Spring (CS), which was subsequently crossed with a spelta wheat ( T. spelta L. var. duhamelianum, accession KT019-001). The F2 population derived from normal CS and KT019-001 was used as control. Linkage maps were constructed using the same set of 494 markers scattered on A and B genome chromosomes. Results : The complete linkage map derived from DT4B-4Ssh was ~11% longer than from CS. The average crossover numbers significantly increased for the entire A and B genome respectively. The observed elevation of recombination frequencies was not concentrated in a particular chromosomal region. In conclusion, our results indicated that the chromosome segment introduced from *Ae. sharonensis *increased recombination frequency globally. This suggests that small alien chromatin may affect meiotic recombination in wheat. 85 Reduced Height Semi-Dwarf Alleles Significantly Impact Wheat End Use Quality Emma Jobson Montana State University The genes responsible for dramatic yield increases during the 1950s and 1960s are mutant forms of the Reduced height ( Rht ) genes. Since then, two semi-dwarfing alleles of Rht , Rht-B1b and Rht-D1b have been widely incorporated into modern wheat cultivars. Despite being some of the most widely utilized yield increasing genes, few studies have examined their effect on wheat end use quality. For this study we compared near isogenic lines created in a standard height spring wheat variety (Fortuna) varying for the presence of the gibberellin insensitive mutations Rht-B1b, Rht-D1b, *or the gibberellin sensitive dwarfing gene *Rht-8 . Our agronomic results agreed with previous findings and we observed a 25% height reduction and 13% yield increase in Rht-B1b/Rht-D1b compared to the tall isoline. Grain protein was decreased (from 15.4 to ~13.6%) as was kernel weight (15%) in the Rht-B1b/Rht-D1b isolines. We also saw a slight decrease in the loaf volume in Rht-B1b/Rht-D1b compared to the tall line. However, we observed statistically significant increases in flour yield (2%), falling number (5%), mixing tolerance (56%), and baking mix time (33%). The fact that flour yield was increased is unexpected since Rht-B1b/Rht-D1b also decrease seed size. For almost all parameters, Rht-8 was intermediate between the tall line and Rht-B1b/Rht-D1b . These findings indicate that although Rht-B1b/Rht-D1b decrease seed size and protein content, they positively impact wheat milling yield and do not negatively impact dough strength. 86 Analysis of Wheat Internode Time Course RNAseq Data to Identify Genes Related to Nutrient Remobilisation Depending on Nitrogen Availability Asier Gonzalez-Uriarte Rothamsted Research The massive and polyploid genome of wheat has make it challenging for researchers to leverage RNAseq to identify candidate genes underlying complex phenotypes. Most studies in wheat have focused on high-level characteristics of gene expression because the available references were incomplete and fragmented and over 100,000 transcribed genes are assayed simultaneously. In other organisms, well designed and carefully analysed RNAseq experiments have contributed to gain insights into mechanisms controlling complex traits and we intend to follow a similar approach in wheat genomics now that near-complete references are available. Here we describe the bioinformatics analysis of a time course RNAseq experiment in which internode samples from hexaploid wheat ( T. aestivum ) plants treated with two nitrogen levels have been collected at 8 time points between anthesis and senescence. The study aims to elucidate the molecular mechanisms involved in nutrient remobilisation from senescing organs to developing tissues and the role of nitrogen availability in senescence. The chloropyll level has been used as a marker of senescence and the DESeq2 Bioconductor package has been used to identify genes that switch their state at its onset. We demonstrate that it is possible to reduce the number of candidate genes from thousands to dozens using statistical methods to identify genes that have an expression profile of interest. In this work, 9 genes have been found to be upregulated and 8 downregulated in senescence and their functions seem to be related to processes like chlorophyll binding, protein breakdown and cell signalling. 87 Towards Chromatin Immunoprecipitation (ChIP)-DNA Isolation and Epigenome Development in Durum Wheat Tissues Antonette Todd Delaware State University Chromatin Immunoprecipitation (ChIP) examines the connections between proteins and DNA contained in the genome of an organism by observing histone modifications. Histone modifications incorporate the ability to relax and condense chromatin, which in turn, helps govern gene expression and repression. In acetylation, the chromatin relaxes, which allows transcription factors to reach their target, causing gene expression. In methylation, the chromatin condenses, restricting transcription factors from reaching their target, obstructing gene expression. Tri-methylated lysine four on histone three (H3K4me3) plays a role in activation in gene promoter regions. Histone-DNA interactions might play an important role in fighting drought, adjusting to heat stress, and combating diseases during plant developmental stages. In this work, we will optimize ChIP-DNA extractions in Durum wheat and observe ChIP-DNA isolates in four tissues (leaf, root, head, and two week old seedling) to detect variances in histone-DNA interactions among the group using Illumina sequencing. By optimizing the ChIP-DNA isolation protocol in Durum wheat we may better understand histone modifications and the role they play in fighting abiotic and biotic stresses. Additionally, we will use quantitative PCR to identify chromosome remodeling gene expression differences among tissue types in wheat. Knowing where these particular genes are located in the genome may help us understand their importance. The objective of this study is to serve as a blueprint for examining spatial histone methylation and acetylation in wheat using the ChIP assay. 88 Assessing the Consequences of Key Events of the Hexaploid Wheat Genome Evolution: Structural and Evolutive Analysis of an Ancestral Chromosomes Fusion Point and of a Region Resulting from Ancient and Recent Polyploidizations Arnaud Bellec French Plant Genomic Center CNRGV - INRA Studying the bread wheat genome’s structure has been a tremendous challenge for decades. Its complexity (hexaploidy, high rate of repetitive elements) and size make wheat genome both complex to decipher and interesting to investigate as the result of multiple evolutionary forces (ancient and recent polyploidization, chromosomes fusions, deletion or sub-functionalization of homeologous genes). To study these events we first aimed at characterizing a chromosomes fusion locus (CF) and comparing the structure of the copies of a 2 Mb region carried by chromosomes 1A, 1B, 1D, 3A, 3B, 3D. Before the release of a wheat reference genome, our strategy was to identify BACs spanning the regions of interest using available resources (chromosome specific BAC libraries, physical maps, genome zipper, WGP) and to sequence BACs using PacBio technology. Despites all these resources, it remained difficult to sequence the CFs which are highly rearranged regions and the six copies of the region of interest. The release of the IWGSC reference genome followed by its annotation have changed our strategy by giving access to the whole genome sequence. Thanks to this sequence, we have redefined the orthologous relationship between hexaploid wheat genes and rice genes (as rice has conserved the structure of the common grass ancestor). We have identified various rearrangements and precisely outlined the CF regions. Following this analysis at the genome scale, we focused on the rearrangements of the CF regions of chromosomes 1A, 1B, 1D and on the fates of homeologous genes among the six copies of a region of interest. 89 Improved Markers for a Pre-Harvest Sprouting QTL on Wheat Chromosome 3B Mark Jordan Agriculture Agri-Food Canada A QTL for sprouting index on chromosome 3B was identified in the AC Domain x RL4452 bi-parental mapping population (Cabral et al. 2014, BMC Plant Biology 14:340). The flanking markers derived from the Illumina iSelect 90K chip define a region of 185 Mbp in the wheat RefSeq 1.0 genome sequence containing over 1180 annotated high confidence genes. Additional markers are needed to narrow down this region for wheat breeding purposes as well as to eventually identify candidate genes. As a first step to identify additional markers SNPs previously validated in the KASP assay were identified by locating QTL flanking markers from the 'AC Domain' x RL4452 3B map on the 'Avalon' x 'Cadenza' map. Validated KASP markers mapped on Avalon x Cadenza in the region between QTL flanking markers were chosen ( http://lgcapps.com/assays/wheat/ ) for genotyping and mapping on the 'AC Domain' x RL4452 population. Subsequently the full genomic region between flanking markers from the IWGSC RefSeq1.0 genome sequence was used to identify SNPs between the parental genotypes in a sequence database derived from exome capture sequencing of Canadian wheat genotypes. 1492 SNPs were identified in 288 annotated genes. The SNPs will be useful to further narrow down the QTL region and provide robust markers for selection of lines with increased tolerance to pre-harvest sprouting. 90 Discovering Superior Alleles Underlying Drought and Heat Tolerance in Common Wheat Ruilian Jing Institute of Crop Science, Chinese Academy of Agricultural Sciences Environmental stresses, drought and heat, especial the stresses in grain filling period are the primary causes of grain yield losses in wheat ( Triticum aestivum L.). Abundant wheat germplasm resources with tolerance to drought (DT) and heat (HT) have been identified. They are important gene resources for wheat improvement. However, very little is known about these resources, such as what tolerant-genes these germplasm possess, in which accessions have the superior alleles underlying the tolerances, and how to use these alleles effectively. Our researches showed that some genes involved in the DT and HT, also contributed to the yield-related traits. Here, we dissect the functions of gene Ta**SnRK2 (sucrose non-fermenting1-related protein kinase 2), TaPP2A (protein phosphatase 2A), and TaSPL (squamosa-promoter binding protein, SBP-box). TaSnRK2 and TaPP2A not only responded to abiotic stress, but also significantly associated with 1000-grain weight under terminal drought and heat stress. Two of the SPL *members, *TaSPL20 and TaSPL21 associated with 1000-grain weight and plant height in multi-environment. According to the functional analysis of naturally occurring variants, favorable alleles/haplotypes were identified with the perfect markers. They increased 1000-grain weight, and reduced plant height in well-watered, drought, and heat environments. Our study suggests that during domestication and breeding of wheat in China, superior alleles of each gene were selected and exploited to varying degrees due to their large effects on the yield-related traits.
31、Meiosis Specific Gene Discovery in Hexaploid Wheat Arun S.K Shunmugam National Research Council Canada Meiosis plays a key role in sexual reproduction of eukaryotic organisms. Understanding the molecular basis of chromosome pairing and recombination during meiosis is essential to exploit the genetic variation available in the gene pool. Meiotic development is governed by a genetic program that coordinates the spatio-temporal expression and function of numerous genes essential for the process. The key step towards the discovery of meiosis specific genes and regulatory networks is to isolate uncontaminated male meiocytes from well-defined stages of meiosis. Male meiocytes are present in a column of enlarged cells called archesporial column within the four loculi of wheat anthers. We have optimized a male meiocyte isolation procedure which involves the extraction of intact archesporial columns using a specialized anther squash method to avoid or minimise contamination from other cell types present in wheat anthers. To comprehensively characterize expression dynamics during meiosis, meiocytes from Chinese Spring anthers were collected from seven different meiotic stages, including leptotene, zygotene, pachytene, diplotene, diakinesis, metaphase I and metaphase II. Total RNA was isolated and sequencing was performed using the Illumina platform. In this presentation, we will discuss (1) our efforts towards establishing a comprehensive catalogue of meiosis-specific genes in wheat and identification of gene regulatory networks governing chromosome pairing behavior and recombination, and (2) future strategies to exploit these resources towards development of novel wheat germplasm. 32、Wheat Hessian Fly Interactions: A Duel till Death Subhashree Subramanyam Purdue University A duel between wheat ( Triticum aestivum ) and its major dipteran insect pest, the Hessian fly ( Mayetiola destructor ) elicits one of two interactions: incompatible (plant wins and larvae die), and compatible (larvae win and plant dies). During an incompatible interaction, the wheat plant surveillance mechanism detects the larval salivary effectors with an appropriate R *gene triggering a gene-for-gene recognition that in turn activates plant defenses rendering the host plant resistant. This recognition event triggers expression of defense-response genes, changes in surface wax composition, accumulation of antifeedant proteins, as well as controlled host-cell permeability that aids in delivery of antinutrients, all leading to larval death. In contrast, during a compatible interaction, the salivary effectors from virulent larvae essentially hijack the host plant system by suppressing defense response, and altering the metabolic pathways leading to physiological changes at the feeding site (crown tissue) that provide the developing larvae a diet rich in essential nutrients making the wheat plant susceptible. Our recent investigations using Next generation RNA-Sequencing technology and quantitative real-time PCR expression studies in wheat and Hessian fly have revealed several differentially expressed genes and associated metabolic pathways providing molecular insight into plausible resistance and susceptibility mechanisms. Development of the Hessian fly *in planta translocation (HIT) feeding assay opened up research avenues to test the effects of various defense and insecticidal proteins on this obligate parasite of wheat. In addition, we have explored the use of model grass genome and nonhost of Hessian fly, Brachypodium distachyon , for functional characterization of candidate defense genes for development of molecular tools to overcome economic devastations caused by this insect pest. 33、Completion of the ‘Jagger’ Winter Wheat Genome Leads to Identification of Aegilops ventricosa 2NS Translocation and Its Impact in Kansas and US Wheat Breeding Liangliang Gao Kansas State University Since its release 23 years ago, the winter wheat cultivar Jagger has had a huge impact on wheat production in the US and around the globe and became a parental germplasm in many of the current cultivars of the central U.S. Importantly, Jagger also possesses the Aegilops ventricosa 2NS translocation fragment, which is associated with disease resistance against multiple wheat pathogens including the devastating wheat blast fungus. Here we present the first de novo assembly and anchoring of the Jagger genome based on the NRGene DeNovoMAGIC 3.0 pipeline and chromosome conformation capture technology (Hi-C). We were able to successfully anchor ~3000 scaffolds with a cumulative length of 14.2 Gb and an N50 of 10.5 Mb to build 21 draft pseudomolecules. Overall, these draft pseudomolecules showed high collinearity with the reference Chinese Spring genome (IWGSC RefSeq v1). The Jagger genome will be a powerful tool in the analysis of the wheat pan genome and the dissection of important agronomic traits. To illustrate its utility, we delineated the Aegilops ventricosa 2NS translocation fragment in Jagger, consisting of a ~30 Mb fragment identified through alignment of Jagger chromosome 2A to ‘Chinese Spring’ chromosome 2A. We also developed a pipeline for identification of 2NS translocations in wheat breeding lines using genotyping by sequencing (GBS) data and reference genomes. Our results suggest that the 2NS translocation segment is widely present in KS and other US breeding materials, and is potentially providing a yield benefit over the span of 26 years. 34、Validation of Grain Yield QTL from Soft Winter Wheat Using a CIMMYT Spring Wheat Panel Dennis Nicuh Lozada University of Arkansas QTL validation is an essential step in identifying genomic regions affecting variation for complex traits such as grain yield (GY) and yield components for marker-assisted breeding. We report the validation of GY-QTL from winter wheat using a population of spring wheat from CIMMYT, Mexico evaluated for GY, grain number (GNO), and thousand grain weight (TGW) across 29 international locations. The objectives of this study were to validate GY and yield component QTL previously identified from soft winter wheat using CIMMYT’s wheat association mapping initiative (WAMI) panel, determine the allele combination for the validated QTL that resulted to highest GYs, and identify candidate genes associated with the validated SNP loci. KASP® assays developed for *wsnp_Ex_c361_708712 *(3A), *wsnp_Ex_c13849_21698240 *(4B), and *wsnp_CAP11_c3599_1741800 *(6B) were associated with GY, GNO, and TGW across different BLUP and BLUE datasets in WAMI. The T-C-C allele combination, which contained favorable (positive) alleles at all three loci resulted to highest mean GY. A negative effect for the minor alleles observed in both the winter and spring panels demonstrated selection for the GY-enhancing major allele and indicated similar selection pressures in both wheat classes. Candidate gene analyses revealed diverse gene functions from repressor of RNA pol III transcription, positive regulation of ubiquitin protein ligase activity, and transcription factor identified for GY-related marker-trait associations demonstrating the complex nature of GY and yield components. Our results showed the potential of the developed assays for marker-assisted selection to improve GY-related traits in both winter and spring wheat classes. 35、Assessing the Potential of Host-Induced Gene Silencing to Reduce Wheat Rust Infection in Transgenic Wheat Ali A. Ahmed UC DAVIS The RNA interference based Host-Induced Gene Silencing (HIGS) has been shown to provide resistance to several plant diseases. We are testing HIGS to enhance resistance in wheat against three rust pathogens. Previously we demonstrated that individual silencing of ten stem rust genes using transient Virus-Induced Gene Silencing significantly reduced stem rust development. Silencing four and three of these genes also decreased the development of stripe rust and leaf rust, respectively. We are currently investigating the potential of silencing these genes to minimize rust infection through stable expression of the RNAi trigger sequence in transgenic wheat. Four stripe rust genes which are highly expressed in haustoria and two leaf rust genes that may be vital for proliferation were also targeted. So far 154 T1 plants have been generated with an average of six independent transgenic events per target gene, of which 140 have been confirmed as containing the respective transgene by PCR. The T1 plants were selfed to generate T2 seed. Ten T2 plants per each T1 are being evaluated for resistance to stripe rust and stem rust on 1-9 and 0-4 scales, respectively. Of 68 T1 progeny tested so far against stripe rust, 6 and 7 infection types were observed for 3 and 13 transgenics, respectively. One, nine and four transgenics showed 2-3, 3 and mixed infection types for stem rust infection, respectively. Seven plants showed some level of reduced infection with both stripe rust and stem rust. The infection assays are underway for the remaining T1 plants. Tests will be repeated to confirm the partial resistance phenotypes on T3 plants. All 140 T1 progeny will also be evaluated for resistance to leaf rust. Transgenic lines containing different RNAi targets that exhibit promising phenotypes will be crossed in order to pyramid individual RNAi effects. 36、Leveraging the Tetraploid Wheat Genomes for Cloning Cdu-B1 , a Major Gene for Cd Accumulation in Durum Wheat Grain Sean Walkowiak University of Saskatchewan Cadmium (Cd) accumulation in the grain of durum wheat presents a serious concern for human health. As a result, durum wheat breeding programs select for low grain Cd. Differences in Cd accumulation among cultivars of durum wheat are attributed to the major-effect gene Cdu-B1 located on chromosome 5B. The objective of this study was to identify the functional determinant of Cdu-B1 . The fine mapped interval for Cdu-B1 was anchored to the complete genome sequences of the durum cultivar ‘Svevo’ (a high Cd accumulator) and the wild emmer wheat accession ‘Zavitan’ (a low Cd accumulator). A sequence comparison of Cdu-B1 between Svevo and Zavitan revealed a gene candidate, HMA3-B1 . This gene encodes a P1B-ATPase transition metal transporter and contains a 17 bp duplication in the first exon in Svevo relative to the wild-type allele in Zavitan. A molecular marker for the 17 bp duplication was used to evaluate a diverse set of breeding lines from global breeding programs and was able to identify low and high Cd accumulators with perfect precision. Furthermore, functional assays using yeast expression systems confirm a role for the wild-type HMA3-B1 gene in regulating Cd accumulation in grain by mediating vacuolar Cd sequestration. In addition, the 17 bp duplication allele present in high Cd genotypes was non-functional. The molecular marker developed from this work is currently deployed in global breeding programs to develop wheat lines with low grain Cd. 37、A Benchmarking Resource to Assess Wheat Genotyping Platforms Mario J Caccamo NIAB Recent advances in both chemistry and data analysis tools have driven down the cost of DNA-based protocols resulting in a varied offer of genotyping platforms, in particular for species with complex genomes such as wheat. One of the challenges for the end users is to be able to evaluate how the different platforms compare and which ones are better suited for the different downstream applications. The aim of our project is to design a benchmarking assay to be made available to the scientific community as a resource to assess the different genotyping platforms in terms of information content, reliability of the results and resources requirements. In order to inform the construction of this resource we generated genotyping data for 384 wheat lines using three reduced-representation approaches: DArTseq, SNP-array (hybridisation-based) and exome capture. The DNA samples were extracted from material that is hosted at the seed bank at CIMMYT and includes varieties from a diversity of backgrounds (including some wild species). We will make the genotyping data publicly available via established resources (such as the CerealsDB database). We will also deploy a Galaxy interface that will provide access to the data together with a number of data analysis tools. This BBSRC Newton-fund project is a collaboration between the Seeds of Discovery initiative at CIMMYT (Mexico), and NIAB, the Earlham Institute and the James Hutton Institute in the UK. 38、A Comprehensive Microbiome Analysis of Wheat and Its Wild Relatives Heather N. Cantor Colorado State University Microbiomes are diverse assemblages of endophytic and free-living microorganisms that can confer competitive advantages to their plant hosts such as water acquisition, nutrient mobilization, drought tolerance, salt tolerance, and disease resistance. Plant domestication and selective breeding have altered the composition of these plant-microbe interactions in several crops. It is thought that the progenitors of the A, B, and D genomes in modern hexaploid wheat manage environmental stress in their native environment by establishing symbioses with a consortium of beneficial microbes. However, these microbial communities are not well understood. The goal of this study is to better understand the core community of microbes in wild wheat relatives and how they differ from the microbiome of cultivated wheat. This study compares the bacterial and fungal taxa found in the leaves, roots, and rhizosphere of three accessions of hard winter wheat and 11 wild relatives. These plants and the agricultural soil they inhabit were sampled from a randomized complete block design with two replications, grown in well-watered and water-limited treatments in Fort Collins, Colorado. DNA was extracted and amplicon sequencing of the 16S-V4 (bacterial) and ITS2 (fungal) rRNA genes was used to describe the diversity of the microbial community associated with the root, rhizosphere and leaf of each accession. Preliminary results indicate that while there was limited difference in microbial communities among accessions, plant compartment appears to have an important effect on structuring the microbial community across accessions. 39、Isolating a Gene that Suppresses Stem Rust Resistance in Wheat Colin W. Hiebert Agriculture and Agri-Food Canada Stem rust, caused by Puccinia graminis f.sp. tritici ( Pgt ), is an important disease of wheat that can be controlled by developing cultivars that carry effective resistance genes. However, as the pathogen evolves virulence, new resistance must be identified and deployed. Previously, a gene on chromosome arm 7DL was described that suppresses resistance to some races of Pgt in the cultivar Canthatch. When the suppressor is knocked-out by mutagenesis resistance is expressed that is normally silenced. Our goals were to map and isolate the suppressor gene, SuSr-D1 . Two EMS-induced mutants, NS1 and NS2, were each crossed to Thatcher, the recurrent parent of Canthatch, and two doubled haploid (DH) mapping populations were generated. The DH populations were phenotyped with Pgt race QTHJC at the seedling stage. Chromosome 7D was isolated from wild-type and mutant stocks by flow cytometry and then sequenced using Illumina technology. Sequences were assembled and SNVs were called between wild-type and mutant contigs. SNVs and SuSr-D1 were mapped in DH populations to define a physical region for detailed bioinformatic analysis. A single gene was found to have nonsense mutations in NS1 and NS2 that also co-segregated with the SuSr-D1 phenotype. Sequencing an additional five independent mutants showed the same gene carried a nonsense mutation in each instance. SuSr1-D1 encodes a subunit of the Mediator complex, which plays a key role in regulating transcription of protein-coding genes. 40、Speed GS: Accelerating Genetic Gain in Wheat Ben Hayes University of Queensland The genetic improvement of modern wheat varieties has been very successful. However annual yield increases need to be doubled over the next few decades and the global production trends in all major wheat growing regions indicate a yield plateau. To overcome this, innovative strategies that efficiently integrate modern technologies in breeding programs are required. Using simulations based on real wheat data sets, we demonstrate how genomic selection and “speed breeding”, a novel rapid generation advancement technology, can be combined to substantially reduce the length of the breeding cycle and maximise genetic gain per unit time. We outline the opportunities and challenges associated with the fusion of these breeding tools and reinforce the importance of integrating novel genetic diversity in breeding programs to achieve sustainable long-term genetic gain. 41、Wheat Mutants with Reduced Puccinia triticina Infection John Fellers USDA ARS Wheat and Puccinia triticina , the fungus causing leaf rust, have a biotrophic relationship that has evolved over time. After a urediniospore lands on the leaf, it will germinate, form an appresoria over the stomate, insert a hyphal tube, find a mesophyll cell, and produces a haustoria which invaginates the host cell plasma membrane. The haustoria will begin to secrete effectors garnering host nutrients, squelching host defenses, and will entice host enzymes and pathways to work for the fungus. Recent cloning of broad-spectrum resistance genes suggests that stable resistance may be found by upsetting the biotrophic interaction between rust and wheat. To identify wheat genes needed by the pathogen, EMS was used to mutate the spring cultivar Thatcher. M2 lines were screened with P. triticina race BBBD, and lines were identified with a reduction in rust infectivity. Lines were taken to the M6 and evaluated in the field under natural, mixed race infections, and 25 lines were identified. Phenotypes included little or no pustules, race specific-like resistance, or reduction in pustule size. These lines were backcrossed to Thatcher and resistant and susceptible F2 lines were pooled and their RNA and DNA sequenced. Phenotypes segregated in a manor consistent with a single recessive gene. Comparisons back to the wheat genome will be made and genes will be identified and reported that are associated with the traits. 42、Cytogenetic Analysis of Karyotypically Unstable Perennial Wheat Amphiploid Breeding Lines Matthew Arterburn Washburn University Perennial wheat breeding lines are amphiploids generated by wide hybridization of annual hexaploid bread wheat ( Triticum aestivum , 2n = 6x = 42, AABBDD) with perennial wheatgrass species such as tall wheatgrass ( Thinopyrum elongatum , 2n = 14, EeEe) and intermediate wheatgrass ( Thinopyrum intermedium , 2n = 6x = 42, EeEeEeEeStSt) and doubling chromosome content with colchicine. This process mimics polyploidization events that have occurred throughout evolutionary history in the plant tribe Triticeae. Such lines demonstrate a perennial habit and are useful in sustainable agriculture systems. Post-hybridization generations of these lines exhibit considerable karyotypic instability, and chromosome loss results. Similarly, when perennial wheat amphiploids are crossed to other wheat cultivars as part of breeding strategies, subsequent generations experience considerable chromosome number variation. To characterize chromosome behavior in early and late generations after amphiploid crosses, and to distinguish perennial wheat breeding lines with promising agronomic characteristics, we performed cytogenetic analysis on 38 lines selected from multiple generations (F1 through F6) after initial crosses involving wheat and various wild perennial wheatgrass species from the Thinopyrum genus. We used genomic in situ hybridization (GISH) to identify the genome origins of the chromosomes present. Among the various lines analyzed, chromosome numbers ranged from 43 to 70, with GISH analysis indicating great variation among the alien chromosomes. Chromosomal aberrations were evident in a number of lines, including telosomes and translocations between wheat and the alien chromosomes. We also employed molecular marker analysis, using cleaved amplified polymorphic sequence (CAPS) markers, to help specifically identify alien chromosomes present. 43、Detoxification of Deoxynivalenol and Resistance to FHB : From the Model Cereal Species Brachypodium distachyon to Bread Wheat Miriam Gatti Institute of Plant Sciences Paris-Saclay Fusarium head blight (FHB) caused by fungi of the Fusarium genus is a widespread disease of wheat ( Triticum aestivum ) and other small-grain cereal crops. The main causal agent of FHB, Fusarium graminearum , can produce mycotoxins belonging to type B trichothecenes, such as deoxynivalenol (DON) that can negatively affect humans, animals and plants. Several quantitative trait loci (QTLs) for resistance to FHB have been identified some of which have been correlated with efficient DON detoxification, through the conjugation of DON into DON-3- O -glucose (D3G), a reaction catalyzed by UDP-glucosyltransferases (UGTs). Nevertheless, only few studies have conducted functional analyses to directly correlate DON glucosylation and resistance in planta and none were performed on wheat UGT gene(s). The search for UGT candidates able to conjugate DON into DON 3- 0- glucoside (D3G) in the cereal model species Brachypodium distachyon resulted in the identification of the Bradi5g03300 gene. Functional analyses of this gene showed increased sensitivity of the mutant lines to the toxin and to F. graminearum . Furthermore, lines overexpressing this gene showed a tolerance to the toxin and quantitative resistance to the fungal pathogen. These results were positively correlated with the detection of increased amounts of D3G, further reinforcing the ability of the B. distachyon *to conjugate DON *in planta . Using a synteny approach between B. distachyon and bread wheat genomes we identified a wheat locus carrying wheat genes orthologous to the B. distachyon Bradi5g03300 gene. One homeolog was selected as the best ortholog by examining the gene expression pattern during wheat infection. It was therefore introduced by transformation into B. distachyon to rapidly determine its ability to conjugate DON into D3G *in planta *and its involvement in FHB resistance. These results contribute to increase the knowledge concerning the functional relationship between DON glucosylation and FHB resistance in different cereal species and provide candidate genes to include in selection processes in wheat. 44、Development of a Genome-Wide ChIP Derived Reference Epigenomes in Durum Wheat Mayavan Subramani Delaware State University Modifications in histones regulate gene expression by relaxing or condensing chromatin. Histone modifications play an important role in plant development and stress response. Very few studies of epigenome have been performed in wheat. The objective of this study is to serve as a blueprint for examining epigenomic regulation involved in developmental stages and stress responses in wheat using the ChIP-seq assay. The goal of our research is to produce a ChIP reference epigenome derived from tetraploid wheat. In this work, we have developed protocols for ChIP-DNA isolation from three tissues -leaf, head, and root of the durum wheat cultivar ‘Langdon’ to detect spatial variances in histone modification H3K4me3 (trimethylation of lysine 4 on the histone H3 protein). Strategies and statistics of read alignment will be summarized and provided as a guideline for future studies. Peak regions with H3K4me3 will be identified and characterized. Differential modification regions of H3K4me3 among different tissues will be extracted. The genes that are close to differential modification regions will be investigated to see whether these genes can explain the differences in these developmental stages. With these results, we will be able to better understand gene activation or repression in relation to this specific histone mark, paving the way for us to examine genome-wide gene regulation in wheat. 45、Wheat WRKY Gene TaWRKY51 Plays Positive Roles in Drought Stress Zhaorong Hu China Agricultural University WRKY-type transcription factors are involved in multiple aspects of plant growth, development and stress response. WRKY genes have been found to be responsive to abiotic stresses; however, their roles in abiotic stress tolerance are largely unknown especially in crops. Wheat ( Triticum aestivum *L.) is one of the major crops largely cultivated and consumed all over the world. The molecular mechanism of the abiotic stress response in wheat is largely unclear. We previously identified multiple stress responsive WRKY genes from wheat. Here, we further characterized the roles of one of these genes, *TaWRKY51 , in abiotic stress tolerance. TaWRKY51 expression was increased by various abiotic stresses. Over-expression and RNAi analysis demonstrated that TaWRKY51 *improves drought tolerance in transgenic wheat lines. Measurement of physiological parameters, including chlorophyll and proline contents, supported this conclusion. TaWRKY51 enhanced expressions of *NCEDs and DREBs *genes. TaWRKY51 protein may regulate the downstream genes through direct binding to the gene promoter or via indirect mechanism. Manipulation of *TaWRKY51 in wheat or other crops should improve their performance under drought stress conditions. 46、Genome-Wide Association Mapping Reveals Major Genomic Regions for Grain Zinc Concentration in Wheat Govindan Velu CIMMYT Bread wheat is a major staple providing 20% of dietary energy and major source of protein and essential micronutrients such as iron (Fe) and zinc (Zn) for world’s population. About two billion people are deficient in some essential micronutrients, including the Zn and Fe deficiency. The magnitude of Fe and Zn deficiency is particularly severe among children and women. To close nutrition gaps in rural households of remote areas, development and dissemination of high-yielding and nutrient-rich wheat varieties offers a cost-effective and sustainable solution. Breeding for enhanced Zn concentration in wheat was initiated by crossing high Zn progenitors such as synthetic hexaploid wheats, T. dicoccum, T. spelta and landraces. These crosses have resulted in several wheat varieties with competitive yields and enhanced grain Zn which were adapted by thousands of small-holder farmers in South Asia and Africa. Here we report one of our genome-wide association studies (GWAS) using the wheat 90K genotyping assay, characterized in 330 bread wheat cultivars. The diverse HarvestPlus Association Mapping (HPAM) panel was phenotyped in a range of environments in India and in Mexico. The GWAS analysis revealed more than 30 marker-trait associations (MTA) for grain Zn in wheat. Interestingly two large effect QTL regions were found on 2 and 7 chromosome groups. Moreover, 3 to 4 known candidate genes associated with Zn homeostasis and metal transporter genes were mapped near these QTL regions. The markers and associated candidate genes identified in this study are being validated in new biparental mapping populations and breeding materials. 47、Allelic Contributions of TaPHS1 and TaMKK3 to Pre-Harvest Sprouting Resistance in Montana Spring and Winter Wheats Justin Vetch Montana State University Pre-harvest sprouting (PHS) is the precocious germination of grain prior to harvest which negatively impacts seed and end use quality. PHS is evaluated in two ways: visual inspection or the falling number (FN) test. A low FN value denotes starch degradation caused by PHS. This negatively impacts producer prices resulting in global losses of up to $1 billion per year. Thus, identifying wheat varieties which are PHS resistant is important. The first goal of our project was to screen Montana wheat varieties for FN and PHS tolerance. Our second goal is to investigate the contribution of allelic variation in the TaPHS1 and TaMKK3 genes which have been reported to be associated with PHS. A PHS screening method was developed and used to screen ~50 Montana grown spring and winter wheat varieties. During the PHS screening, high variability in PHS was observed in both spring and winter wheat varieties. Among MT grown winter wheats, TaPHS1 allelic variation was associated with significant PHS variation. MT grown spring wheats did not vary for the previously reported TaPHS1 resistant and susceptible alleles. Both spring and winter wheats varied for TaMKK3 alleles with those carrying the resistant allele trending lower in PHS. We hypothesize that there is unpublished allelic variation in TaPHS1 contributing to PHS variation in MT spring wheats and we are currently identifying additional TaPHS1 sequence variants. The results of this study will be used to develop PHS resistant spring and winter wheat varieties adapted to Montana. 48、Unique Sources of Resistance to Fusarium Head Blight for Durum Wheat George Fedak Agriculture and Agri-Food Canada There was a major epidemic of FHB in the durum wheat crop in Canada in 2016. There is not as much variability for FHB resistance in the primary gene pool of T. durum as there is in bread wheat. In a recent screening of synthetic hexaploids and their parents for FHB resistance by point inoculation, a number of T. dicoccon accessions appeared to have enhanced levels of FHB resistance. The floret infection frequencies ranged from 10-12% while the values for Langdon durum were 73%. These inoculations were repeated for a second time with similar results. The T. dicoccon accessions were accessed from various gene banks. Records indicate that some of these accessions were collected in Russia and Georgia in the 1930s by N. I. Vavilov and deposited in the genebanks. As would be expected from T. dicoccon accessions collected in the wild, some are deficient in useful agronomic traits. For example some are very tall and others have smaller spikes. However such traits could easily be removed by a few backcrosses so as to minimize any linked drag. On the other hand other accessions had very large seeds, a trait that could be an asset to a breeding program. Another potential source of FHB resistance for durum wheat is that found in the amphiploid Triticum durum x Hordeum chilense with the genomes AABBHH. This source of resistance will be more difficult to integrate into durum wheat. 49、QTL Mapping of Flag Leaf-Related Traits in Wheat ( Triticum aestivum L.) Jinkun Du China Agricultural University This study aimed to advance our understanding of the genetic mechanisms underlying morphological traits of the flag leaves of wheat ( Triticum aestivum L.). A recombinant inbred line (RIL) population derived from ND3331 and the Tibetan semi-wild wheat Zang1817 was used to identify quantitative trait loci (QTL) controlling flag leaf length (FLL), flag leaf width (FLW), flag leaf area (FLA) and flag leaf angle (FLANG). Using an available high-density simple sequence repeat (SSR) genetic linkage map, 24 putative QTL for FLL, FLW, FLA, and FLANG were detected on chromosomes 1B, 2B, 3A, 3D, 4B, 5A, 6B, 7B, and 7D. Individual QTL explained 4.2–68.52% of the phenotypic variance in different environments. Four QTL for FLL, two for FLW, four for FLA and five for FLANG were detected in at least two environments. Eighteen QTL for flag leaf-related traits originated from ND3331 alleles, and six originated from Zang1817 alleles. QTL with pleiotropic effects or multiple linked QTL were also identified on chromosomes 1B, 4B, and 5A; these are potential target regions for fine mapping and marker-assisted selection in wheat breeding programs. 50、Identifying Novel Genetic Sources for FHB Resistance in Ontario Wheat Harwinder Singh Sidhu University of Guelph Fusarium head blight (FHB) caused by Fusarium graminearum is one of the most detrimental diseases of wheat ( Triticum aestivum L.). Reduced yield due to fusarium damaged kernels and mycotoxin contamination causes significant economic loss. Inadequate disease control strategies render breeding for FHB resistant wheat varieties as a favorable approach. The objective of this research is to identify the genomic regions associated with FHB resistance in a Canadian Winter Wheat Diversity Panel (n=450) and develop genomic selection models for FHB resistance breeding. The diversity panel was phenotyped in two FHB nurseries in Ontario, in 2017. The disease incidence ranged from 10% to 100% with an average of 65%. Disease severity ranged from 7% to 100% with an average of 25% 21 days after inoculation. The diversity panel was genotyped using the 90K Illumina iSelect chip, which provided dense coverage for all chromosomes with more than 50K markers. Phylogenetic trees, Principal Component Analysis, and STRUCTURE analysis alluded to the presence of population structure in the panel. Genome-wide association studies, following correction for population structure, identified a genomic region on chromosome 5A (698 mbp, maf 0.43) associated with FHB severity, in addition to other suggestive QTLs in multiple chromosomes. This research is expected to further the development of a source wheat germplasm as well as optimizing a genomic selection breeding strategy for FHB resistance breeding. 51、Genome-Wide Association Mapping of Phenotype Traits Related to Phosphorus Use Efficiency in Synthetic Hexaploid Wheat Emily K. Gordon University of Guelph Phosphorus (P) is a non-renewable macronutrient required for many plant processes, where P fertilizer uptake rates are typically 30% of what is applied. Not only are current application rates unsustainable, fertilizer application from agriculture production is a major source of P loading into water bodies around the world. Breeding for more P efficient crops may improve the P balance efficiency of the entire cropping system by preventing dissolved P from being lost, exported and accumulated in the field. As a major cereal crop worldwide, wheat ( Triticum aestivum L.) yields must continue to increase in order to meet expected food demands under lower P inputs. Wheat has the potential to be improved in terms of its genetic diversity for P use efficiency. To investigate this, a panel of 194 synthetic hexaploid wheat (SHW) derived accessions from the International Maize and Wheat Improvement Centre (CIMMYT) were genotyped with the Illumina iSelect 90k single nucleotide polymorphism (SNP) chip and phenotyped under 0 and 60 kg P ha-1 in three trials over two years in Ontario, Canada. We identified genomic regions on chromosomes 2B and 5B associated with yield under high P. Additionally, a region on chromosome 3B showed association with P deficiency tolerance. Further identification of genomic regions associated with the phenotypic traits analysized in this study will be presented. 52、A Tailored Quantitative Genetic Framework Reveals the Important Role of Epistatic Effects for Grain Yield Heterosis Yong Jiang Leibniz Institute of Plant Genetics and Crop Plant Research Increasing wheat yield is a key global challenge to produce sufficient food for a growing human population. Wheat grain yield can be boosted by exploiting heterosis, the superior performance of hybrids over the midparent values. Here we present a tailored quantitative genetic framework to study the genetic basis of midparent heterosis in hybrid populations based on crosses among diverse parents and applied it to a particularly extensive dataset assembled for winter wheat. Grain yield was assessed for 1,604 hybrids and their 135 parental elite breeding lines in 11 environments. The hybrids outperformed on average the midparent values by 10%. This equals approximately fifteen years of breeding progress in wheat, thus further substantiating the remarkable potential of hybrid wheat breeding. Genome-wide prediction and association mapping implemented based on the developed quantitative genetic framework revealed that dominance effects played a less prominent role than epistatic effects for grain yield heterosis in wheat. 53、Genetic Mapping of Leaf Rust Resistance in the Tetraploid Wheat Cross Strongfield/Blackbird Xiangyu Pei University of Manitoba Leaf rust, caused by Puccinia triticina *Eriks. ( Pt ), is an economically important disease of wheat worldwide. Deploying wheat cultivars with effective leaf rust resistance (Lr) genes is an efficient method for disease management. The genetic basis of leaf rust resistance was studied a doubled haploid (DH) population of the cross Strongfield/Blackbird. Strongfield is a widely grown durum wheat variety ( Triticum turgidum* var. durum *L.; genome AABB) in Canada, which was developed at Agriculture and Agri-Food Canada, Swift Current. Strongfield is highly resistant to *Pt in Canada. Blackbird ( Triticum carthlicum ; genome AABB) is susceptible to Pt at the seedling stage but possesses partial adult plant resistance. The genetic basis of leaf rust resistance was studied in a doubled haploid (DH) population of the cross Strongfield/Blackbird which was previously genotyped with SSR markers and the 90K wheat Infinium SNP array. Four QTLs were found on chromosomes 1B, 2B, 3A, and 3B based analysis of leaf rust reaction from inoculated field nurseries in 2016 and 2017. This population was then screened for leaf rust resistance with multiple races at the seedling stage indoors . One Lr gene was identified on chromosome 3A, mapping to the same location as the 3A QTL detected with the field leaf rust data. 54、Deciphering Structural Variations in the Wheat Genome Using Resequencing Data Romain De Oliveira INRA GDEC Structural variations (SVs) such as copy number and presence-absence variations (CNVs, PAVs) are polymorphisms that are known to be involved in the expression of phenotypes. In the absence of a reference genome sequence, their study has long been hampered in wheat. The recent advent of new wheat genomic resources has led to a paradigm shift, making possible to investigate the extent of SVs among cultivated and wild populations. Our project aims at characterizing SVs in a Triticeae diversity panel of 44 accessions from seven tetraploid and hexaploid Triticeae species. To cope with the wheat genome complexity, we developed strategies combining shotgun sequencing of sorted chromosomes 3B with bioinformatics tools and we studied SVs affecting not only genes but also transposable elements (TEs). Our results show that 14% of the genes are variable within this panel. In addition, they reveal a very high level of intra- and interspecific variability affecting TEs, contrasting with the weak polymorphism rate usually reported with SNPs. Chromosomal extremities are the regions where we see most of the variability, confirming previous hypotheses made when comparing wheat with the other grasses. 55、Diversity of Responses of Wheat to Heat Stress as Revealed by Grain Transcriptome Profiling Parimalan Rangan ICAR Adapting major crops to climate change requires an understanding of the influence of temperature on plant performance. Wheat is a crop that often matures in a warming environment and is prone to heat stress especially late in the growth of the crop. We have examined the impact of heat stress at mid and late seed development using the transcriptome of the developing wheat grain. Genotypes displayed remarkable diversity in response at the transcript level and in the associated impact on grain size and yield. Genotypes also displayed differences in the timing of susceptibility to heat stress. Short periods of heat stress and longer periods of continuous high temperatures may require different genetic adaptation. Higher temperatures are likely to impact not only on wheat productivity but also on the composition of the wheat grain. This has implications for both the functional (especially end use quality) and nutritional quality of the grain. However, these studies suggest significant potential to select genotypes that are better adapted to heat stress and provide a better understanding of the genetic basis of heat stress tolerance. 56、Hi-C and Chromosome-Scale Assembly to Detect Large Chromosomal Rearrangements in Wheat Genomes Cécile Monat Leibniz Institute of Plant Genetics and Crop Plant Research High-quality sequence assemblies of multiple individuals have emerged as important tools towards a deeper understanding of the full diversity within a species. The comprehensive and robust assessment of the different type of variation based on sequence assemblies can only be achieved through the collection of genome-wide sequence data with complementary technologies that retain information about physical linkage between sequence fragments. In the context of the Wheat Ten plus Genomes Project, in which we are assembling at pseudomolecules level wheat genomes with the final goal to get on overview of the wheat pan-genome, we are studying structural variation in bread wheat ( Triticum aestivum L.). We have developed a pipeline to use chromosome capture (Hi-C) sequencing data to construct chromosome-scale sequence assemblies. Hi-C uses three-dimensional contact probabilities of chromatin in the nucleus to reconstruct the linear order of sequence scaffolds. The first step of our pipeline is the alignment of Hi-C data to a genetically anchored sequence assembly. Subsequently, residual misassemblies are detected and corrected and chromosome-scale physical genome maps are constructed from Hi-C contact matrices. Here, we present the outcome of this computational pipeline for three wheat cultivars. Highly contiguous sequence assemblies of three wheat genomes with scaffold N50 values 10 Mb were constructed using the DeNovoMAGIC™ technology (NRGene, Ness Ziona, Israel) from paired-end and mate-pair Illumina data as well 10X Chromium linked-reads. These assemblies were ordered into 21 pseudomolecules representing 95 % of the genome using Hi-C. Sequence alignments and Hi-C contact matrices revealed megabase-scale chromosomal rearrangements between cultivars such as inversions and inter-chromosomal translocations. 57、Characterization of Meiosis and the Pairing Homoeologous 1 ( Ph1 ) Locus in Wheat Sateesh Kagale National Research Council Canada Meiotic recombination between related but diverged sequences (homoeologous recombination) influences genome stability in polyploid crop species and the ability to introgress desirable traits through inter-specific crosses. Disruption of genetic barriers, such as sequence divergence and strict regulation of chromosome pairing, is the key to enable ‘genetic accessibility’ of natural variation and introgression of favorable traits from related or wild species into polyploid crops. In wheat, a single locus on Chromosome 5B known as Ph1 ( pairing homoeologous 1 ) controls orderly pairing of homologous chromosomes during meiosis. A Ph1 deficient stock in Chinese Spring (CS- Ph1b ) produced through radiation treatment has been used for inducing homoeologous recombination between wheat chromosomes and their alien homoeologues. Using the reference genome sequence of wheat and RNA sequencing of meiocytes from CS and Cs- Ph1b , we have identified the complete repertoire of genes in the Ph1 locus region. Comprehensive structural and expression analysis of these genes suggest Ph1 is a complex locus carrying multiple candidate genes with redundant functions. These findings along with our efforts towards (1) characterizing gene regulatory networks that are specifically involved in complex chromosome pairing behavior and subsequent recombination initiation during meiosis in wheat, (2) suppression of Ph1 through mutagenesis in an elite wheat cultivar, and (3) developing pollen based single cell genomic sequencing approach for monitoring recombination frequency in F1 wheat plants will be discussed. 58、Vitamin A Biofortification of Wheat Grains using a TILLING Mutant-Based Approach Shu Yu University of California, Davis Vitamin A deficiency (VAD) has been widely recognized as a major public health problem in many parts of the world. While wheat provides about 20% of dietary calories and proteins worldwide, wheat grains (particularly endosperm/flour) are generally low in vitamins (e.g. provitamin A) and minerals. We are breeding for increased accumulation of beta-carotene, a provitamin A molecule, in tetraploid wheat grain endosperm using induced mutations. Our spatial gene expression analysis indicated that specific carotenoid metabolic gene homoeologs are involved in beta-carotene accumulation in wheat grain endosperm. We have also isolated Targeting Induced Local Lesions in Genomes (TILLING) mutants of the carotenoid metabolic gene homoeologs. Building upon the molecular knowledge and the genetic resources, we are currently determining the contribution of the key carotenoid metabolic gene homoeologs, singly and in combination, to beta-carotene accumulation in the endosperm using TILLING mutants. Our results on gene expression analysis and progress on mutant identification and characterization will be presented. 59、TaZIM1, a Major QTL and Novel Negative Regulator of Heading Date and Kernel Weight, Experienced Strong Selection during Wheat Breeding Xueyong Zhang Institute of Crop Sciences, Chinese Academy of Agricultural Sciences Heading date is a critical determinant of regional adaptation for crops and it has a significant impact on crop yield. We identified an atypical GATA-like transcription factor,* TaZIM1* as a negative regulator of wheat heading. We showed that TaZIM1 possesses a weak transcription repression activity and its CCT domain functions as the major inhibitory region. Expression of TaZIM1 demonstrated a typical circadian clock oscillation pattern under different illumination conditions. Overexpression of TaZIM1 *in wheat causes a delay in the heading date and a decrease of thousand kernel weight (TKW) under long-day conditions. Moreover, TaZIM1 can directly bind to the promoters of *TaCO1 and TaFT and down-regulate their expression. Sequence analysis of common wheat cultivar collection identified three and two haplotypes for TaZIM1-7A and TaZIM1-7B , respectively. Association analysis revealed that TaZIM1-7A-HapI/Hap-III and TaZIM1-7B-HapI have undergone strong positive selection during modern breeding probably due to their association with earlier heading and higher TKW. We developed diagnostic markers for these haplotypes, which can be utilized in further improvement of wheat cultivars via marker-assisted breeding. 60、Leveraging the Tetraploid Wheat Genomes for Cloning Cdu-B1 , a Major Gene for Cd Accumulation in Durum Wheat Grain Sean Walkowiak University of Saskatchewan Cadmium (Cd) accumulation in the grain of durum wheat presents a serious concern for human health. As a result, durum wheat breeding programs select for low grain Cd. Differences in Cd accumulation among cultivars of durum wheat are attributed to the major-effect gene Cdu-B1 located on chromosome 5B. The objective of this study was to identify the functional determinant of Cdu-B1 . The fine mapped interval for Cdu-B1 was anchored to the complete genome sequences of the durum cultivar ‘Svevo’ (a high Cd accumulator) and the wild emmer wheat accession ‘Zavitan’ (a low Cd accumulator). A sequence comparison of Cdu-B1 between Svevo and Zavitan revealed a gene candidate, HMA3-B1 . This gene encodes a P1B-ATPase transition metal transporter and contains a 17 bp duplication in the first exon in Svevo relative to the wild-type allele in Zavitan. A molecular marker for the 17 bp duplication was used to evaluate a diverse set of breeding lines from global breeding programs and was able to identify low and high Cd accumulators with perfect precision. Furthermore, functional assays using yeast expression systems confirm a role for the wild-type HMA3-B1 gene in regulating Cd accumulation in grain by mediating vacuolar Cd sequestration. In addition, the 17 bp duplication allele present in high Cd genotypes was non-functional. The molecular marker developed from this work is currently deployed in global breeding programs to develop wheat lines with low grain Cd.
1 The Reference Sequence for the Bread Wheat Genome Frederic Choulet INRA GDEC The generation of a high-quality reference genome sequence for bread wheat, linked to genetic and genomic resources, has been the goal of the International Wheat Genome Sequencing Consortium (IWGSC) since its foundation in 2005. Here, we report on the assembly and deep analysis of the 21 chromosomes of the allohexaploid bread wheat cv. Chinese Spring: IWGSC RefSeq v1.0. We used an Illumina-based whole genome shotgun approach integrated with a wealth of community resources and were able to assemble 21 high-quality pseudomolecules representing 94% of the predicted wheat genome size, with a scaffold N50 of 23 Mb. We predicted 107,886 high confidence gene models and ~4 million transposable elements accounting for 85% of the genome. Comparative analyses of the A-B-D sub-genomes revealed no subgenome dominance, and a highly conserved gene set although only 55% of the homeologous groups correspond to 1:1:1 triplets, meaning that A-B-D have been strongly impacted by lineage-specific gene duplications. Insights into gene expression have been described through a transcriptome atlas developed from 850 RNASeq datasets representing all stages of wheat phenological development. With a sequence assembly that now supports the resolution of complex gene families associated with important traits, the community now has a key resource in place for future research and breeding. 2、Characterisation of the Pentatricopeptide Repeat Protein Family in the Wheat IWGSC Refseq v1.0 Reference Genome Joanna Melonek The University of Western Australia The family of pentatricopeptide repeat (PPR) proteins is one of the largest gene families in flowering plants and has agronomical importance as a source of restorer of fertility (Rf) genes used to suppress cytoplasmic male sterility during the development of F1 hybrids. Typically, flowering plant genomes contain 550-700 PPR genes, in the wheat IWGSC RefSeq v1.0 reference genome we found 1686 PPRs. The large number of PPR genes is primarily due to polyploidy and it’s actually lower than expected from simply adding genes present in the progenitor diploid genomes. This implies PPR gene inactivation and loss during polyploidization, for which we found evidence in the form of truncated or frame-shifted gene fragments. 207 PPRs were identified as restorer of fertility-like (RFL) genes in the wheat reference genome, far more than in any other plant genome analysed to date. We show that locations of some of the previously mapped restorer genes overlap with the genomic locations of RFL clusters identified in our study. This is the first comprehensive analysis of the PPR and RFL families in wheat. The sequence knowledge gained from this project has the potential to accelerate hybrid wheat breeding programs by facilitating the identification of active restorer genes in potential restorer lines. Hybrid wheat varieties are expected to have higher and more consistent yields by better adaptation to increasingly unpredictable weather conditions in the era of global climate change. 3、Map-Based Cloning of Powdery Mildew Resistance QTL Introgressed to Bread Wheat from the Timopheevi Group Reveals a Highly Divergent Region with Suppressed Recombination containing a Cluster of NLR Gene Homologues Miroslav Valárik Institute of Experimental Botany Introgression of QPm.tut-4A locus from Triticum militinae into the distal end of bread wheat chromosome 4AL confers improved resistance against powdery mildew. The locus was high-density mapped and delimited to 0.024 cM using 8327 individuals and 75 markers. Using additional 2052 ph1 *lines seven new recombinations were identified. After chromosome walking, final flanking markers *owm169 *and *owm228 were mapped and the region was found 640.8 kbp and 480.2 kbp long in cv. Chinese Spring (CS) and *T. militinae *(TM), respectively. The cM/Mb ratio is much smaller compared to these commonly found at the end of wheat chromosomes. The sequenced region was annotated and 16 and 12 protein coding genes were identified in CS and TM, respectively. Out of them, seven CS and six TM genes were not syntenic. Furthermore, intergenic regions do not show a significant similarity between CS and TM. The TM region containing the remaining six genes has a syntenic counterpart in CS, but that region was duplicated and one of the duplications was inverted. The duplication and inversion were accompanied by gene loss and four of the TM genes have their counterparts in both duplicated regions in CS. Finally, three genes from the CS region do not have their homologs in the TM region. These structural and sequence differences are major reasons for the discrepancy between the expected and observed cM/Mb ratio. This work was supported by award LO1204 from the National Program of Sustainability I and by the Estonian Ministry of Agriculture. 4、Hunting Yellow Rust Resistance Genes in Bread Wheat Clemence Marchal John Innes Centre Achieving wheat yields to meet current and future demands is crucial. This, however, remains challenging in part due to the numerous pathogens threatening wheat production, including yellow (stripe) rust ( Puccinia striiformis fsp tritici; Pst ). Despite over 70 designated yellow rust resistance genes (Yr) in wheat, few have been cloned. This lack of knowledge hinders efficient marker assisted breeding and exploitation of novel allelic variation. We recently exome sequenced a mutant population of UK cultivar Cadenza which carries the major gene Yr7 . Screening 1,000 mutagenized individuals with Pst identified seven susceptible lines presumed to carry mutations in Yr7 . To test this, mutational resistance gene enrichment sequencing (MutRenSeq) was conducted on the susceptible lines and a candidate for Yr7 was identified. Taking advantage of the IWGSC RefSeqv1.0 assembly, we quickly determined the physical position of the closest Chinese Spring homolog within the Yr7 region and confirmed this linkage in an F2 population. Previously, Yr5 was proposed to be allelic to Yr7 . Therefore, a similar approach was carried out on Yr5 susceptible mutants and a single candidate gene, different from Yr7 , was identified. The Yr5 homolog is located in close physical proximity to Yr7 on IWGSC RefSeqv1.0. This suggests that Yr5 and Yr7 are very closely linked genes rather than true alleles. The closest homologs to both Yr7 and Yr5 reside in a complex disease resistance cluster in RefSeqv1.0. We will present a phylogenetic analysis of this resistance gene cluster in Chinese Spring and additional commercial varieties and discuss the implications for breeding. 5、Reconstructing Wheat Evolutioanry History Caroline Pont INRA Polyploidization have been reported as a major evolutionary force during plant paleohistory. Following the triplication reported in *Brassiceae *~10 million years ago, and at the basis of rosids ~100 million years ago, bias in organisation and regulation, known as subgenome dominance, has been reported between the three post-polyploidy compartments referenced to as less fractionated (LF), medium fractionated (MF1) and more fractionated (MF2), that have been proposed to derive from an hexaploidization event involving ancestor intermediate of 7-14-21 chromosomes. Modern bread wheat experienced similar paleohistory during the last half million year of evolution opening a new hypothesis where the wheat genome is at the earliest stages on the road of diploidization through subgenome dominance driving asymmetry in gene content, gene expression abundance, transposable element content as dynamics and epigenetic regulation between the A, B and D subgenomes. 6、Tetraploid Wheat Germplasm Diversity SCAN Based on the Durum Wheat Genome Assembly Marco Maccaferri DipSA, Department of Agricultural Science, University of Bologna The genome of modern durum wheat (DW) cultivar Svevo has been assembled based on a combination of whole genome shotgun sequencing (270X), NRGene deNovoMagic assembler, high-resolution genetic mapping obtained from the cross between Svevo DW and Zavitan wild emmer wheat (WEW) and scaffold ordering based on chromosome conformation capture sequencing (Hi-C). The assembly consisted of 9.96 Gb of ordered sequences with 66,559 high-confidence (HC) genes. We used this resource to investigate the genetic diversity and ancestry of tetraploid wheat germplasm. iSelect 90K SNP array was used to genotype a global collection of 1,858 non-redundant accessions covering the whole range of tetraploid genetic resources from WEW, cultivated emmer (CEW), durum landraces (DWL) and modern durum cultivars (DWC). We performed a whole-genome scan for population genetic structure, selective sweeps together with the tetraploid QTLome projection. Average whole-genome genetic diversity were pWEW= 0.285, pCEW = 0.254, pDWL = 0.201, pDWC = 0.192, with an overall WEW-DWC decrease in diversity equal to 32.6%. Diversity depletions were more relevant in peri-centromeric regions (pWEW_C = 0.269, pDWC_C = 0.151) as compared to the highly-recombinogenic distal regions (pWEW_R = 0.287, pDWC_R = 0.250). From WEW to DWC, 68 chromosome regions were subjected to diversity depletion, affecting up to 38% of the genome in total: 19 of these were associated to WEW-CEW transition, 41 to CEW-DWL and 8 to DWL-DWC. The gene content of these regions is being explored in relation to known QTL content and haplotype analysis. Overall, the analysis pointed out the chromosome regions subjected to strong selective sweeps during the domestication and breeding selection, on one side, and those regions that would benefit from targeted genetic diversity restoration on the other side. 7、Exploring Epigenomic Diversity in Polyploid Wheat Laura-Jayne Gardiner Earlham Institute Wheat has been domesticated into a large number of agricultural environments, a key question is what drives the ability for crops to rapidly adapt. To address this question, we survey genotype and DNA methylation across the core Watkins bread wheat landrace collection that is representative of global wheat genetic diversity. We identify independent variation in methylation, genotype and transposon copy number. These three sources of variation are likely to be driving phenotypic differences across this diverse wheat collection. Methylation and transposon diversity could therefore be used alongside single nucleotide polymorphism (SNP) based markers for breeding. 8、Mutations in the Branched Head Homoeo-Allele Bht-B1 Modify Inflorescence Architecture in Tetraploid Wheat Gizaw M Wolde Leib-Inst Plant Gen Crop Plant Res Inflorescence morphology directly affects the reproductive success and yield of crops. The wheat inflorescence, also known as spike, forms an unbranched inflorescence where individual spikelets are arranged distichously on the central axis of the spike, the rachis. Previously, we reported the causative mutation in the branched headt ( bht ) gene of tetraploid wheat ( TtBH-A1 ) being responsible for the loss of spikelet meristem identity, converting the non-branching wheat spike into a branched spike. Since spike-branching in wheat is a quantitatively inherited trait, we further performed whole-genome quantitative trait loci (QTL) analysis and Genome Wide Association Scans (GWAS) based on 146 recombinant inbred lines (RILs) and a collection of 302 tetraploid wheat accessions, respectively. Results showed that besides the previously found gene at the bht-A1 locus on the short arm of chromosome 2A, mutations in the homoeologous gene, TtBH-B1 , was linked to the increased penetrance and expressivity of the supernumerary spikelet (SS) and /or mini-spike formation during spike-branching thereby increasing spikelet and grain number per plant. Furthermore, we developed bht-A1 *Near Isogenic Lines ( bht-A1-*NILs) using an elite durum wheat cultivar, Floradur, for the molecular genetic dissection of the wheat spike morphogenesis and the agronomic implications of the homoeo-allele(s) for increasing grain yield production in wheat. 9、Wheat Leaf Rust Resistance Gene from Marquis Wheat Brent McCallum Agriculture and Agri-Food Canada Marquis wheat, released in 1911, was one of the most widely grown cultivars in Canada and the north-central USA. It was susceptible to all leaf rust ( Puccinia triticina ) isolates tested, up to the emergence of a group of races in the early 2000s, predominantly TDBG. Marquis had an unusual mesothetic resistance phenotype when inoculated with TDBG. To characterize this resistance the Marquis backcross line RL6071was crossed with a leaf rust resistant accession from the Kyoto University wheat germplasm collection KU168-2 to create a doubled haploid population. Seedling resistance from RL6071 was inherited as a single resistance gene that mapped to chromosome 7BL. Tightly linked molecular markers, along with seedling leaf rust testing and pedigree analysis revealed that this gene, temporarily named LrMar , was present in Marquis, Red Fife and a number of cultivars derived from Red Fife, such as White Fife, Percy and Renfrew. The same group of races that were avirulent to LrMar were also avirulent to LrCen , previously mapped to 7AL, with a similar mesothetic infection type. Both genes are only effective against this small group of P. triticina isolates, are ineffective in conditioning field resistance against the broader Canadian population, and neither were detected prior to the emergence of these races. These could be homeologous resistance genes based on their respective positions on chromosomes 7BL and 7AL, and phenotypic similarities. 10、The Genome of Triticum urartu , a Progenitor of Wheat a Genome Hong-Qing Ling Institute of Genetics and Developmental Biology, CAS Triticum urartu , a wild diploid wheat, is the progenitor of the A subgenome of tetraploid and hexaploid wheat. Ample genetic studies have shown the value of T. urartu for investigating the structure, function, and evolution of polyploid wheat genomes. Here, we report the generation of a high-quality genome sequence of T. urartu by combining BAC-by-BAC sequencing, single molecule real-time (SMRT) sequencing, and next-generation mapping (BioNano genome map and 10x Genomics linked reads) technologies. We produced seven chromosome-scale pseudomolecules that spanned 4,666 Mb and annotated 37,516 high confidence and 3,991 low confidence protein-coding genes. By comparing collinear segments between T. urartu and its grass relatives rice, sorghum, and Brachypodium , we propose an evolution model of T. urartu chromosomes, and found that T. urartu and Brachypodium *were independently evolved from the grass ancestor with 12 chromosomes. Furthermore, the ancient genome duplications, which are well maintained in rice, sorghum, and *Brachypodium, were strongly corrupted in T. urartu because of extensive amplifications of transposable elements and widespread gene loss. Overall, the T. urartu genome sequence described here provides a valuable reference for systematic studies of Triticeae genomes and for genetic improvement of wheat. 11、Identification of QTLs Associated with Kernel Texture Variation in a Soft-Kernel Durum Wheat ( Triticum turgidum ssp. durum ) Population Maria Itria Ibba Washington State University Kernel texture is one of the major determinants of wheat quality. This trait is primarily controlled by the Puroindoline genes, located at the Hardness ( Ha ) locus on the short arm of chromosome 5D. However additional factors contribute to minor variations in endosperm texture. Durum wheat ( Triticum turgidum *sbsp. *durum ) lacks the Ha *locus and, therefore, its kernels exhibit an extremely hard texture that limits its end-uses. Recently, the *Puroindoline *genes from the chromosome 5DS of common wheat ( T. aestivum* L.) were introgressed into the durum wheat cultivar Langdon through the Ph1b -mediated homoelogous recombination, thus obtaining soft-textured kernel durum wheat lines. In the present study, soft durum wheat line Langdon 1-678 was crossed with the durum wheat variety Creso. The progeny were analyzed for kernel texture through the single kernel characterization system (SKCS) and only the lines exhibiting a hardness index (HI) 40 were advanced, obtaining 590 soft-textured kernel F6 lines. These lines were phenotyped through SKCS and exhibited a wide variation of kernel hardness (HI ranging from -0.3 to 37). In order to identify the genetic factors associated with variation of this phenotype, the same lines were genotyped using a targeted amplicon sequencing (TAS) approach. The identification of QTLs significantly associated with kernel hardness is in progress. To date, this is the first study to investigate the genetic control at the basis of endosperm texture in durum wheat. These results will facilitate the selection of soft durum wheat lines with superior milling properties and novel end-use applications. 12、Development and Validation of a Single Nucleotide Polymorphic Marker for the Yield Component Kernel Weight in Wheat Santosh Kumar Agriculture and Agri-Food Canada Canada is a major producer and exporter of hard red spring (HRS) wheat. The HRS wheat is well known for its excellent milling and baking quality. With high protein requirement in the HRS class of wheat, it lags in yield compared to other classes of wheat. Yield is of utmost importance to producers and is one of the primary focuses of wheat breeding programs. An important yield component is the thousand kernel weight (TKW) and is highly heritable. Selection for high TKW in early generations of wheat breeding is effective, but is difficult to access phenotypically due to limited seed availability. Marker-assisted selection (MAS) using single nucleotide polymorphisms (SNPs) and insertion-deletion (indels) mutations will allow selection in early generations breeding lines based on genotype. Kompetitive Allele Specific PCR (KASP) assays based on SNPs and indels are high-throughput, easy to use, and requiring limited amounts of DNA. Trehalose-6-phosphate (T6P) is a regulator of starch accumulation, the most important contributor of TKW. Trehalose 6-phosphate phosphatase (T6PP) activity can affect T6P levels, and a wheat T6PP gene has been cloned. This gene was found to be polymorphic in Chinese accessions of wheat using a cleaved amplified polymorphic sequence assay and linked to TKW. Here we developed a much simpler and high-throughput KASP assay and showed that this gene is polymorphic in Canadian wheat germplasm. This should allow selection for TKW in early generations of wheat breeding in Canada. 13、Genome-Wide Homology Analysis Reveals New Insights into the Origin of the Wheat B Genome Wei Zhang North Dakota State University Wheat is a typical allopolyploid with three homoeologous subgenomes (A, B, and D). The ancestors of the subgenomes A and D had been identified, but not for the subgenome B. The goatgrass Aegilops speltoides (genome SS) has been controversially considered a candidate ancestor of the wheat B genome. However, the relationship of the Ae. speltoides S genome with the wheat B genome remains largely obscure, which has puzzled the wheat research community for nearly a century. In the present study, we performed genome-wide homology analysis to assess the B-S relationship using an integrative molecular cytogenetics and comparative genomics approach. Noticeable homology was detected between wheat chromosome 1B and Ae. speltoides chromosome 1S, but not between other chromosomes in the B and S genomes. An Ae. speltoides -originated segment spanning a genomic region of approximately 10.46 Mb was identified on the long arm of chromosome 1B (1BL) in all wheat species containing the B genome. The Ae. speltoides -originated segment on 1BL was found to co-evolve with the rest of the B genome in wheat species. Thereby, we conclude that Ae. speltoides had been involved in the origin of the wheat B genome, but should not be considered an exclusive ancestor of this genome. The wheat B genome might have a polyphyletic origin with multiple ancestors involved, including Ae. speltoides . These findings provide new insight into the origin and evolution of the wheat B genome, and will facilitate genome studies in wheat and its relatives. 14、Comparison of Durum Wheat and Wild Emmer Genomes Provides Insights into Genomic Diversity in Tetraploid Wheat Luigi Cattivelli CREA - Research Centre for Genomics and Bioinformatics The domestication of wild emmer wheat ~10,000 years ago by early agrarian societies led to the selection of modern durum wheat widely grown today, mainly for pasta. We report the fully-assembled genome of a modern durum wheat variety (cv. Svevo) and present, via comparison with the previously published genome of wild emmer accession Zavitan, a genome-wide account of the modifications imposed by 10,000 years of selection and breeding. The durum wheat genome was assembled with the NR-Gene DeNovoMAGICTM pipeline (N50 = 6 Mb) and ordered by chromosome conformation capture sequencing (Hi-C), resulting in 14 pseudomolecules plus one group of unassigned scaffolds. A total of 66,559 high-confidence (HC) genes have been identified on the durum wheat assembly. This first genome-wide comparison between a wild and cultivated form of tetraploid wheat revealed several thousand copy-number and presence-absence variations with significantly expanded gene families in durum wheat (e.g. for disease resistance), as well as of widespread polymorphism with putative impacts on gene function. While the gene sets of durum wheat and wild emmer are highly similar, the compositions of the pseudogene sets differ in both number and enrichment for particular GO categories. Inspection at the pseudogenes in syntenic regions of durum wheat and wild emmer indicates potentially distinct duplication and pseudogenization dynamics. The comparison of the two genomes offers an overall picture of the genomic diversity between the cultivated tetraploid wheat and its wild relative progenitor. 15、Genomic Dissection of Nonhost Resistance to Wheat Stem Rust in Brachypodium distachyon Rafael Della Coletta University of Campinas Wheat stem rust caused by the fungus Puccinia graminis f.sp. tritici ( Pgt ) is a devastating disease that has largely been controlled for decades by the deployment of resistance genes. However, new races of this pathogen have emerged that overcome many important wheat stem rust resistance genes used by breeding programs, and their spread toward major wheat production areas poses a threat to global wheat production. Nonhost resistance in plants, which provides durable and broad-spectrum resistance to non-adapted pathogens, holds great promise for helping to control wheat stem rust, but the genetic and molecular basis of nonhost resistance is poorly understood. This study employed the model plant Brachypodium distachyon (Brachypodium), a nonhost of Pgt , to genetically dissect nonhost resistance to wheat stem rust. Using bulked segregant analysis, next-generation sequencing, cumulative allele frequency differences and statistical analysis, seven quantitative trait loci (QTL) that contribute to stem rust resistance were identified in a recombinant inbred population derived from a cross between two Brachypodium genotypes with differing levels of resistance. The QTL effects vary in their magnitude, and act both additively and in some cases interact, indicating that the resistance is genetically complex. The delineation of regions of the Brachypodium genome that harbor these QTLs will guide future research aiming to identify genes essential to the nonhost resistance response and their mechanisms of action. 16、Development of a Complete Set of Wheat-Barley Group-7 Robertsonian Translocation Chromosomes Conferring an Increased Content of ß-Glucan Tatiana V. Danilova Kansas State University Many valuable genes for agronomic performance, disease resistance and increased yield have been transferred from relative species to wheat ( Triticum aestivum L.) through whole-arm Robertsonian translocations (RobT). Although of a great value, the sets of available translocations from barley ( Hordeum vulgare L.) are limited. Here we present the production of a complete set of six compensating RobT chromosomes involving barley chromosome 7H and three group-7 chromosomes of wheat. The barley group-7 long arm RobTs had a higher grain ß-glucan content compared to the wheat control. The ß-glucan levels varied depending on the temperature and were higher under hot conditions. Implicated in this increase, the barley cellulose synthase-like F6 gene ( CslF6 ) responsible for ß-glucan synthesis was physically mapped near the centromere in the long arm of barley chromosome 7H. Likewise, wheat *CslF6 *homoeologs were mapped near the centromere in the long arms of all group-7 wheat chromosomes. With the set of novel wheat-barley translocations, we demonstrate a valuable increase of ß-glucan, along with a resource of genetic stocks that are likely to carry many other important genes from barley into wheat. 17、Nitrogen Use Efficiency Is Regulated By Interacting Proteins Relevant to Development in Wheat Lei Lei Oklahoma State University Nitrogen (N) is the most important nutrient for plant development and growth, and soil is often supplemented with N fertilizer to ensure successful seed production and high grain yield for non-N-fixing food crops such as wheat ( Triticum aestivum L.). Only 30–35% of added N fertilizers are taken up and used by wheat plants in the year of application, and the remaining 65–70% (assuming fertilizer–soil equilibrium) is lost. Developing varieties of wheat that require less N input yet maintain the same or higher grain yield is an economically and environmentally sustainable goal in international agriculture. In this study, a major quantitative trait locus (QTL) for N-related agronomic traits was cloned from wheat. The vernalization gene TaVRN-A1 was tightly linked with the gene at the QTL. Due to the Ala180/Val180 substitution, Ta VRN-A1a and Ta VRN-A1b proteins had differential interactions with Ta ANR1 protein, which is encoded by a wheat orthologue of Arabidopsis nitrate regulated 1 ( ANR1 ). A natural mutant of TaANR1 was found which is missing exon 6 in its mRNA, which had genetic effect on wheat development and growth. The transcripts of both TaVRN-A1 and TaANR1 were down-regulated by N. Genetically incorporating favorable alleles from TaVRN-A1 , TaANR1 , and TaHOX1 increased grain yield from 9.83% to 11.58% in a winter wheat population tested in the field. 18、Gene and Trait Discovery for Improvement of Processing and Nutrition Quality in Wheat Anuradha Singh National Institute of Plant Genome Research (NIPGR) Bread wheat (Triticum aestivum L.) is one of the most important food crops in the world, and its flour processed into various end-use food products such as bread, biscuits, and chapatti. The suitability of wheat grains for end-uses are largely affected by the biochemical composition of seeds including storage proteins, starch, and photochemical and hence, it indirectly affects the processing, cooking, and organoleptic qualities of wheat seed. Knowledge of genetics and molecular basis of processing quality related traits are important for their improvement. Thus, the present investigation was designed for the identification of candidate genes related to processing quality through genome-wide transcriptome analysis of wheat during seed development. The study also emphasizes the understanding of expression pattern of starch metabolic genes during seed development and the correlation of variation in physical and biochemical traits of seeds and the physicochemical properties of starches on large sets of Indian wheat varieties. Genome-wide transcriptome study using 61k wheat genome arrays in developing seeds of wheat genotypes identified 110 candidate probe sets for processing quality mainly chapatti. Further, quantitative expressions of the 25 starch metabolic genes, during seed development also identify the highly expressed key genes of starch metabolism, which are candidates for a development of markers for starch quality. Thus, these candidate genes would be useful for designing wheat improvement programs for processing quality or nutrition quality either by changing their expression (over-expression, silencing or genome editing) or development of bi-parental mapping populations for molecular breeding. Further, Physical (kernel length, kernel width and thousand kernel weights), Biochemical (total starch content, amylose content, total protein content and starch granules associated proteins) and Physico-chemical (starch granules size distribution, swelling power, starch solubility, Pasting, thermal, and gelatinization) traits of diverse sets of Indian wheat varieties and starch isolated from them showed strong correlation with each other. The detail analysis of these properties could lead to an appropriate selection of wheat cultivar, well-adapted to industrial end-uses, without encountering processing or end-products quality problems and with most cost-competitive production. 19、Wheat miR9678 Controls Seed Germination By Generating Phased ta-siRNAs and Modulating Abscisic Acid/Gibberellin Signaling Yingyin Yao China Agricultural University Seed germination is important for wheat yield and quality. However, our knowledge of mechanisms regulating seed germination in wheat remains limited. In this study, we found microRNA9678 (miR9678) is specifically expressed in the scutellum of developing and germinating wheat seeds. Overexpression of miR9678 delays germination and improves resistance to pre-harvest sprouting (PHS) in wheat; miR9678 silencing enhances germination rates. miR9678 triggers phased trans-acting small interfering RNAs (ta-siRNAs) by cleaving the long non-coding RNA, and ta-siRNAs also delay seed germination. In addition, miR9678 overexpression also reduces bioactive gibberellin (GA) levels through a ta-siRNAs independent mechanism. Finally, abscisic acid (ABA) signaling proteins bind the promoter of miR9678 precursor and activate its expression, indicating miR9678 regulates germination by modulating the GA/ABA signaling. 20、A Genome Wide Association Study for Yield Traits in Soft Red Winter Wheat Dylan Lee Larkin University of Arkansas Wheat (*Triticum aestivum *L.) is a widely produced grain crop, significantly contributing to global food security. As the global population continues to grow, so will the demand for food. In order to meet such demands, breeders must work to increase wheat yield potential. Wheat yield can be impacted by multiple quantitative traits which rely on several quantitative trait loci (QTL). A genome wide association study (GWAS) was conducted on 360 inbred soft red winter wheat genotypes adapted to the southern United States in an association mapping panel (AMP) in order to identify novel QTL associated with wheat yield traits, including yield, test weight, heading date, maturity date, and plant height. The AMP was grown over eight location-years between 2013 and 2017 in randomized complete block and augmented designs. Each location-year was evaluated for the five aforementioned traits impacting yield. Best linear unbiased estimates for the five traits were obtained from a spatial linear mixed model for each location-year and combined to obtain best linear unbiased predictions from SAS 9.4 software. Genotype-by-sequencing (GBS) identified 71,428 high quality single nucleotide polymorphisms (SNP) markers across all 21 wheat chromosomes. Marker-trait associations will be determined using the FarmCPU function in R software. Data analysis for the five phenotypic traits are still in progress. Marker-trait associations will also be performed in the near future, resulting in potential SNP that can be implemented by the University of Arkansas wheat breeding and genetics program through marker assisted selection or genomic selection in order to improve wheat yield. 21、Exploring Allelic Diversity Underlying Breeding Progress in European Wheat Kai P Voss-Fels The University of Queensland Despite the remarkable successes that were achieved in the history of wheat breeding, future wheat production remains challenging. Climatic changes that lead to unprecedented extreme weather scenarios are accompanied by a rising disease pressure and a declining fertiliser availability. While the dramatic global population growth necessitates a significant further improvement of wheat productivity in the upcoming decades, a stagnation of wheat yield increases has recently been reported in all major production areas worldwide. This has mainly been attributed to a drastic loss of genetic diversity in elite breeding pools due to strong selective breeding and intensive germplasm exchange. At the same time there are public concerns that modern agriculture can only sustain productivity under extremely high resource inputs involving chemical fertilisers and plant protection, while the actual impact of genetic improvements remains elusive. Here, we present the first large-scale investigation of the impact of wheat breeding on all major trait complexes in a historic panel of almost 200 registered European winter wheat varieties, including important representatives of the last five decades of winter wheat production. Presenting phenotype data from multiple locations and three different cropping systems that range from fully extensive to fully intensive, we are able to demonstrate the great impact of genetic improvement on performance increase under any environmental scenario. Linking this to genome-wide marker information we are able to track the influence of artificial selection on genetic parameters throughout the history of wheat breeding and to define target regions with the highest impacts on agronomically important traits. Our study gives first insights into the genetic basis of the improvement of high-yielding winter wheat and assesses the potential for further genetic gain in the European elite germplasm pool in the short- and mid-term 22、Development of Wheat-*Haynaldia villosa *Alien Chromosome Lines and their use in Gene Mining and Wheat Breeding Xiue Wang Nanjing Agricultural University Wild relatives provide rich gene resources for wheat breeding.* Haynaldia villosa (2n=14, genome VV), is a diploid wild species and has proved to be resistant to several wheat diseases, such as powdery mildew, wheat yellow mosaic etc. The development of alien translocation lines conferring useful genes is the most effective way for the utilization of alien genes. In Cytogenetics Institute if Nanjing Agricultural University, a research platform for the induction of alien chromosome structural variation and for effective identification of alien chromatin has been established. A wheat- H. villosa* alien translocation pool was constructed and the their chromosome constitution was characterized. Genes conferring resistances to powdery mildew, wheat yellow mosaic virus, strip rust as well as loci controlling grain quality has been assigned specific regions of H. villosa chromosomes. The whole arm translocation lines carrying useful genes have been released and utilized in breeding programs. Using the T6VS/6AL translocation carrying the powdery mildew resistance gene Pm21 and the strip rust resistance gene Yr26 , about 30 wheat varieties have been developed and commercially released in China. 23、Characterization, Validation, and Deployment of Chromosome 6BL and 7AL QTLs for Grain Yield Components in Hard Winter Wheat Andrew M. Katz Colorado State University The United Nations has estimated that food production will need to double by 2050 to adequately feed a global population of 9 billion people. Improvements in wheat yields, which account for 30% of coarse grain production, will be essential to meet this goal. Yield is a complex trait due to a multitude of influential factors. To address this complexity we have identified individual yield components that are less complex and contribute to overall yield. A GWAS of a hard winter wheat association-mapping panel identified QTLs on the 7AL chromosome arm for spikelet number and the 6BL chromosome arm for kernel width. The Great Plains winter wheat cultivar Platte and experimental line CO940610 were identified as polymorphic in the 7AL and 6BL regions. A population of recombinant inbred lines was generated from the two parents and used to validate the 7AL and 6BL QTLs’ effects. Individual SNPs have been identified which will be used to introgress spikelet number and kernel width QTL into Colorado advanced lines and high biomass lines from the International Maize and Wheat Improvement Center (CIMMYT). Exome sequencing data generated from the parental lines will enable high-resolution mapping of the causative genetic variant underlying these QTL. The employment of novel genomic tools and resources enable unprecedented opportunities to identify allelic variation underlying individual yield components in wheat. This will ultimately aid in the development of higher yielding wheat varieties. 24、Genetic Basis of the Short Life Cycle of ‘Apogee’ Wheat Carol Powers Oklahoma State University ‘Apogee’ is a wheat cultivar that was developed for utilization of the NASA-ALSS food system and has the shortest life cycle in wheat in the world, with flowering only 25 days after planting under long day conditions and constant warm temperature without vernalization. This growth habit can be utilized to accelerate breeding cycles. It is intriguing to unravel the genetic mystery of this agronomic characteristic. In this study, Apogee was crossed with a strong winter wheat cultivar ‘Overland’, and over 800 F2 plants were generated and tested in a greenhouse under temperature and photoperiod controlled conditions. Apogee was found to have vrn-A1a and vrn-D3a that are the same alleles as observed in the winter wheat cultivar ‘Jagger’, Vrn-B1 that has a deletion in intron one, and PPD-D1b that is insensitive to photoperiod. The super-short life cycle of ‘Apogee’ wheat resulted from pyramiding of the early alleles for the four flowering time genes, whose effects are vrn-A1 VRN-B1 vrn-D3 PPD-D1 . The dominant vrn-D3a alone was not sufficient to induce the transition from vegetative to reproductive development in winter plants without vernalization, but did accelerate heading in those plants that have been induced by vrn-A1a or Vrn-B1 . This study greatly advanced the molecular understanding of the multiple flowering genes under different genetic backgrounds and provided useful molecular tools that can be used to accelerate winter wheat breeding schemes. 25、Hybrid Wheat from a Practical Breeder’s Perspective P. Stephen Baenziger Department of Agronomy and Horticulture, University of Nebraska-Lincoln Hybrid wheat has proven to be elusive. From its previous highpoint in the 1980s, currently, only a few companies are producing hybrids in Europe, India, and South Africa. However, interest in hybrids has recently increased due to the need for greater and more efficient production to meet the projected future needs coupled with the availability of advanced breeding tools and insights. While most hybrid wheat discussions concentrate on the theoretical or genetic aspects, this talk will present how an applied wheat breeder is trying to make hybrid wheat a reality. Hybrid wheat requires: converting a self-pollinated crop into a cross-pollinated crop, the ability to make experimental hybrids, the use of genome-wide molecular markers and theory to develop genome-based high-yielding heterotic groups and patterns augmented by improved crossing block designs such as balanced incomplete factorial, and a path to commercial hybrid production. Preliminary results indicate that pollinator lines with good pollen shed can be readily found in existing breeding programs and anther extrusion genes can be mapped in doubled haploid populations from crosses that greatly differ in anther extrusion; identifying pollen receptive lines need more research perhaps through using genetic male sterility and random-mating populations; chemical hybridizing agents can be used to make experimental hybrids in sufficient seed quantity for multi-location trials; the genome-wide markers and algorithms are being developed to build heterotic groups which like maize will need to be bred, not discovered; and chemical hybridizing agents and cytoplasmic male sterility systems appear to be commercially viable. 26、The Interplay Among Subgenomes Shapes Genomic Variations and Transcriptomic Changes during Wheat Hexaploidization Events Mingming Xin CHINA AGRICULTURAL UNIVERSITY Genomic variations and transcriptomic changes extensively occur in newly formed polyploids to reconcile immediate challenges caused by divergent subgenomes in one nucleus. To comprehensively investigate sequence elimination and expression alteration in wheat hexaploidization, here we performed whole exome capture experiments coupled with high throughput sequencing analysis by exploiting three sets of newly synthesized wheat species. We observed that the whole wheat chromosomes was subjected to extensive genomic elimination partially regulated by sequence homology in response to hexaploidization. But homeologous subgenomes exhibited distinct features that DNA sequences were preferentially eliminated on DD genome compared with AA and BB genome. In addition, a higher proportion of eliminated sequences occurred in exonic regions than in intergenic regions on DD genome, whereas a significant enrichment was observed in the repeat-rich intergenic regions for AA and BB genome, exhibiting a contrast distribution pattern compared to the gene density. Furthermore, we detected 488 overlapped genes with sequence elimination on DD genome but few on the other two genomes across three nascent hexaploid wheats. Interestingly, GO enrichment analysis showed genes with sequence elimination were enriched in distinct functional pathways between subgenomes. Transcriptome analysis indicates polyploidization enhanced gene expression differentiation between root and leaf and led to rapid and extensive gene expression changes in synthetic hexaploid wheat. AA and BB genome exhibited synergistic expression profiling which was distinct from DD genome, and interestingly, expression bias was observed for a proportion of homeologs in synthetic hexaploid wheat. Strikingly, only 3.3-23.6% genes with sequence elimination exhibited expression changes in synthetic hexaploid wheat compared with their respective progenitors, indicating genomic variation is not the major cause resulting in the transcirptomic changes during wheat polyploidization events, whereas epigenetic modifications might play an important role in regulating expression profiling alterations. 27、Delimitation of Wheat ph1b Deletion and Development of the ph1b-Specific DNA Markers Yadav Gyawali North Dakota State University The Ph1 (pairing homoeologous) locus has been considered a major genetic system responsible for the diploidized meiotic behavior of the allohexaploid genome in wheat. It functions as a defense system against homoeologous pairing in meiosis of polyploid wheat. A large deletion of the genomic region harboring the Ph1 locus on the long arm of chromosome 5B (5BL) led to the ph1b mutant in hexaploid wheat ‘Chinese Spring’ (CS), which has been widely used to induce meiotic homoeologous pairing/recombination for gene introgression from wild grasses into wheat. However, knowledge of the breakpoints and actual physical size for the ph1b deletion remains limited. In the present study, we first anchored the deletion region on 5BL by wheat 90K SNP assay, and then delimited the deletion to a genomic region of 60,014,523 bp by chromosome walking. The nucleotide positions of the distal and proximal breakpoints (DB and PB) were identified for the ph1b deletion. This will facilitate understanding of the genetic and molecular mechanism underlying the Ph1 activity in wheat. In addition, we developed user-friendly molecular markers specific for the ph1b deletion based on the DNA sequences immediately proximal to PB and distal to DB. These ph1b deletion-specific markers have dramatically improved the efficacy of the ph1b mutant in the meiotic recombination-based gene introgression and genome studies in wheat and its relatives. Also, these markers have been used to assist selection in the introgression of the ph1b deletion from CS into adapted wheat genotypes. 28、Efficient Wheat Transformation Can be Performed on Cold-Conserved Immature Hybrid Embryos Robin Michard INRA UMR 1095 GDEC Bread wheat is one of the three most cultivated crops in the world and a major economic challenge. However, since a few years, wheat production has reached a plateau. Despite the major role of conventional breeding programs in crop improvement, genetic engineering has become the fastest way to introduce new and well-characterized genes in plants leading researchers to elaborate each day new genetic transformation protocols. As wheat has become a new model plant for crop studying, especially in the word of genetic transformation, the need for an efficient protocol is without appeal. The present study aims to propose improvement of current immature embryo Biolistic® transformation protocols using cold conservation and hybrid immature embryos. We were able to show that using 4°C conservation for immature embryo storage do not affect regeneration and transformation efficiency. Moreover, using immature hybrid embryos can allow simultaneous transformation of two wheat genotypes, even if one of the genotypes is recalcitrant to genetic transformation. We think that those processes can be generalized to optimize wheat Biolistic® protocols. 29、Effect of Glutenin Genes and Glutenin Gene By Environmental Interaction on Quality in Spring Wheat Emily Delorean Department of Plant Pathology, Kansas State University Wheat quality, comprised of milling yield, dough and baking quality, is a critical objective in the spring wheat breeding program at the International Maize and Wheat Improvement Center (CIMMYT). The glutenin genes encode the proteins that are part of the gluten matrix that gives rise to strength, extensibility and elasticity for which wheat dough is famous and are known to be an important determinate in processing and end-use quality. Previous studies have found significant genotype, environment and genotype by environment effects on grain quality traits. Recently, these same trends were also found in a population of 56 hard spring wheat lines grown in 6 environments representing 2 levels each of irrigation, drought or heat stress. It was hypothesized that glutenin genes were underlying the significant genotype effects and glutenin alleles may interact with environments. The effects of glutenin alleles as well as the environment by glutenin effects on quality were tested with a mixed linear model on this population. Glutenin loci were found to have a significant association with most grain quality phenotypes, with the high molecular weight glutenins ( Glu-A1 , Glu-B1 , and Glu-D1 ) having larger effects. Additionally, the glutenin by environment interaction was significant for some of the glutenin loci. The results of this study confirm that glutenin alleles do underlie some of the genotype effect on quality traits in wheat and different glutenin alleles are performing different in contrasting environments. This information can help breeders at CIMMYT to target wheat quality profiles of lines to specific environments. 30、VERNALIZATION1* Modulates Root System Architecture in Wheat and Barley Lee Hickey Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland As the primary interface for resource acquisition, plant roots play a key role in growth regulation. Evidence from rice, maize and sorghum demonstrates that the below-ground plant architecture significantly impacts plant performance under abiotic constraints. Roots assume critical functions in water uptake, nutrient acquisition and anchorage, an essential characteristic to maintain plant stability under increased grain load. Despite their fundamental importance, knowledge about genetic control of root growth in major grain crops is limited and very little is known about interactions between below-ground and above-ground plant development. Here we demonstrate that VERNALIZATION1 *( VRN1*), a key regulator of flowering behavior in cereals, also modulates root architecture in wheat and barley. Associations of *VRN1 *haplotypes to root growth habit were discovered in wheat by genome-wide association studies, and confirmed by allelic analyses in wheat and barley populations. Functional characterization in transgenic barley confirmed that *VRN1 *influences root growth angle directly, via gravitropism. These discoveries provide unexpected insight into underground functions of a major player in the well-characterized flowering pathway, revealing the intersection of above-ground gene regulation with the largely unexplored genetic architecture of plant root development. Understanding the pleiotropic involvement of this key developmental gene in overall plant architecture will help to breed cereal cultivars adapted to specific environmental scenarios.
2018年第一周小麦文献推荐（1.7） 本期作者 麦萌 小麦生信联盟 Hi,大家好！欢迎来到一周一次的小麦文献推荐。今天是2018年的第一次推荐，在此有必要对此简单的介绍下。首先，我们周一至周六会解读一些文献，但是限于我们主编的背景知识，在选择文献上可能具有一定的偏好性，再加上现在小麦研究越来越热门，发表的文章也会越来越多，研究的质量也会越来越高，所以总是会漏掉一些文献，这些漏掉的文献不代表不重要。为了弥补这个遗憾，我们特别在周末汇总这一周和小麦相关的文献，供大家浏览和参考，这些文献有些可能会被我们解读，有些则不会。每一篇文献会有题目，作者，发表杂志以及摘要信息，供大家决定是否需要进一步阅读。 想要特别声明一点，无论是我们推荐的文章还是我们做过导读的文章，都不能代替您亲自读文章，不能代表您对这篇文章的思考。同样一篇文献，每个人get到的点一定不一样。一个人多次阅读文章，可能每次引起的思考也会不同。 突然想起来颜宁说过她在国外上课时，老师都会给一些经典的生物文献，并且要求找出文献的问题。这种训练教会她学会质疑。科学没有挑战权威的质疑精神，就不可能有创新。同样的，这种讨论也应该存在于导师指导过程中，学生也要敢于向导师说出自己的想法，也许会由于思虑不周或欠缺相关背景知识而显得幼稚，或者观点错误，这些都没关系，立即改正过来就行。当然了，实际情况可能要复杂，导师也不是你想要和他讨论他就能和你讨论的。导师也是一个普通人，每个人都有自己的风格。 说的多了，我们正式开始我们的文献推荐。 1 Genetic diversity and virulence of wheat and barley strains of Xanthomonas translucens from the Upper Midwestern United States Bacterial leaf streak (BLS) of wheat and barley, caused by Xanthomonas translucens pv. undulosa and Xanthomonas translucens pv. translucens, has been of growing concern in small grains production in the Upper Midwestern United States. To optimize disease resistance breeding, a greater awareness is needed of the pathovars and genetic diversity within the pathogens causing BLS in the region. Multilocus sequencing typing (MLST) and analysis (MLSA) of four common housekeeping genes (rpoD, dnaK, fyuA and gyrB) was used to evaluate the genetic diversity of 82 strains of X. translucens isolated between 2006 and 2013 from wheat, barley, rye and intermediate wheatgrass. In addition, in planta disease assays were conducted on 75 strains to measure relative virulence in wheat and barley. All strains were determined by MLSA to be related to X. translucens pv. undulosa and X. translucens pv. translucens. Clustering of strains based on Bayesian, network, and minimum spanning trees correlated with relative virulence levels in inoculated wheat and barley. Thus, phylogeny based on rpoD, dnaK, fyuA and gyrB correlated with host of isolation and was an effective means for predicting virulence of strains belonging to X. translucens pv. translucens and X. translucens pv. undulosa. 2 Analysis of contributors to grain yield in wheat at the individual quantitative trait locus level In wheat, strong genetic correlations have been found between grain yield (GY) and tiller number per plant (TN), fertile spikelet number per spike (FSN), kernel number per spike (KN) and thousand-kernel weight (TKW). To investigate their genetic relationships at the individual quantitative trait locus (QTL) level, we performed both normal and multivariate conditional QTL analysis based on two recombinant inbred lines (RILs) populations. A total of 79 and 48 normal QTLs were identified in the International Triticeae Mapping Initiative (ITMI)/SHW-L1 9 Chuanmai 32 (SC) populations, respectively, as well as 55 and 35 conditional QTLs. Thirty-two QTL clusters in the ITMI population and 18 QTL clusters in the SC population explained 0.9%– 46.2% of phenotypic variance for two to eight traits. A comparison between the normal and conditional QTL mapping analyses indicated that FSN made the smallest contribution to GY among the four GY components that were considered at the QTL level. The effects of TN, KN and TKW on GY were stronger at the QTL level. 3 Genome-Wide Association Mapping of Loci for Resistance to Stripe Rust in North American Elite Spring Wheat Germplasm Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a major yield-limiting foliar disease of wheat (Triticum aestivum) worldwide. In this study, the genetic variability of elite spring wheat germplasm from North America was investigated to characterize the genetic basis of effective all-stage and adult plant resistance (APR) to stripe rust. A genome-wide association study was conducted using 237 elite spring wheat lines genotyped with an Illumina Infinium 90K single-nucleotide polymorphism array. All-stage resistance was evaluated at seedling stage in controlled conditions and field evaluations were conducted under natural disease pressure in eight environments across Washington State. High heritability estimates and correlations between infection type and severity were observed. Ten loci for race-specific all-stage resistance were confirmed from previous mapping studies. Three potentially new loci associated with race-specific all-stage resistance were identified on chromosomes 1D, 2A, and 5A. For APR, 11 highly significant quantitative trait loci (QTL) (false discovery rate 0.01) were identified, of which 3 QTL on chromosomes 3A, 5D, and 7A are reported for the first time. The QTL identified in this study can be used to enrich the current gene pool and improve the diversity of resistance to stripe rust disease. 4 Fluorescence in situ hybridization karyotyping reveals the presence of two distinct genomes in the taxon Aegilops tauschii The distribution of sites hybridizing to the two probes oligo-pTa-535 and (CTT)10 split the Ae. tauschii accessions into two clades, designated Dt and Ds, which corresponded perfectly with a previously assembled phylogeny based on marker genotype. The Dt cluster was populated exclusively by ssp. tauschii accessions, while the Ds cluster harbored both ssp. strangulata and morphologically intermediate accessions. As a result, it is proposed that Ae. tauschii ssp. tauschii is restricted to carriers of the Dt karyotype: their spikelets are regularly spaced along the rachis, at least in the central portion of their spike. Accessions classified as Ae. tauschii ssp. strangulata carry the Ds karyotype; their spikelets are irregularly spaced. Based on this criterion, forms formerly classified as ssp. tauschii var. meyeri have been re-designated ssp. strangulata var. meyeri . According to the reworking of the taxon, the bread wheat D genome was most probably donated by ssp. strangulata var. meyeri . Chromosomal differentiation reveals intra-species taxon of Ae. tauschii . Ae. tauschii ssp. tauschii has more distant relationship with breed wheat than ssp. strangulata and can be used for breeding improving effectively. 5 Asymmetrical changes of gene expression, small RNAs and chromatin in two resynthesized wheat allotetraploids Polyploidy occurs in some animals and all flowering plants including important crops such as wheat. The consequences of polyploidy on crops remain elusive partly because their progenitors are unknown. Using two resynthesized wheat allotetraploids SlSlAA and AADD with known diploid progenitors, we analyzed mRNA and small RNA transcriptomes in the endosperm, compared transcriptomes between endosperm and root in AADD, and examined chromatin changes in the allotetraploids. In the endosperm, there were more nonadditively expressed genes in SlSlAA than in AADD. In AADD, nonadditively expressed genes were developmentally regulated, and the majority (62-70%) were repressed. The repressed genes in AADD included a group of histone methyltransferase gene homologs, which correlated with reduced histone H3K9me2 levels and activation of various transposable elements in AADD. In SlSlAA, there was a tendency of expression dominance of Sl over A homoeologs, but the histone methyltransferase gene homologs were additively expressed, correlating with insignificant changes in histone H3K9me2 levels. Moreover, more 24-nt small inferring RNAs (siRNAs) in the A subgenome were disrupted in AADD than in SlSlAA, which were associated with expression changes of siRNA-associated genes. Our results indicate that asymmetrical changes in siRNAs, chromatin modifications, transposons, and gene expression coincide with unstable AADD genomes and stable SlSlAA genomes, which could help explain evolutionary trajectories of wheat allotetraploids formed by different progenitors. 6 Genetic characterization of type II Fusarium head blight resistance derived from transgressive segregation in a cross between Eastern and Western Canadian spring wheat Fusarium head blight (FHB) caused by Fusarium graminearum is a devastating disease affecting global wheat production, causing significant losses to yield and grain quality. The Eastern Canadian line FL62R1 was developed using a systemic breeding approach and boasts high levels of FHB resistance with good yield, desirable agronomics, and end-use quality traits. The objective of this study was to identify genetic determinants of type II resistance in a cross between FL62R1 and cv. Stettler, a Canada Western Red Spring variety rated moderately susceptible to FHB. Although neither parent displayed strong resistance to FHB spread within spikes following point inoculation (type II resistance) in greenhouses, strong type II resistance was observed in a large number of progeny, including 6% with resistance comparable to the best check line, Sumai 3. Quantitative trait locus (QTL) mapping identified a locus from chromosome 2BL of Stettler which provides Sumai 3 level type II resistance when combined with favorable FHB resistance QTLs with minor effects from FL62R1. This study provides insight into transgressive segregation for FHB, which despite its importance is poorly understood, rare, and difficult to predict. It also begins to dissect the genetic architecture of FHB resistance in wheat derived from the systemic breeding approach. 7 Brassinosteroids Modulate Meristem Fate and Differentiation of Unique Inflorescence Morphology in Setaria viridis(狗尾草,禾本科) Inflorescence architecture is a key determinant of yield potential in many crops and is patterned by the organization and developmental fate of axillary meristems. In cereals, flowers and grain are borne from spikelets, which differentiate in the final iteration of axillary meristem branching. In Setaria spp., inflorescence branches terminate in either a spikelet or a sterile bristle, and these structures appear to be paired. In this work, we leverage Setaria viridis to investigate a role for the phytohormones brassinosteroids (BRs) in specifying bristle identity and maintaining spikelet meristem determinacy. We report the molecular identification and characterization of the Bristleless 1 (Bsl1) locus in S. viridis, which encodes a rate-limiting enzyme in BR biosynthesis. Loss-of-function bsl1 mutants fail to initiate a bristle identity program, resulting in homeotic conversion of bristles to spikelets. In addition, spikelet meristem determinacy is altered in the mutants, which produce two florets per spikelet instead of one. Both of these phenotypes provide avenues for enhanced grain production in cereal crops. Our results indicate that the spatiotemporal restriction of BR biosynthesis at boundary domains influences meristem fate decisions during inflorescence development. The bsl1 mutants provide insight into the molecular basis underlying morphological variation in inflorescence architecture. 8 Critical and speculative review of the roles of multi-protein complexes instarch biosynthesis in cereals Starch accounts for the majority of edible carbohydrate resources generated through photosynthesis. Amylopectin is the major component of starch and is one of highest-molecular-weight biopolymers. Rapid and systematic synthesis of frequently branched hydro-insoluble amylopectin and efficient accumulation into amyloplasts of cereal endosperm is crucial. The functions of multiple starch biosynthetic enzymes, including elongation, branching, and debranching enzymes, must be temporally and spatially coordinated. Accordingly, direct evidence of protein-protein interactions of starch biosynthetic enzymes were first discovered in developing wheat endosperm in 2004, and they have since been shown in the developing seeds of other cereals. This review article describes structural characteristics of starches as well as similarities and differences in protein complex formation among different plant species and among mutant plants that are deficient in specific starch biosynthetic enzymes. In addition, evidence for protein complexes that are involved in the initiation stages of starch biosynthesis is summarized. Finally, we discuss the significance of protein complexes and describe new methods that may elucidate the mechanisms and roles of starch biosynthetic enzyme complexes. 9 Developmental responses of bread wheat to changes in ambient temperature following deletion of a locus that includes FLOWERING LOCUS T1 FLOWERING LOCUS T ( FT ) is a central integrator of environmental signals that regulates the timing of vegetative to reproductive transition in flowering plants. In model plants, these environmental signals have been shown to include photoperiod, vernalization and ambient temperature pathways, whilst in crop species the integration of the ambient temperature pathway remains less well understood. In hexaploid wheat, at least 5 FT-like genes have been identified, each with a copy on the A, B and D genomes. Here we report the characterization of FT-B1 through analysis of FT-B1 null and over-expression genotypes under different ambient temperature conditions. This analysis has identified that the FT-B1 alleles perform differently under diverse environmental conditions; most notably the FT-B1 null produces an increase in spikelet and tiller number when grown at lower temperature conditions. Additionally, absence of FT-B1 facilitates more rapid germination under both light and dark conditions. These results provide an opportunity to understand the FT-dependent pathways that underpin key responses of wheat development to changes in ambient temperature. This is particularly important for wheat, for which development and grain productivity is sensitive to changes in temperature. 10 On the Origin of the Non-brittle Rachis Trait of Domesticated Einkorn Wheat Einkorn and emmer wheat together with barley were among the first cereals domesticated by humans more than 10,000 years ago, long before durum or bread wheat originated. Domesticated einkorn wheat differs from its wild progenitor in basic morphological characters such as the grain dispersal system. This study identified the Non-brittle rachis 1 ( btr1 ) and Non-brittle rachis 2 ( btr2 ) in einkorn as homologous to barley. Re-sequencing of the Btr1 and Btr2 in a collection of 53 lines showed that a single non-synonymous amino acid substitution (alanine to threonine) at position 119 at btr1 , is responsible for the non-brittle rachis trait in domesticated einkorn. Tracing this haplotype variation back to wild einkorn samples provides further evidence that the einkorn progenitor came from the Northern Levant. We show that the geographical origin of domesticated haplotype coincides with the non-brittle domesticated barley haplotypes, which suggest the non-brittle rachis phenotypes of einkorn and barley were fixed in same geographic area in today’s South-east Turkey. 11 Pyramiding of transgenic Pm3 alleles in wheat results in improved powdery mildew resistance in the field Allelic Pm3 resistance genes of wheat confer race-specific resistance to powdery mildew ( Blumeria graminis f. sp. tritici , Bgt ) and encode nucleotide-binding domain, leucine-rich repeat (NLR) receptors. Transgenic wheat lines overexpressing alleles Pm3a, b, c, d, f, and g have previously been generated by transformation of cultivar Bobwhite and tested in field trials, revealing varying degrees of powdery mildew resistance conferred by the transgenes. Here, we tested four transgenic lines each carrying two pyramided Pm3 alleles, which were generated by crossbreeding of lines transformed with single Pm3 alleles. All four allele-pyramided lines showed strongly improved powdery mildew resistance in the field compared to their parental lines. The improved resistance results from the two effects of enhanced total transgene expression levels and allele-specificity combinations. In contrast to leaf segment tests on greenhouse-grown seedlings, no allelic suppression was observed in the field. Plant development and yield scores of the pyramided lines were similar to the mean scores of the corresponding parental lines, and thus, the allele pyramiding did not cause any negative effects. On the contrary, in pyramided line, Pm3b × Pm3f normal plant development was restored compared to the delayed development and reduced seed set of parental line Pm3f. Allele-specific RT qPCR revealed additive transgene expression levels of the two Pm3 alleles in the pyramided lines. A positive correlation between total transgene expression level and powdery mildew field resistance was observed. In summary, allele pyramiding of Pm3 transgenes proved to be successful in enhancing powdery mildew field resistance. 12 Chemical hybridizing agent SQ-1-induced male sterility in Triticum aestivum L.: a comparative analysis of the anther proteome We performed proteomic analyses using the wheat Triticum aestivum L.to identify those proteins involved in physiological male sterility (PHYMS) induced by the chemical hybridizing agent CHA SQ-1. A total of 103 differentially expressed proteins were found by 2D–PAGE and subsequently identified by MALDI-TOF/TOF MS/MS. In general, these proteins had obvious functional tendencies implicated in carbohydrate metabolism, oxidative stress and resistance, protein metabolism, photosynthesis, and cytoskeleton and cell structure. In combination with phenotypic, tissue section, and bioinformatics analyses, the identified differentially expressed proteins revealed a complex network behind the regulation of PHYMS and pollen development. Accordingly, we constructed a protein network of male sterility in wheat, drawing relationships between the 103 differentially expressed proteins and their annotated biological pathways. To further validate our proposed protein network, we determined relevant physiological values and performed real-time PCR assays. Our proteomics based approach has enabled us to identify certain tendencies in PHYMS anthers. Anomalies in carbohydrate metabolism and oxidative stress, together with premature tapetum degradation, may be the cause behind carbohydrate starvation and male sterility in CHA SQ-1 treated plants. Here, we provide important insight into the mechanisms underlying CHA SQ-1-induced male sterility. Our findings have practical implications for the application of hybrid breeding in wheat. 13 Effects of Three Parastagonospora nodorum Necrotrophic Effectors on Spring Wheat under Norwegian Field Conditions The wheat (Triticum aestivum L.) disease Septoria nodorum blotch (SNB) is caused bythe necrotrophic fungus Parastagonospora nodorum (Berk.) Quaedvlieg, Verkley Crousand causes significant yield and quality losses in several wheat growing regions. Theresistance mechanisms are quantitative and progress in resistance breeding has beenslow. However, gene-for-gene interactions involving necrotrophic effectors (NEs) andsensitivity genes (Snn) are involved, providing hope for more effective breeding. Althoughthe interactions are significant determinants of seedling SNB susceptibility, their role inadult plant leaf blotch resistance in the field is less understood. In this study, the frequencyof SnTox genes was investigated in 62 P.nodorum isolates collected in Norway. A panel of Norwegian and international spring wheat lines and cultivars was screened under natural SNB infection in a mist-irrigated field nurseryacross 7 yr. The lines were infiltrated in the greenhouse with the purified NEs SnToxA,SnTox1, and SnTox3, and the prevalence of corresponding sensitivity was investigated, aswell as correlation between NE sensitivity and resistance level in the field. The frequencies of SnToxA, SnTox1, and SnTox3 in the isolates were 0.69, 0.53 and 0.76, respectively.Sensitivity to SnToxA, SnTox1, and SnTox3 was present in 45, 12, and 55% of the plant material. Sensitivity to SnToxA was associated with significantly higher disease severity in the field than insensitivity. This indicates that elimination of SnToxA sensitivity in the breeding material by effector infiltrations or marker-assisted selection can be an effective way to increase field resistance to SNB. 14 Proteomic analysis of low-molecular-weight glutenin subunits and relationship with their genes in a common wheat variety Although many studies on low-molecular-weight glutenin subunit (LMW-GS) function have been reported, a comprehensive comparison between specific genes and their protein product is still lacking. This study aimed to link the 43 genes isolated from the Korean wheat variety “Jokyoung” in the authors’ previous study to their protein products. Proteins were separated using two-dimensional gel electrophoresis (2-DGE) and identified by tandem mass spectrometry (MS/MS) at the gene haplotype level. Using MS/MS analysis of 17 protein spots, two spots were identified in the Glu-A3 locus and the corresponding haplotype was GluA3-13(Glu-A3c). Six spots were identified in the Glu-B3 locus and the corresponding haplotypes were GluB3-33 and GluB3-43 (Glu-B3h). Eight spots were identified in the Glu-D3 locus and the corresponding haplotypes were GluD3-11, GluD3-21, GluD3-31, GluD3-5, and GluD3-6 (Glu-D3a), and one spot was contaminated with gamma gliadin. Phylogenetic analysis and alignment of nucleotide and amino acid sequences assigned 35 of the 43 genes to seven haplotypes: GluA3-13, GluB3-43, GluD3-11, GluD3-21, GluD3-31, GluD3-42, and GluD3-5. Taken together, except for GluB3-33 and GluD3-6, which were not isolated, linking of each gene to the corresponding protein products at the gene haplotype level was accomplished using proteomic tools and phylogenetic analysis. 欢迎关注“小麦研究联盟”
1/6 本期作者：The Crop Journal The Crop Journal“小麦功能基因组”专辑 中国是世界上最大的小麦种植和消费国家。小麦研究联盟回顾的2017年大事件中与我国小麦科学家相关的占一半以上。但是，革命尚未成功，同志还需努力，特别是随着小麦参考基因组的释放，未来竞争将更加激烈。 The Crop Journal (《作物学报》英文版)致力于刊载作物科学相关领域最新成果和应用技术, 开展国际学术交流, 促进我国作物科学研究水平及国际影响力的提升。The Crop Journal刚刚被SCI收录，我们希望能够在宣传中国小麦研究成果方面尽一份力。因此，我们将于今年2月份推出一期小麦功能基因组专辑。 该专辑详细而又特色地论述了小麦功能基因组，基因组测序、转化和基因组编辑，抗逆，籽粒品质，发育转录组学，小麦病原菌基因组学，以及我国西南地区——中国春故乡的小麦育种历史和经验等。综述文章来自中国农业科学院作物科学研究所、中国科学院遗传与发育生物学研究所、山东大学、中国农业大学、南京农业大学、西北农林科技大学、四川农业大学等单位，撰稿人包括新科院士康振生教授、孙其信校长、夏光敏教授等国内大腕儿，也包括马正强教授、王道文研究员、刘登才教授等国内小麦研究骨干。特约编辑为毛龙研究员、凌宏清研究员。 值得一提的是，李爱丽研究员9岁的女儿创作了本专辑的封面画 ，该画作描述了在初旭映红的麦田上，古老的中国象形字和现代DNA双螺旋交相辉映，寓意着中国小麦功能基因组研究将蒸蒸日上。 本专辑总结了我国小麦人“十五”以来的部分代表性进展，是在多倍体、重复序列多、转化困难、缺乏高质量参考基因组等不利条件下，埋头苦干，不言放弃，取得成就的感人经历的总结，向世界展示了中国小麦基因组研究成果，也是展望小麦功能基因组研究未来和方向的一个窗口。欢迎大家一睹为快啊。 Wheat functional genomics in the era of next generation sequencing: An update Meiling Jia, Jiantao Guan, Zhiwen Zhai, Shuaifeng Geng, Xueyong Zhang, Long Mao, Aili Li Bread wheat is not only an important cereal crop but also a model for study of an allopolyploid plant with a large, highly repetitive genome. Advances in next-generation sequencing (NGS) technology provide needed throughput to conquer the enormous size of the wheat genome. Multiple high quality reference genome sequences will soon be available. Full-scale wheat functional genomics studies are dawning. In this review we highlight the available tools and methodologies for wheat functional genomics research developed with the assistance of NGS technology and recent progress, particularly the concerted effort in generating multiple reference genomes, strategies to attain genome-wide genetic variation, genome-wide association studies, mutant population generation, and NGS-supported gene cloning and functional characterization. These resources and platforms lay a solid foundation for wheat research, leading to a new era of wheat functional genomics that will bridge the gap between genotype and phenotype. Dissection of wheat genomes and gene functions should assist in genomics-assisted selection and facilitate breeding of elite varieties for sustainable agriculture in China and the world. Current advances in genome sequencing of common wheat and its ancestral species Xiaoli Shi, Hong-Qing Ling Common wheat is an important and widely cultivated food crop throughout the world. Much progress has been made in regard to wheat genome sequencing in the last decade. Starting from the sequencing of single chromosomes/chromosome arms whole genome sequences of common wheat and its diploid and tetraploid ancestors have been decoded along with the development of sequencing and assembling technologies. In this review, we give a brief summary on international progress in wheat genome sequencing, and mainly focus on reviewing the effort and contributions made by Chinese scientists. Wheat genome editing expedited by efficient transformation techniques: Progress and perspectives Ke Wang, Bisma Riaz, Xingguo Ye Genome editing is one of the most promising biotechnologies to improve crop performance. Common wheat is a staple food for mankind. In the past few decades both basic and applied research on common wheat has lagged behind other crop species due to its complex, polyploid genome and difficulties in genetic transformation. Recent breakthroughs in wheat transformation permit a revolution in wheat biotechnology. In this review, we summarize recent progress in wheat genetic transformation and its potential for wheat improvement. We then review recent progress in plant genome editing, which is now readily available in wheat. We also discuss measures to further increase transformation efficiency and potential applications of genome editing in wheat. We propose that, together with a high quality reference genome, the time for efficient genetic engineering and functionality studies in common wheat has arrived. Genetic improvement of heat tolerance in wheat: Recent progress in understanding the underlying molecular mechanisms Zhongfu Ni, Hongjian Li, Yue Zhao, Huiru Peng, Zhaorong Hu, Mingming Xin, Qixin Sun As a cool season crop, wheat (Triticum aestivum L.) has an optimal daytime growing temperature of 15 °C during the reproductive stage. With global climate change, heat stress is becoming an increasingly severe constraint on wheat production. In this review, we summarize recent progress in understanding the molecular mechanisms of heat tolerance in wheat. We firstly describe the impact of heat tolerance on morphology and physiology and its potential effect on agronomic traits. We then review recent discoveries in determining the genetic and molecular factors affecting heat tolerance, including the effects of phytohormone signaling and epigenetic regulation. Finally, we discuss integrative strategies to improve heat tolerance by utilization of existing germplasm including modern cultivars, landraces and related species. The landscape of molecular mechanisms for salt tolerance in wheat Meng Wang, Guangmin Xia Wheat is one of the most important food crops, and its yield is seriously restricted by high salinity and other abiotic stresses. Many attempts have been made to elucidate the major physiological processes associated with salt tolerance and to identify the genes controlling the processes. In this review, the major role of high-affinity potassium transporter (HKT) genes in enhancing the salt tolerance of wheat is summarized. The link between maintenance of reactive oxygen species (ROS) homeostasis and salt tolerance through a comprehensive study of a wheat introgression line is examined, and the contribution of a set of genes involved in this process is depicted. New research strategies to uncover the mechanisms underlying salt tolerance in wheat based on recent advances in omics will be discussed. A journey to understand wheat fusarium head blight resistance in the Chinese wheat landrace Wangshuibai Haiyan Jia, Jiyang Zhou, Shulin Xue, Guoqiang Li, Haisheng Yan, Congfu Ran, Yiduo Zhang, Jinxing Shi, Li Jia, Xin Wang, Jing Luo, Zhengqiang Ma Fusarium head blight (FHB) or scab caused by Fusarium graminearum is a major threat to wheat production in China as well as in the world. To combat this disease, multiple efforts have been carried out internationally. In this article, we review our long-time effort in identifying the resistance genes and dissecting the resistance mechanisms by both forward and reverse genetics approaches in the last two decades. We present recent progress in resistance QTL identification, candidate functional gene discovery, marker-assisted improvement of FHB resistant varieties, and findings in investigating association of signal molecules, such as Ca++, SA, JA, and ET, with FHB response, with the assistance from rapidly growing genomics platforms. The information will be helpful for designing novel and efficient approaches to curb FHB. Understanding the lifestyles and pathogenicity mechanisms of obligate biotrophic fungi in wheat: The emerging genomics era Chunlei Tang, Qiang Xu, Mengxin Zhao, Xiaojie Wang, Zhensheng Kang Obligate biotrophic fungi cause serious and widespread diseases of crop plants, but are challenging to investigate because they cannot be cultured in vitro. The two economically important groups of biotrophic fungi parasitizing wheat are the rust and powdery mildew pathogens, but their obligate biotrophic lifestyles and pathogenicity mechanisms are not well understood at the molecular level. With the advent of next generation sequencing technology, increasing numbers of pathogen genomes are becoming available. Research in plant pathology has entered a new genomics era. This review summarizes recent progress in understanding the biology and pathogenesis of biotrophic fungal pathogens attacking wheat based on pathogen genomics. We particularly focus on the three wheat rust and the powdery mildew fungi in regard to genome sequencing, avirulence gene cloning, effector discovery, and pathogenomics. We predict that coordinated study of both wheat and its pathogens should reveal new insights in biotrophic adaptation, pathogenicity mechanisms, and population dynamics of these fungi that will assist in development of new strategies for breeding wheat varieties with durable resistance. Molecular genetic and genomic analysis of wheat milling and end-use traits in China: Progress and perspectives Daowen Wang, Kunpu Zhang, Lingli Dong, Zhenying Dong, Yiwen Li, Abrar Hussain, Huijie Zhai Wheat is the most widely cultivated staple food crop, and multiple types of food derivatives are processed and consumed globally. Wheat grain quality (WGQ) is central to food processing and nutritional value, and is a decisive factor for consumer acceptance and commercial value of wheat cultivars. Hence, improvement in WGQ traits is top priority for both conventional and molecular wheat breeding. In this review we will focus on two important WGQ traits, grain milling and end-use, and will summarize recent progress in China. Chinese scientists have invested substantial effort in molecular genetic and genomic analysis of these traits and their effects on end-use properties. The insights and resources generated have contributed to the understanding and improvement of these traits. As high-quality genomics information and powerful genome engineering tools are becoming available for wheat, more fundamental breakthroughs in dissecting the molecular and genomic basis of WGQ are expected. China will strive to make further significant contributions to the study and improvement of WGQ in the genomics era. Wheat breeding in the hometown of Chinese Spring Dengcai Liu, Lianquan Zhang, Ming Hao, Shunzong Ning, Zhongwei Yuan, Shoufen Dai, Lin Huang, Bihua Wu, Zehong Yan, Xiujin Lan, Youliang Zheng The common wheat landrace Chinese Spring (CS) was made famous by the work of Ernie Sears, a great cytogenetist, who developed a number of CS-based aneuploid series that were used to identify individual wheat chromosomes. Based on this, a standard karyotype and nomenclature system was developed for wheat chromosomes that allowed wheat researchers to analyze and manipulate the wheat genome with unprecedented precision and efficiency. Nevertheless, not much is known about the utilization of CS at its hometown, Chengdu in Sichuan province, during early wheat breeding activity. In this review, we follow the speculation that CS is a selection from the Cheng-du-guang-tou (CDGT) landrace. We provide a description of how CDGT became a founder landrace for wheat breeding activities in early times. We show that CDGT-derived varieties were reinforced genetically by crosses to six more exotic parents. These varieties remained the major elite cultivar for several decades. Later, synthetic hexaploid wheats were introduced into the breeding program, firstly using those from CIMMYT and later using materials produced with local tetraploid wheat and goat grass. Finally, we discuss the strategies and future directions to improve wheat yield and resistance through an expanded genetic basis, especially by recapturing lost genetic variations from landraces and related wild species, a process that may set an example for wheat breeders in China and elsewhere. Mapping stripe rust resistance genes by BSR-Seq: YrMM58 and YrHY1 on chromosome 2AS in Chinese wheat lines Mengmai 58 and Huaiyang 1 are Yr17 Yong Wang, Huaizhi Zhang, Jingzhong Xie, Bingmin Guo, Yongxing Chen, Huaiyu Zhang, Ping Lu, Qiuhong Wu, Miaomiao Li, Deyun Zhang, Guanghao Guo, Jian Yang, Panpan Zhang, Yan Zhang, Xicheng Wang, Hong Zhao, Tingjie Cao, Zhiyong Liu Stripe rust (yellow rust), caused by Puccinia striiformis f. sp. tritici (PST), is one of the most devastating fungal diseases in common wheat (Triticumaestivum L.) in China and worldwide. Resistance breeding is the most effective strategy to control diseases in crop plants. Chinese wheat lines Mengmai 58 and Huaiyang 1 are highly resistant to PST race CYR34 (V26) at the adult plant stage. To genetically map the underlying resistance genes we developed segregating populations by crossing Mengmai 58 and Huaiyang 1 with the susceptible cultivar Nongda 399. The stripe rust resistances in Mengmai 58 and Huaiyang 1 were both controlled by single dominant genes, provisionally designated YrMM58 and YrHY1 , respectively. Bulked segregant RNA-Seq (BSR-Seq) analysis showed that YrMM58 and YrHY1 were located in the same distal ~ 16 Mb region on chromosome2AS. Comparative genomics analysis with the physical map of Aegilops tauschii proved useful for developing additional markers to saturate the genetic linkage map. YrMM58 and YrHY1 were mapped to the distal end of chromosome arm 2AS, with the closest marker WGGB148being 7.7 cM and 3.8 cM from the resistance gene, which was considered to be Yr17. These markers can be used in marker-assisted selection. 欢迎关注 “小麦研究联盟”， 了解小麦新进展 投稿、转载、合作以及信息分布等请联系： wheatgenome
12 31 本期作者：麦萌 又到了周日，有没有感到时光飞逝？今天恰好是2017年的最后一天。岁末年初，还是挺忙的。今晚胖丫仍然猫在实验室，我问她为啥没出去跨年啊。胖丫淡淡的说，“热闹是他们的,我什么也没有 ”。 下面是17年12份小麦相关的文献列表。 一周文献汇总 一周文献推荐（2017.12.9） 小麦一周文献推荐（12.17） 小麦一周文献推送（12.23） 1 Interspecific and intergeneric hybridization as a source of variation for wheat grain quality improvement Wheat quality and its end-uses are mainly based on variation in three traits: grain hardness, gluten quality and starch. In recent times, the importance of nutritional quality and health-related aspects has increased the range of these traits with the inclusion of other grain components such as vitamins, fibre and micronutrients. One option to enlarge the genetic variability in wheat for all these components has been the use of wild relatives, together with underutilised or neglected wheat varieties or species. In the current review, we summarise the role of each grain component in relation to grain quality, their variation in modern wheat and the alternative sources in which wheat breeders have found novel variation. 2 Functional and DNA–protein binding studies of WRKY transcription factors and their expression analysis in response to biotic and abiotic stress in wheat (Triticum aestivum L.) WRKY, a plant-specific transcription factor family, plays vital roles in pathogen defense, abiotic stress, and phytohormone signalling. Little is known about the roles and function of WRKY transcription factors in response to rust diseases in wheat. In the present study, three TaWRKY genes encoding complete protein sequences were cloned. They belonged to class II and III WRKY based on the number of WRKY domains and the pattern of zinc finger structures. Twenty-two DNA–protein binding docking complexes predicted stable interactions of WRKY domain with W-box. Quantitative real-time-PCR using wheat near-isogenic lines with or without Lr28 gene revealed differential up- or down-regulation in response to biotic and abiotic stress treatments which could be responsible for their functional divergence in wheat. TaWRKY62 was found to be induced upon treatment with JA, MJ, and SA and reduced after ABA treatments. Maximum induction of six out of seven genes occurred at 48 h post inoculation due to pathogen inoculation. Hence, TaWRKY (49, 50, 52, 55, 57, and 62) can be considered as potential candidate genes for further functional validation as well as for crop improvement programs for stress resistance. The results of the present study will enhance knowledge towards understanding the molecular basis of mode of action of WRKY transcription factor genes in wheat and their role during leaf rust pathogenesis in particular. 3 Durum wheat diversity for heat stress tolerance during inflorescence emergence is correlated to TdHSP101C expression in early developmental stages The predicted world population increase along with climate changes threatens sustainable agricultural supply in the coming decades. It is therefore vital to understand crops diversity associated to abiotic stress response. Heat stress is considered one of the major constrains on crops productivity thus it is essential to develop new approaches for a precocious and rigorous evaluation of varietal diversity regarding heat tolerance. Plant cell membrane thermostability (CMS) is a widely used method for wheat thermotolerance assessment although its limitations require complementary solutions. In this work we used CMS assay and explored TdHSP101C genes as an additional tool for durum wheat screening. Genomic and transcriptomic analyses of TdHSP101C genes were performed in varieties with contrasting CMS results and further correlated with heat stress tolerance during fertilization and seed development. Although the durum wheat varieties studied presented a very high homology on TdHSP101C genes (99%) the transcriptomic assessment allowed the discrimination between varieties with good CMS results and its correlation with differential impacts of heat treatment during inflorescence emergence and seed development on grain yield. The evidences here reported indicate that TdHSP101C transcription levels induced by heat stress in fully expanded leaves may be a promising complementary screening tool to discriminate between durum wheat varieties identified as thermotolerant through CMS. 4 Virulence of some Puccinia triticina races to the effective wheat leaf rust resistant genes Lr 9 and Lr 19 under Egyptian field conditions Leaf rust ( Puccinia triticina Eriks.) is the most widespread disease of wheat ( Triticum aestivum L.) in Egypt and worldwide. The two leaf rust resistance genes i.e. Lr 9 and Lr 19 were previously highly effective against the predominant Puccinia triticina races in Egypt. In 2015/2016 growing season, susceptible field reaction was recorded on these two genes, where rust severity reached to 40% (S) for Lr 9 and 5% (S) for Lr 19 under Egyptian field conditions at four locations i.e. El-Behira, El-Minufiya, El-Qalubiya and El-Fayom governorates. In this study, 39 leaf rust monogenic lines and 16 commercial wheat cultivars were tested at seedling stage. While, 12 leaf rust monogenic lines and the same 16 wheat cultivars were evaluated at adult plant stage. Eight leaf rust field samples were collected from these governorates (four from each of Lr 9 and Lr 19). Forty single isolates were derived from the collected samples of Lr 9 and Lr 19 (each with 20 isolates). Eight pathotypes were identified from Lr 9, while only two pathotypes were identified from Lr 19. The most frequent pathotype (virulent to Lr 9) was KTSPT (30% frequency), followed by TTTMS (25% frequency). The other pathotypes ranged from only 5%–10% frequency. Whereas, the most frequent pathotype (virulent to Lr 19) was CTTTT (85% frequency), while the lowest frequent one was PKTST (15% frequency). Pathotypes i.e. PRSTT, NTKTS and TTTMS (identified from Lr 9) were more aggressiveness on the most of the tested leaf rust monogenic lines than others, as they were virulent to 36, 35 and 35 lines from a total of 39 monogenic lines, respectively. Also, the two pathotypes; PKTST and CTTTT (identified from Lr 19) were virulent to 36 and 35 monogenic lines, respectively. Moreover, leaf rust pathotypes i.e. NPTNK and PRSTT (from Lr 9) and PKTST (from Lr 19) were the most aggressive on the tested wheat cultivars at seedling stage. Lr 2a was the most effective leaf rust resistance gene against the tested pathotypes at adult plant stage. On the other hand, the three wheat cultivars Misr 1, Misr 2 and Nubariya 1 proved to be the highly resistant cultivars against all the tested leaf rust pathotypes at adult plant stage. 5 Resistance of Aegilops longissima to the rusts of wheat | Plant Disease Stem rust (caused by Puccinia graminis f. sp. tritici), leaf rust (P. triticina), and stripe rust (P. striiformis f. sp. tritici) rank among the most important diseases of wheat worldwide. The development of resistant cultivars is the preferred method of controlling rust diseases because it is environmentally benign and also cost-effective. However, new virulence types often arise in pathogen populations, rendering such cultivars vulnerable to losses. The identification of new sources of resistance is key to providing long-lasting disease control against the rapidly evolving rust pathogens. Thus, the objective of this research was to evaluate the wheat wild relative Aegilops longissima for resistance to stem rust, leaf rust, and stripe rust at the seedling stage in the greenhouse. A diverse collection of 394 accessions of the species, mostly from Israel, was assembled for the study, but the total number included in any one rust evaluation ranged from 308 to 379. With respect to stem rust resistance, 18.2% and 80.8% of accessions were resistant to the widely virulent U.S. and Kenyan P. graminis f. sp. tritici races of TTTTF and TTKSK, respectively. The percentage of accessions exhibiting resistance to the U.S. P. triticina races of THBJ and BBBD was 65.9% and 52.2%, respectively. Over half (50.1%) of the Ae. longissima accessions were resistant to the U.S. P. striiformis f. sp. tritici race PSTv-37. Ten accessions (AEG-683-23, AEG-725-15, AEG-803-49, AEG-1274-20, AEG-1276-22, AEG-1471-15, AEG-1475-19, AEG-2974-0, AEG-4005-20, and AEG-8705-10) were resistant to all races of the three rust pathogens used in this study. Distinct differences in the geographic distribution of resistance and susceptibility were found in Ae. longissima accessions from Israel in response to some rust races. To P. graminis f. sp. tritici race TTKSK, populations with a very high frequency of resistance were concentrated in the central and northern part of Israel, whereas populations with a comparatively higher frequency of susceptibility were concentrated in the southern part of the country. The reverse trend was observed with respect to P. striiformis f. sp. tritici race PSTv-37. The results from this study demonstrate that Ae. longissima is a rich source of rust resistance genes for wheat improvement. 6 Genes WHEAT FRIZZY PANICLE and SHAM RAMIFICATION 2 independently regulate differentiation of floral meristems in wheat Here we characterized diploid and tetraploid wheat lines of various non-standard spike morphotypes, which allowed for identification of a new mutant allele of the WHEAT FRIZZY PANICLE ( WFZP ) gene that determines spike branching in diploid wheat Ttiticum monococcum L. Moreover, we found that the development of SSs and spike branching in wheat T. durum Desf. was a result of a wfzp-A/TtBH-A1 mutation that originated from spontaneous hybridization with T. turgidum convar. сompositum (L.f.) Filat. Detailed characterization of the false-true ramification phenotype controlled by the recessive sham ramification 2 ( shr2 ) gene in tetraploid wheat T. turgidum L. allowed us to suggest putative functions of the SHR2 gene that may be involved in the regulation of spikelet meristem fate and in specification of floret meristems. The results of a gene interaction test suggested that genes WFZP and SHR2 function independently in different processes during spikelet development, whereas another spike ramification gene(s) interact(s) with SHR2 and share(s) common functions. 7 Allelic composition and associated quality traits of the Glu-1 and Glu-3 loci in selected modern Ethiopian durum wheat varieties Gluten protein determines the processing quality of both durum wheat and bread wheat. The glutenin subunits compositions and associated quality traits of 20 Ethiopian durum wheat varieties were systematically analyzed using SDS-PAGE and Payne numbers. A total of 16 glutenin patterns were identified. At the Glu-A1 locus, all varieties scored the null allele. The predominant glutenin alleles at the Glu-B1 locus were Glu-B1b (7+8) and Glu-B1e (20). In Glu-3, the most abundant glutenin subunits were Glu-A3a and Glu-B3c. Based on the Payne scores, the varieties Yerer, Ginchi, Candate, and Foka were identified to have allelic composition suitable for pasta making. The cluster analysis using agglomerative hierarchical clustering (AHC) method classified the varieties into four similarity classes. Based on the findings of this experiment, suggestions were made for allelic composition improvement through introgression of superior alleles from known Glu-1 and Glu-3 sources. 8 The NB-LRR gene Pm60 confers powdery mildew resistance in wheat 欢迎对这篇文章感兴趣的小伙伴给我们写个解读或导读。 Powdery mildew is one of the most devastating diseases of wheat. To date, few powdery mildew resistance genes have been cloned from wheat due to the size and complexity of the wheat genome. Triticum urartu is the progenitor of the A genome of wheat and is an important source for powdery mildew resistance genes. Using molecular markers designed from scaffolds of the sequenced T. urartu accession and standard map-based cloning, a powdery mildew resistance locus was mapped to a 356-kb region, which contains two nucleotide-binding and leucine-rich repeat domain (NB-LRR) protein-encoding genes. Virus-induced gene silencing, single-cell transient expression, and stable transformation assays demonstrated that one of these two genes, designated Pm60 , confers resistance to powdery mildew. Overexpression of full-length Pm60 and two allelic variants in Nicotiana benthamiana leaves induced hypersensitive cell death response, but expression of the coiled-coil domain alone was insufficient to induce hypersensitive response. Yeast two-hybrid, bimolecular fluorescence complementation and luciferase complementation imaging assays showed that Pm60 protein interacts with its neighboring NB-containing protein, suggesting that they might be functionally related. The identification and cloning of this novel wheat powdery mildew resistance gene will facilitate breeding for disease resistance in wheat. 9 Identification of QTL for flag leaf length in common wheat and their pleiotropic effects Leaf size is an important factor contributing to the photosynthetic capability of wheat plants. It also significantly affects various agronomic traits. In particular, the flag leaves contribute significantly to grain yield in wheat. A recombinant inbred line (RIL) population developed between varieties with significant differences in flag leaf traits was used to map quantitative trait loci (QTL) of flag leaf length (FLL) and to evaluate its pleiotropic effects on five yield-related traits, including spike length (SL), spikelet number per spike (SPN), kernel number per spike (KN), kernel length (KL), and thousand-kernel weight (TKW). Two additional RIL populations were used to validate the detected QTL and reveal the relationships in different genetic backgrounds. Using the diversity arrays technology (DArT) genetic linkage map, three major QTL for FLL were detected, with single QTL in different environments explaining 8.6–23.3% of the phenotypic variation. All the QTL were detected in at least four environments, and validated in two related populations based on the designed primers. These QTL and the newly developed primers are expected to be valuable for fine mapping and marker-assisted selection in wheat breeding programs. 10 The repetitive landscape of the 5100 Mbp barley genome Here, we present an analysis of the repetitive fraction of the 5100 Mb barley genome, the largest angiosperm genome to have a near-complete sequence assembly. Genes make only about 2% of the genome, while over 80% is derived from TEs. The TE fraction is composed of at least 350 different families. However, 50% of the genome is comprised of only 15 high-copy TE families, while all other TE families are present in moderate or low copy numbers. We found that the barley genome is highly compartmentalized with different types of TEs occupying different chromosomal “niches”, such as distal, interstitial, or proximal regions of chromosome arms. Furthermore, gene space represents its own distinct genomic compartment that is enriched in small non-autonomous DNA transposons, suggesting that these TEs specifically target promoters and downstream regions. Furthermore, their presence in gene promoters is associated with decreased methylation levels. 11 TaNTF2, a contributor for wheat resistance to the stripe rust pathogen Nuclear Transport Factor 2 (NTF2) functions as a critical regulator in balancing the GTP-and GDP-bound forms of Ran, a class of evolutionarily conserved small GTP-binding protein. During the incompatible interaction between wheat-Puccinia striiformis f. sp. tritici (Pst), a cDNA fragment encoding a putative wheat NTF2 gene was found to be significantly induced, suggesting a potential role in wheat resistance to Pst. In this work, the full length of TaNTF2 was obtained, with three copies located on 7A, 7B and 7D chromosomes, respectively. QRT-PCR further verified the up-regulated expression of TaNTF2 in response to avirulent Pst. In addition, TaNTF2 was also induced by exogenous hormone applications, especially JA treatment. Transient expression of TaNTF2 in tobacco cells confirmed its subcellular localization in the cytoplasm, perinuclear area and nucleus. And virus induced gene silencing (VIGS) was used to identify the function of TaNTF2 during an incompatible wheat-Pst interaction. When TaNTF2 was knocked down, resistance of wheat to avirulentPst was decreased, with a bigger necrotic spots, and higher numbers of hyphal branches and haustorial mother cells. Our results demonstrated that TaNTF2 was a contributor for wheat resistance to the stripe rust pathogen, which will help to comprehensively understand the NTF2/Ran modulating mechanism in wheat-Pst interaction. 12 Loss of AvrSr50 by somatic exchangein stem rust leads to virulence forSr50 resistance in wheat 13 Variation in the AvrSr35 genedetermines Sr35 resistance againstwheat stem rust race Ug99 14 ZmCCT9 enhances maize adaptation to higher latitudes 最后一篇是关于玉米的文章，该文发表在PNAS上，要推荐给做图位克隆的小伙伴。 欢迎关注 “ 小麦研究联盟 ”， 了解小麦新进展 请点击此处输入图片描述 投稿、转载、合作以及信息分布等请联系： wheatgenome
12 29 本期作者：大汉武 胖丫 前几天关于锈病无毒基因解读的年末大餐（ 年末的惊喜一：小麦锈病史上具有里程碑意义的进展！ ， 再析小麦锈病里程碑进展-植物病害流行学角度 ），不知大家感受如何？小编悄悄看了下阅读量，创了历史新高，这倒不是解读的好，主要是结果太震撼了！同时也看出大家的关注程度，抗病这块在小麦育种中还是举足轻重。 就在文章刚刚出来那会，小编第一时间联系到了文章的作者陈嘉鹏博士和 Zhang Peng 老师（这里首先感谢同门晓果同学和河北农大李在峰老师积极的联系）,了解到文章背后的一些小故事。多说一句，通讯作者Robert F. Park和Peter N. Dodds可谓是植物病理界冉冉升起的新秀。 在介绍本篇文章之前，首先要回顾两个常识，锈菌有两个核；锈菌是活体寄生，通过自身发育的吸器进入寄主细胞壁与细胞膜形成类似三明治结构。 本文用到两个小种，即野生型 Pgt279 和发生自然变异的 Pgt632 ，前者不可以侵染含有抗病基因 Sr50 的小麦材料，后者可以。作者对这两个小种的基因组进行了全基因组重测序，经过多步生信分析和筛选，两个小种与锈菌参考基因组PGTAus-pan相比分别约有110万个杂合变异（包括单碱基/多碱基的变异, single/multiple nucleotide variants, SNVs/MNVs ; 和小片段插入及缺失）。（为什么作者费力的要挖掘杂合差异？在这里先卖个关子，后面会详细说明。）根据现有的认知，亚麻锈的无毒基因在吸器中表达，因此，作者优先鉴定了编码吸器分泌蛋白haustorial secreted protein (以下简称HSP)的基因592个。尽管没有新的非同义突变nonsynonymous（这次搞对了，哈哈） ，但是有18个HSP基因在 Pgt632 内发生了杂合性丢失（loss-of-heterozygosity，以下简称LOH，可以理解为在染色体发生重组时，其中一条染色体上的一小段发生了丢失）。通过比较这18个HSP基因的物理位置发现，LOH横跨了大约2.5Mb的物理区间，该区间包含4个完整的scaffolds以及1个scaffolds的部分，如下图 Pgt632 的杂合性丢失可能是突变体发生了片段缺失，这会使该区域的DNA拷贝数减半；或者是两个单倍核发生体细胞重组，此时DNA拷贝数不会变化。所以只要检测DNA拷贝数是否变化就可以验证 Pgt632 的杂合性丢失是如何发生的。这个问题就简单了，统计该区域标准化之后的reads覆盖度发现，野生型 Pgt279 和突变型 Pgt632 之间DNA拷贝数相同。进一步对该区域内的一些基因位点进行覆盖度统计和分析，发现两个小种之间也没有差异。如下图A-C 进一步的定量PCR实验验证拷贝数未发生变化。 我想作者此刻的心情是无比兴奋的，他坚定地得出以下结论：该区域的杂合性丢失是由锈菌中的两个单倍核型发生了交换引起的。于是给出了以下几句话（我个人觉得这是本文最重要的发现之一）：Although it is not clear how genetic exchange occurs between the two separate haploid nuclei, which are thought to replicate independently , genetic evidence suggests that nuclear exchange and recombination between coinoculated rust isolates can result in previously unknown virulence combinations . There is also evidence for nuclear fusion in Pgt , and somatic hybridization has been postulated as a mechanism underlying the emergence of new lineages in asexual rust populations . 大意是虽然目前还不清楚两个单独的单倍体细胞核之间是如何发生遗传交换的，但遗传证据却表明以前被认为独立复制的两个核的确发生了遗传物质的交换，这种遗传交换会引起小种毒力的变化，以往已经有很多证据，比如核融合，体细胞杂交等都是除了有性重组之外引起遗传物质变化的重要原因。 既然推出了突变型突变的可能原因，那么接下来如何拿到候选基因呢？此刻一个不容忽视的问题摆在了面前，该区间约有2.5Mb。作者率先将该区域所有可能的HSP基因注释了一遍，共有24个，然后比较他们在突变菌Pgt632上丢失但是在野生菌Pgt279杂合率接近0.5的，再进行实验验证。最后只有一个AvrSr50 candidate, 当HSP#8 (HSGS210 |asmbl_13131|m.9539) 与Sr50共表达后能够成功引起细胞坏死实验，并通过酵母双杂等一系列实验验证了结果。这个无毒基因编码132氨基酸，且与已知的鉴定出来的无毒蛋白没有同源性，AvrSr35编码的是578氨基酸，目前同样也是独一的，看来小麦锈菌的无毒蛋白多样 性还很丰富。 还有一张图，见下。作者主要对秆锈菌编码外泌蛋白的基因表达进行了聚类分析，分别从吸器，牙管，及侵染小麦叶片2-7天的这几个层面。 到了这里，本篇解析基本完毕。但是标题说了，还有背后的故事，哈哈。确实有点小故事，彩蛋来了。话说当年Park教授在温室中像往常一样对秆锈菌进行扩繁或者鉴定工作，当他用 Pgt279 （野生型，不侵染 Sr50 基因材料）对含有 Sr50 的小麦材料接种时，突然发现后代出现了致病反应，Park很兴奋，小心的把它保存起来，在排除了锈菌污染和小麦材料可能是假杂种后，他们于2015年便开展了上述研究。另外，同年Lagudgh（偶像之一）率领的团队成功克隆到 Sr50 基因，为Park后期的工作奠定了坚实的基础。小编不由感慨，如果Park当时认为是由污染引起的而忽略它，可能就没有今天这个故事了，所以，科研实验还是要善于观察，留心记录的，另外还要有丰富的基础知识，大胆提出假设。这两篇文章的一作貌似都是做生物信息出身的（再次对生信人顶礼膜拜！），他们通过科学的算法使得科研思路能够实现。当然，也非一帆风顺，本篇一作嘉鹏博士邮件里跟我说，他们后面总共在候选区域预测了25个候选基因，实际上是一个一个进行了验证，当验证到第15个的时候，结果出来了.....看来科研还需要一颗恒心，一次两次失败不要紧，三次四次不要紧，起码像人家弄到15次，哈哈。每一个成功的背后都是辛苦的付出，探究永远在路上！ 欢迎关注 “ 小麦研究联盟 ”， 了解小麦新进展 请点击此处输入图片描述 投稿、转载、合作以及信息分布等请联系： wheatgenome
小麦一周文献推送 大家不要忘了我们昨日的约定。俗话说计划赶不上变化，本来这周的文献推荐应该明天推送，但明天辉哥有重要的事情要说。所以，索性我们就调整下，今天来推送一周的文献速览。 1 AetMYC1, the Candidate Gene Controlling the Red Coleoptile Trait in Aegilops tauschii Coss. Accession As77 The red coleoptile trait can help monocotyledonous plants withstand stresses, and key genes responsible for the trait have been isolated from Triticum aestivum , Triticum urartu , and Triticum monococcum , but no corresponding research has been reported for Aegilops tauschii . In this research, transcriptome analysis was performed to isolate the candidate gene controlling the white coleoptile trait in Ae. tauschii . There were 5348 upregulated, differentially-expressed genes (DEGs) and 4761 downregulated DEGs in red coleoptile vs. white coleoptile plants. Among these DEGs, 12 structural genes and two transcription factors involved in anthocyanin biosynthesis were identified. The majority of structural genes showed lower transcript abundance in the white coleoptile of accession ‘As77’ than in the red coleoptile of accession ‘As60’, which implied that transcription factors related to anthocyanin biosynthesis could be the candidate genes. The MYB and MYC transcription factors AetMYB7D and AetMYC1 were both isolated from Ae. tauschii accessions ‘As60’ and ‘As77’, and their transcript levels analyzed. The coding sequence and transcript level of AetMYB7D showed no difference between ‘As60’ and ‘As77’. AetMYC1p encoded a 567-amino acid polypeptide in ‘As60’ containing the entire characteristic domains, bHLH-MYC_N, HLH, and ACT-like, belonging to the gene family involved in regulating anthocyanin biosynthesis. AetMYC1w encoded a 436-amino acid polypeptide in ‘As77’ without the ACT-like domain because a single nucleotide mutation at 1310 bp caused premature termination. Transient expression of AetMYC1p induced anthocyanin biosynthesis in ‘As77’ with the co-expression of AetMYB7D , while AetMYC1w could not cause induced anthocyanin biosynthesis under the same circumstances. Moreover, the transcript abundance of AetMYC1w was lower than that of AetMYC1p . AetMYC1 appears to be the candidate gene controlling the white coleoptile trait in Ae. tauschii , which can be used for potential biotech applications, such as producing new synthetic hexaploid wheat lines with different coleoptile colors. 2 Production and molecular characterization of bread wheat lines with reduced amount of α-type gliadins Here, three bread wheat deletion lines (Gli-A2, Gli-D2 and Gli-A2/Gli-D2) at the Gli-2 loci were generated by the introgression in the bread wheat cultivar Pegaso of natural mutations, detected in different bread wheat cultivars. The molecular characterization of these lines allowed the isolation of 49 unique expressed genes coding α-type gliadins, that were assigned to each of the three Gli-2 loci. The number and the amount of α-type gliadin transcripts were drastically reduced in the deletion lines. In particular, the line Gli-A2/Gli-D2 contained only 12 active α-type gliadin genes (−75.6% respect to the cv. Pegaso) and a minor level of transcripts (−80% compared to cv. Pegaso). Compensatory pleiotropic effects were observed in the two other classes of gliadins (ω- and γ-gliadins) either at gene expression or protein levels. Although the comparative analysis of the deduced amino acid sequences highlighted the typical structural features of α-type gliadin proteins, substantial differences were displayed among the 49 proteins for the presence of toxic and immunogenic epitopes. 3 Physiological and transcriptomic analyses of a yellow-green mutant with high photosynthetic efficiency in wheat (Triticum aestivum L.) Optimizing the antenna size by reducing the chlorophyll (Chl) content is an effective strategy to improve solar energy conversion efficiencies in dense crop monocultures. To elucidate the physiological and molecular mechanisms that regulate Chl biosynthesis and understand the effects of lower Chl content on the photosynthetic process, a light-intensity-dependent yellow-green wheat mutant ( Jimai5265yg ) was characterized to determine its morphological, histological, physiological, and transcriptional differences with wild type. In addition to lower Chl content with a higher Chl a/b ratio, Jimai5265yg has spherical chloroplasts with few plastoglobule. It is counterintuitive that the photochemical quantum yield of both photosystem I and photosystem II and the following CO2 assimilation rate significantly increased, but the value of nonphotochemical quenching decreased, indicating a reduction of the photoprotective capacity of this yellow-green mutant. Analysis of intermediate pools and the expression of genes in the Chl synthesis pathway indicated that Mg-protoporphyrin IX (Mg-Proto IX) synthesis was partially blocked due to the imbalanced expression of Mg-chelatase subunits. Interestingly, the expression of photosynthesis-associated nuclear genes (PhANGs) was upregulated, resembling gun mutants which have defects in the Mg-Proto IX-mediated plastid-to-nucleus signaling pathway. A genetic analysis indicated that the yellow-green phenotype was controlled by two nuclear recessive genes located on chromosomes 4AL and 4BL. Jimai5265yg is a novel chlorina mutant which could be used for understanding photosynthesis improvement mechanisms. 4 Mapping QTLs for grain yield components in wheat under heat stress The current perspective of increasing global temperature makes heat stress as a major threat to wheat production worldwide. In order to identify quantitative trait loci (QTLs) associated with heat tolerance, 251 recombinant inbred lines (RILs) derived from a cross between HD2808 (heat tolerant) and HUW510 (heat susceptible) were evaluated under timely sown (normal) and late sown (heat stress) conditions for two consecutive crop seasons; 2013–14 and 2014–15. Grain yield (GY) and its components namely, grain weight/spike (GWS), grain number/spike (GNS), thousand grain weight (TGW), grain filling rate (GFR) and grain filling duration (GFD) were recorded for both conditions and years. The data collected for both timely and late sown conditions and heat susceptibility index (HSI) of these traits were used as phenotypic data for QTL identification. The frequency distribution of HSI for all the studied traits was continuous during both the years and also included transgressive segregants. Composite interval mapping identified total 24 QTLs viz ., 9 (timely sown traits), 6 (late sown traits) and 9 (HSI of traits) mapped on linkage groups 2A, 2B, and 6D during both the crop seasons 2013–14 and 2014–15. The QTLs were detected for GWS (6), GNS (6), GFR (4), TGW (3), GY (3) and GFD (2). The LOD score of identified QTLs varied from 3.03 ( Qtgns . iiwbr-6D ) to 21.01 ( Qhsitgw . iiwbr-2A ) during 2014–15, explaining 11.2 and 30.6% phenotypic variance, respectively. Maximum no of QTLs were detected in chromosome 2A followed by 6D and 2B. All the QTL detected under late sown and HSI traits were identified on chromosome 2A except for QTLs associated with GFD. Fifteen out of 17 QTL detected on chromosome 2A were clustered within the marker interval between gwm448 and wmc296 and showed tight linkage with gwm122 and these were localized in 49–52 cM region of Somers consensus map of chromosome 2A i.e. within 18–59.56 cM region of chromosome 2A where no QTL related to heat stress were reported earlier. Besides, three consistent QTLs, Qgws . iiwbr-2A , Qgns . iiwbr-2A and Qgns . iiwbr-2A were also detected in all the environments in this region. The nearest QTL detected in earlier studies, QFv/Fm . cgb-2A was approximately 6cM below the presently identified QTLs region, respectively Additionally, QTLs for physiological and phenological traits and plant height under late sown and HSI of these traits were also detected on chromosome 2A. QTL for HSI of plant height and physiological maturity were located in the same genomic region of chromosome 2Awhereas QTLs for physiological and phonological traits under late sown were located 8cM and 33.5 cM below the genomic location associated with grain traits, respectively in consensus map of Somers. This QTL hot-spot region with consistent QTLs could be used to improve heat tolerance after validation. 5 Inferring defense-related gene families in Arabidopsis and wheat We employed three bioinformatics and genomics approaches to identifying candidate genes known to affect plant defense and to classifying these protein-coding genes into different gene families in Arabidopsis. These approaches predicted up to 1790 candidate genes in 11 gene families for Arabidopsis defense to biotic stresses. The 11 gene families included ABC, NLR and START, the three families that are already known to confer rust resistance in wheat, and eight new families. The distributions of predicted SNPs for individual rust resistance genes were highly skewed towards specific gene families, including eight one-to-one uniquely matched pairs: Lr21-NLR, Lr34-ABC, Lr37-START, Sr2-Cupin, Yr24-Transcription factor, Yr26-Transporter, Yr36-Kinase and Yr53-Kinase . Two of these pairs, Lr21 - NLR and Lr34 - ABC , are expected because Lr21 and Lr34 are well known to confer race-specific and race-nonspecific resistance to leaf rust ( Puccinia triticina ) and they encode NLR and ABC proteins. 6 Single Nucleotide Polymorphisms in B-Genome Specific UDP-Glucosyl Transferases Associated with Fusarium Head Blight Resistance and Reduced Deoxynivalenol Accumulation in Wheat Grain An in vitro spike culture method was optimized to evaluate Fusarium head blight (FHB) resistance in wheat ( Triticum aestivum ) and used to screen a population of ethyl methane sulfonate treated spike culture-derived variants (SCDV). Of the 134 SCDV evaluated, the disease severity score of 47 of the variants was ≤30%. Single nucleotide polymorphisms (SNP) in the UDP-glucosyltransferase ( UGT ) genes, TaUGT-2B , TaUGT-3B , and TaUGT-EST , differed between AC Nanda (an FHB-susceptible wheat variety) and Sumai-3 (an FHB-resistant wheat cultivar). SNP at 450 and 1,558 bp from the translation initiation site in TaUGT-2B and TaUGT-3B , respectively were negatively correlated with FHB severity in the SCDV population, whereas the SNP in TaUGT-EST was not associated with FHB severity. Fusarium graminearum strain M7-07-1 induced early expression of TaUGT-2B and TaUGT-3B in FHB-resistant SCDV lines, which were associated with deoxynivalenol accumulation and reduced FHB disease progression. At 8 days after inoculation, deoxynivalenol concentration varied from 767 ppm in FHB-resistant variants to 2,576 ppm in FHB-susceptible variants. The FHB-resistant SCDV identified can be used as new sources of FHB resistance in wheat improvement programs. 7 Characterization of Leaf Rust and Stripe Rust Resistance in Spring Wheat ‘Chilero’ Since 1984, the ‘Chilero’ spring wheat line developed by CIMMYT has proven to be highly resistant to leaf rust and stripe rust. Amid efforts to understand the basis of resistance of this line, a recombinant inbred line (RIL) population derived from a cross between Avocet and Chilero was studied. The parents and RILs were characterized in field trials for leaf rust and stripe rust in three locations in Mexico between 2012 and 2015 and genotyped with DArT-array, DArT-GBS, and SSR markers. A total of 6,168 polymorphic markers were used to construct genetic linkage maps. Inclusive composite interval mapping detected four colocated resistance loci to both rust diseases and two stripe rust resistant loci in the Avocet × Chilero population. Among these, the quantitative trait locus (QTL) on chromosome 1BL was identified as a pleotropic adult plant resistance gene Lr46/Yr29 , whereas QLr.cim-5DS/QYr.cim-5DS was a newly discovered colocated resistance locus to both rust diseases in Chilero. Additionally, one new stripe rust resistance locus on chromosome 7BL was mapped in the current population. Avocet also contributed two minor colocated resistance QTLs situated on chromosomes 1DL and 4BS. The flanking SNP markers can be converted to breeder friendly Kompetitive Allele Specific PCR (KASP) markers for wheat breeding programs. 8 Analysis of aneuploid lines of bread wheat to map chromosomal locations of genes controlling root hair length BACKGROUND AND AIMS: Long root hairs enable the efficient uptake of poorly mobile nutrients such as phosphorus. Mapping the chromosomal locations of genes that control root hair length can help exploit the natural variation within crops to develop improved cultivars. Genetic stocks of the wheat cultivar 'Chinese Spring' were used to map genes that control root hair length. METHODS: Aneuploid stocks of 'Chinese Spring' were screened using a rapid method based on rhizosheath size and then selected lines were assayed for root hair length to identify chromosomes harbouring genes controlling root hair length. A series of lines with various fractional deletions of candidate chromosomes were then screened to map the root hair loci more accurately. A line with a deletion in chromosome 5A was analysed with a 90 000 single nucleotide polymorphism (SNP) array. The phosphorus acquisition efficiency (PAE) of one deletion line was compared with that of euploid 'Chinese Spring' by growing the seedlings in pots at low and luxury phosphorus supplies. KEY RESULTS: Chromosomes 1A, 1D and 5A were found to harbour genes controlling root hair length. The 90 000 SNP array identified two candidate genes controlling root hair length located on chromosome 5A. The line with a deletion in chromosome 5A had root hairs that were approx. 20 % shorter than euploid 'Chinese Spring', but this was insufficient to reduce its PAE. CONCLUSIONS: A rapid screen for rhizosheath size enabled chromosomal regions controlling root hair length to be mapped in the wheat cultivar 'Chinese Spring' and subsequent analysis with an SNP array identified candidate genes controlling root hair length. The difference in root hair length between euploid 'Chinese Spring' and a deletion line identified in the rapid screen was still apparent, albeit attenuated, when the seedlings were grown on a fully fertilized soil. 9 Introgression of the Aegilops speltoides Su1-Ph1 Suppressor into Wheat Meiotic pairing between homoeologous chromosomes in polyploid wheat is inhibited by the Ph1 locus on the long arm of chromosome 5 in the B genome. Aegilops speltoides (genomes SS), the closest relative of the progenitor of the wheat B genome, is polymorphic for genetic suppression of Ph1. Using this polymorphism, two major suppressor loci, Su1-Ph1 and Su2-Ph1 , have been mapped in Ae. speltoides. Su1-Ph1 is located in the distal, high-recombination region of the long arm of the Ae. speltoides chromosome 3S. Its location and tight linkage to marker Xpsr1205-3S makes Su1-Ph1 a suitable target for introgression into wheat. Here, Xpsr1205-3S was introgressed into hexaploid bread wheat cv. Chinese Spring (CS) and from there into tetraploid durum wheat cv. Langdon (LDN). Sequential fluorescence in situ hybridization and genomic in situ hybridization showed that an Ae. speltoides segment with Xpsr1205-3S replaced the distal end of the long arm of chromosome 3A. In the CS genetic background, the chromosome induced homoeologous chromosome pairing in interspecific hybrids with Ae. peregrina but not in progenies from crosses involving alien disomic substitution lines. In the LDN genetic background, the chromosome induced homoeologous chromosome pairing in both interspecific hybrids and progenies from crosses involving alien disomic substitution lines. We conclude that the recombined chromosome harbors Su1-Ph1 but its expression requires expression of complementary gene that is present in LDN but absent in CS. We suggest that it is unlikely that Su1-Ph1 and ZIP4-1 , a paralog of Ph1 located on wheat chromosomes 3A and 3B and Ae. tauschii chromosome 3D, are equivalent. The utility of Su1-Ph1 for induction of recombination between homoeologous chromosomes in wheat is illustrated. 10 Evolutionary history of the NAM-B1 gene in wild and domesticated tetraploid wheat Background The NAM-B1 gene in wheat has for almost three decades been extensively studied and utilized in breeding programs because of its significant impact on grain protein and mineral content and pleiotropic effects on senescence rate and grain size. First detected in wild emmer wheat, the wild-type allele of the gene has been introgressed into durum and bread wheat. Later studies have, however, also found the presence of the wild-type allele in some domesticated subspecies. In this study we trace the evolutionary history of the NAM-B1 in tetraploid wheat species and evaluate it as a putative domestication gene. Genotyping of wild and landrace tetraploid accessions showed presence of only null alleles in durum. Domesticated emmer wheats contained both null alleles and the wild-type allele while wild emmers, with one exception, only carried the wild-type allele. One of the null alleles consists of a deletion that covers several 100 kb. The other null-allele, a one-basepair frame-shift insertion, likely arose among wild emmer. This allele was the target of a selective sweep, extending over several 100 kb. The NAM-B1 gene fulfils some criteria for being a domestication gene by encoding a trait of domestication relevance (seed size) and is here shown to have been under positive selection. The presence of both wild-type and null alleles in domesticated emmer does, however, suggest the gene to be a diversification gene in this species. Further studies of genotype-environment interactions are needed to find out under what conditions selection on different NAM-B1 alleles have been beneficial. 11 De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.) Background During asexual reproduction the embryogenic callus can differentiate into a new plantlet, offering great potential for fostering in vitro culture efficiency in plants. The immature embryos (IMEs) of wheat ( Triticum aestivum L.) are more easily able to generate embryogenic callus than mature embryos (MEs). To understand the molecular process of embryogenic callus formation in wheat, de novo transcriptome sequencing was used to generate transcriptome sequences from calli derived from IMEs and MEs after 3d, 6d, or 15d of culture (DC). In total, 155 million high quality paired-end reads were obtained from the 6 cDNA libraries. Our de novo assembly generated 142,221 unigenes, of which 59,976 (42.17%) were annotated with a significant Blastx against nr, Pfam, Swissprot, KOG, KEGG, GO and COG/KOG databases. Comparative transcriptome analysis indicated that a total of 5194 differentially expressed genes (DEGs) were identified in the comparisons of IME vs. ME at the three stages, including 3181, 2085 and 1468 DEGs at 3, 6 and 15 DC, respectively. Of them, 283 overlapped in all the three comparisons. Furthermore, 4731 DEGs were identified in the comparisons between stages in IMEs and MEs. Functional analysis revealed that 271transcription factor (TF) genes (10 overlapped in all 3 comparisons of IME vs. ME) and 346 somatic embryogenesis related genes (SSEGs; 35 overlapped in all 3 comparisons of IME vs. ME) were differentially expressed in at least one comparison of IME vs. ME. In addition, of the 283 overlapped DEGs in the 3 comparisons of IME vs. ME, excluding the SSEGs and TFs, 39 possessed a higher rate of involvement in biological processes relating to response to stimuli, in multi-organism processes, reproductive processes and reproduction. Furthermore, 7 were simultaneously differentially expressed in the 2 comparisons between the stages in IMEs, but not MEs, suggesting that they may be related to embryogenic callus formation. The expression levels of genes, which were validated by qRT-PCR, showed a high correlation with the RNA-seq value. This study provides new insights into the role of the transcriptome in embryogenic callus formation in wheat, and will serve as a valuable resource for further studies addressing embryogenic callus formation in plants. 12 Chromosome Pairing in Hybrid Progeny between Triticum aestivum and Elytrigia elongata In this study, the intergeneric hybrids F1, F2, BC1F1, BC1F2, and BC2F1 from Elytrigia elongata and Triticum aestivum crosses were produced to study their chromosome pairing behavior. The average E. elongata chromosome configuration of the two F1hybrids agreed with the theoretical chromosome configuration of 21I+7II, indicating that the genomic constitution of this F1 hybrid was ABDStStEeEbEx. Compared with the BC1F1 generation, the BC2F1 generation showed a rapid decrease in the number of E. elongata chromosomes and the BC1F2 generation showed a more extensive distribution of E. elongata chromosomes. In addition, pairing between wheat and E. elongata chromosomes was detected in each of the wheat -E. elongata hybrid progenies, albeit rarely. Our results demonstrated that genomic in situ hybridization (GISH) using an E. elongata genomic DNA probe offers a reliable approach for characterizing chromosome pairing in wheat and E. elongata hybrid progenies. 13 POTAGE - Popseq Ordered Triticum Aestivum Gene Expression 一个小麦数据库 http://crobiad.agwine.adelaide.edu.au/potage/ 14 A novel wheat NAC transcription factor, TaNAC30, negatively regulates resistance of wheat to stripe rust 据说赤霉病抗性也与NAC转录因子有关？ NAC transcription factors are widespread in the plant kingdom and play essential roles in the transcriptional regulation of defense responses. In this study, we isolated a novel NAC transcription factor gene, TaNAC30 , from a cDNA library constructed from wheat ( Triticum aestivum ) plants inoculated with the stripe rust pathogen Puccinia striiformis f. sp. tritici ( Pst ). TaNAC30 contains a typical NAM domain and localizes to the nucleus. Yeast one-hybrid assays revealed that TaNAC30 exhibits transcriptional activity and that its C-terminus is necessary for the activation of transcription. The expression of TaNAC30 increased when host plants were infected with a virulent race (CYR31) of the rust fungus Pst . Silencing of TaNAC30 by virus-induced gene silencing (VIGS) inhibited colonization of the virulent Pst isolate CYR31. Moreover, detailed histological analyses showed that silencing of TaNAC30 enhanced resistance to Pst by inducing a significant increase in the accumulation of H2O2. Finally, we overexpressed TaNAC30 in fission yeast and found that cell viability was severely reduced in TaNAC30 -transformed cells grown on medium containing H2O2. These results suggest that TaNAC30 negatively regulates plant resistance in a compatible wheat- Pst interaction. 15 Molecular Characterization and Functional Analysis of PR-1-like Proteins Identified from the Wheat Head Blight Fungus Fusarium graminearum 好吧，说赤霉病，赤霉病就来了。 The group 1 pathogenesis-related (PR-1) proteins originally identified from plants and their homologues are also found in other eukaryotic kingdoms. Studies on non-plant PR-1-like (PR-1L) proteins have been pursued widely in humans/animals but rarely in filamentous ascomycetes. Here we report the characterization of four PR-1L proteins identified from the ascomycete fungus Fusarium graminearum, the primary cause of Fusarium head blight of wheat and barley. Molecular cloning revealed that the four FgPR-1L proteins are all encoded by small open reading frames (612 to 909 bp) that are often interrupted by introns, in contrast to plant PR-1 genes that lack introns. Sequence analysis indicated that all FgPR-1L proteins contain the PR-1-specific three-dimensional structure, and one of them features a C-terminal transmembrane (TM) domain that has not been reported for any stand-alone PR-1 proteins. Transcriptional analysis revealed that the four FgPR-1L genes are expressed in axenic cultures and in planta with different spatial/temporal expression patterns. Phylogenetic analysis indicated that fungal PR-1L proteins fall into three major groups, one of which harbors FgPR-1L-2-related TM-containing proteins from both phytopathogenic and human-pathogenic ascomycetes. Low-temperature SDS-PAGE and proteolytic assays indicated that the recombinant FgPR-1L-4 protein exists as a monomer and is resistant to subtilisin of the serine protease family. Functional analysis confirmed that deletion of the FgPR-1L-4 gene from the fungal genome results in significantly reduced virulence on susceptible wheat. This study provides the first example that the F. graminearum–wheat interaction involves a pathogen-derived PR-1-like protein that affects fungal virulence on the host. 16 Physiologic Specialization of Puccinia triticina on Wheat in the United States in 2016 Leaves of wheat infected with the leaf rust fungus, Puccinia triticina, were obtained from farm fields and breeding plots at experimental stations in the Great Plains, Ohio River Valley, and southeastern states in 2016 in order to identify virulence phenotypes prevalent in the United States in different wheat growing regions. A total of 496 single uredinial isolates derived from the leaf rust collections were tested for virulence to 20 lines of Thatcher wheat that differ for single leaf rust resistance genes. A total of 71 virulence phenotypes were described in the United States in 2016. The three most common virulence phenotypes across the United States were MBTNB, MBDSD, and TNBJJ. Phenotype MBTNB is virulent to Lr11, and was most common in the soft red winter wheat region of the southeastern states and Ohio Valley. Phenotype MBDSD is virulent to Lr17 and Lr39, and was most common in the hard red winter wheat area of the southern Great Plains. Phenotype TNBJJ is virulent to Lr24 and Lr39, which are present in the hard red winter wheat cultivars. The P. triticina population in the United States was characterized by two major regional groups of virulence phenotypes in the Great Plains region where hard red winter and spring wheat cultivars are grown, and in the southeastern states and Ohio Valley region where soft red winter wheat cultivars are grown. Isolates from New York state differed the most for virulence compared to the other two major regions. 17 Genetic Relationship of Stripe Rust Resistance Genes Yr34 and Yr48 in Wheat and Identification of Linked KASP Markers The Australian continent was free from wheat stripe rust caused by Puccinia striiformis f. sp. tritici until exotic incursions occurred in 1979 and 2002. The 2002 incursion enabled the identification of a new stripe rust resistance gene (Yr34) in the advanced breeding line WAWHT2046. In this study, we developed and validated markers closely linked with Yr34, which is located in the distal region in the long arm of chromosome 5A. Four kompetitive allele-specific polymerase chain reaction (KASP) and three sequence-tagged site (STS) markers derived from the International Wheat Genome Sequencing Consortium RefSeq v1.0 scaffold-77836 cosegregated with Yr34. Markers sun711, sun712, sun725, sunKASP 109, and sunKASP 112 were shown to be suitable for marker-assisted selection in a validation panel of 71 Australian spring wheat genotypes, with the exception of cultivar Orion that carried the Yr34-linked alleles for sunKASP 109 and sunKASP 112. Markers previously reported to be linked with adult plant stripe rust resistance gene Yr48 also cosegregated with Yr34. Wheat genotypes carrying Yr34 and Yr48 produced identical haplotypes for the Yr34-linked markers identified in this study and those previously reported to be linked with Yr48. Phenotypic testing of genotypes carrying Yr34 and Yr48 showed that both genes conferred similar seedling responses to pre-2002 and post-2002 P. striiformis f. sp. tritici pathotypes. Further testing of 600 F2 plants from a cross between WAWHT2046 and RIL143 (Yr48) with P. striiformis f. sp. tritici pathotype 134 E16A+Yr17+Yr27+ failed to reveal any susceptible segregants. Our results strongly suggest that Yr34 and Yr48 are the same gene, and that Yr48 should be considered a synonym of Yr34. 欢迎关注 小麦研究联盟 ，了解小麦新进展
利用近等基因系进行RNA-Seq定位目标QTL——论材料的重要性 时间都去哪了？在昏沉的下午，胖丫望着实验室一众忙碌的身影，有点茫茫然。2017年就走到头了，又是不堪回首的一年。跟着我 左手右手 一个慢动作，一年到头休息的日子就数过来了，而看看取得的成果貌似一只手都绰绰有余。前几日师兄调戏胖丫说，2017胖丫最重要的收获就是体重，胖丫已经完全放弃治疗，完全放飞自我。胖丫一遍梳理刘海，一边回应道，师兄最重要的收获是肚子吧。油腻中年男人端着泡着枸杞的茶杯，就不要站着说话不腰疼了。果然都是亲师兄亲师妹，取笑起来不含糊。 一年一度的基金申请也快开始了，免不了又要掉几根烦恼丝。趁着岁末年初，何不整理下自己领域的研究进展，规整规整文献，数数看了几篇文献，这好歹也算是收获之一。从即日起，欢迎各位小伙伴将整理好的自己研究方向的小麦文献列表发给我们一份，整理汇总之后我们会推送出来。现在可以闭上眼睛想想，今年看了几篇文献，可以放下手机，跟着我左手右手一个。。。。。。，如果想不起来那就整理下吧。不能只顾往前走，也得回头看看脚印走的漂亮不漂亮。 好了，言归正传正传之前，别忘了刚刚说过的事。今天小编简要介绍一篇关于大麦抗冠腐病QTL定位的文章。题为“ A multiple nearisogenic line (multi‑NIL) RNA‑seq approach to identify candidate genesunderpinning QTL ”。通讯作者是Chunji Liu。 话说Chunji Liu老师小编也是一直关注着他（她），Liu发了很多测序的文章，感兴趣的大家可以搜一下。QTL定位的文章目前很多，除了利用传统的遗传群体外，还有GWAS，关于这一块，我们的瑞哥很有经验，做了很多推送， QTL mapping 思路总结（二）GWAS-1 ， GWAS思路总结-2 。 这篇文章利用多对抗感近等基因系进行RNA-Seq，分析差异SNP并进行物理定位后，发现3对近等基因系共同差异的SNP重叠区域在6.3Mb左右，这部分区域很可能与QTL极为关联，从而迅速锁定了该候选区域，见下图。 分析差异表达基因发现，至少在两对近等基因系中都差异表达的基因也在这个范围，约9.8Mb，进一步确认了该区域为目标QTL区域。基因分析对四个可能为候选基因的转录本进行了定量PCR测定。当然，这一结果还需更精细的定位手段进行验证。 本文提供了一个QTL定位新思路，其实也不算什么新思路了，算是定位过程中一叠开胃菜。不过当我兴致勃勃的跟胖丫聊天谈及此事时，胖丫弱弱的说了一句：“辉哥，这个对于效应值较大的QTL很实用，要是效应值很小的，表型都拿捏不准的还是算了吧”。嗯，大家还是根据自身的实际情况来决定吧，不过创建材料真的很重要！很重要！每年的小麦杂交季大家千万不要错过，设计好试验方案，多多创建一些材料，为后期的研究奠定基础吧，技术什么的都好说，材料可不是一天两天就能出来的。研究永远在路上！最近听说，老美分了8个粒重基因图位克隆的工作给各家单位，效应好的基因研究的人也多，大家好加把劲呢。 最后，再推荐两篇小麦的利用近等基因系定位抗穗发芽的文章，题为“ Transcriptomicanalysis of wheat near-isogenic lines identifies PM19-A1 and A2 as candidatesfor a major dormancy QTL ”，可以参见我们公众号的解读 抗穗发芽Phs-A1位点研究进展 。 另外一篇是上次解读漏掉的“ The wheat Phs-A1 pre-harvestsprouting resistance locus delays the rate of seed dormancy loss and maps 0.3cM distal to the PM19 genes in UK germplasm ”。 欢迎关注 小麦研究联盟 ，了解小麦新进展
小麦GWAS思路总结-2 首先感谢上次小伙伴们积极参与话题的讨论，其实关于Manhattan图那个问题是我毕业答辩的时候一个美国教授问我的，我在他的循循善诱之下终于回答出来了。另外，有一位小伙伴留言说“One of the biggest limitation of GWA approach is the spurious association, I think one can never get over”前半句所指出的问题还是很中肯的，不过小编认为后半句中的 “never” 在科研语境中还是少用较好。其实对于spurious association，不同的实验目的本身就可以避免这个问题，比如spotblotch和rust等主效基因的GWAS鉴定就可以直接忽略那些highp value的associations。另外，对于像FHB抗性这样的GWAS鉴定，虽说必然会有很多lowconfidence的associations，但是如果我们的实验目的是为了抗病育种，那么Genomicselection也算是一种解决办法吧。下面的统计学思路中我们会从统计学角度再提一下这个问题。 GWAS 一般思路 5. 利用 sub-panel 做 association 分析。 比如做小麦谷蛋白含量的GWAS分析，就必须要考虑到不同小麦class（硬/软）自身所含蛋白质的差别，所以如果所用的群体包含不同种类的小麦，用不同sub-class panel单独分析也可以做为文章重要的一部分。又比如做大麦的GWAS，row-type是一个很明显的区别，Wang et al. 2017 是关于大麦的spot blotch 抗病，作者分别用Whole, Two-rowed 和Six-rowed 三个panels做了association analysis,原因有两个：在统计学上有两篇重量级的文章(Zhao et al. 2007; Zhao et al. 2011) 来讨论sub-structure association mapping的必要性，另外生物学意义上，确实有观察到不同row type 大麦对spot blotch抗性不同。 6. Sub-panel 分析继续深入，鉴定出一小批有价值的 validation lines ，可应用于以后 Genecloning 项目中，比如可以用于 target capture 。 还是 Wang et al. 2017 这篇 ( 其实这就是小编自己的文章，哈哈 ), 作者利用一步步的 sub-panel 最终发现在 six-rowed breeding lines （ 120 lines 左右，用 cluster 分析再精简到 50 个 line 左右）所得出的抗病 association 的 p value 最低，证明目标基因以及相应表型在这个小群体中有很好的分离。所以这个小群体可以作为未来基因克隆的宝贵种质资源，至少可以用来做单倍型分析来 validate 目标基因。 GWAS 进阶思路 前两点是我在最初接触 GWAS 的时候所学到的，我当时关注这两点是基于两个思考： 1 ）我所用的 barley panel 是美国农部 NSGC core accessions ，很多其他实验室都在利用这个 Panel 做不同的 traits ，我们能不能把所有的 traits 联合起来做分析呢？ 2 ）我做的是 spot blotch ，用了三种不同的致病菌种来获得三套不同的 phenotyping data ，如果单独分析，得到的就是针对三个不同致病种的抗性，那如果把三套 data 合起来，得到的结果是不是可以算是广谱抗性的鉴定呢？根据我所看到的文章，我的想法应该是可行的。可惜的是在我们小麦和大麦领域，我目前还没有看到相关的文章。我大胆的预测，以后随着更多统计学背景以及做模式植物的大牛们转向小麦，类似下面两点的文章一定会在小麦中出现。 1. Phenome-wide association study (PheWAS) or Pleiotropic association “Phenomic approaches are complementary to the more prevalent paradigm of genome-wide association studies (GWAS), which have provided some information about the contribution of genetic variation to a wide range of diseases and phenotypes. While a typical GWAS evaluates the association between the variation of hundreds of thousands, to over a million, genotyped SNPs and one or a few phenotypes, a common limitation of GWAS is the focus on a pre-defined and limited phenotypic domain. An alternate approach is that of PheWAS, which utilizes all available phenotypic information and all genetic variants in the estimation of association between genotype and phenotype. By investigating the association between SNPs and a diverse range of phenotypes, a broader picture of the relationship between genetic variation and networks of phenotypes is possible.”(Sarah et al. 2013) 2. Meta-analysis of many genome-wide association studies “The advent of genome-wide association studies has allowed considerable progress in the identification and robust replication of common gene variants that confer susceptibility to common diseases and other phenotypes of interest. These genetic effect sizes are almost invariably moderate to small in magnitude and single studies, even if large, are underpowered to detect them with confidence. Meta-analysis of many genome-wide association studies improves the power to detect more associations, and to investigate the consistency or heterogeneity of these associations across diverse datasets and study populations.” (Zeggini et al. 2009) 刚才又 Google 了一下，发现有两篇在 rice/maize 上做 Metabolite-pathway-based Phenome-Wide Association Scan (M-PheWAS) ： Lu et al. 2015; Chen et al. 2016. 期待我们小麦在这个领域也追赶上来。 下面三点是统计学方法上的一些思路，主要是从 Frontiers researchtopics 上摘抄下来的，外加我自己的一些理解和总结（ https://www.frontiersin.org/research-topics/7228/the-applications-of-new-multi-locus-gwas-methodologies-in-the-genetic-dissection-of-complex-traits 有兴趣的小伙伴赶紧投稿啊，小编也正琢磨着投一篇）。 3. Multi-locusGWAS method . How to use some available multi-locus GWAS methods and how to select them. 可以参考 Wen et al. 2017 和 Tamba et al. 2017, 这两篇文章通讯作者都是原来我在南农的大田试验统计学老师章元明，章老师棒棒的！ 4. New technical clue and method to obtain high power and low false positive rate in GWAS. 这又回到了我们开篇所提到的 spurious association ，其实统计学背景的同行们一直都在努力解决！可以参考 Yang, et al. 2014 和 Li et al. 2012 ，都是早期不错的 GWAS 文章，一个是在 rice 上，一个是在 human 上。 5.Heritability missing in GWAS is a common phenomenon. 下面这篇文章提了三点可能的原因以及可能的解决办法（ Zhou et al. 2013 ）。另外， multi-locus GWAS methods 也可能把丢掉的遗传给找回来。 “This missing heritability may be explained by (1) the existence of a large number of minor-effect alleles that remain unidentified; (2) incomplete LD between SNP markers and the causal gene, contributing to the underestimation of single QTL effects; and (3) the existence of gene-by-gene interactions (i.e. epistasis), since only single marker effects were tested in this study. One way to increase heritability is to increase the density of markers. In Arabidopsis, the amount of phenotypic variation accounted for in 44 different traits was moderately high (at least one significant SNP marker with MAF C15 % was found to explain at least 20 % of phenotypic variation) because 250,000 SNP markers were used in the analysis.” 其它思路 小编能力有限，除了上边的思路以外，当然还可以应用 GWAS 玩出更多花样，比如凯凯以前的推送 “ plant journal 上看到一篇小麦株高关联分析的文章 ” ，还有利用 GWAS 来鉴定基因的，比如 “ 抗穗发芽 Phs-A1 位点研究进展 ” 。最后，随着小麦序列和 marker 越来越多，大家可以更多的借鉴在 rice 和拟南芥上做的 GWAS 文章，笔者在这里就不更多列举了。 参考文献 ( 今天的文献有点多，是按文献在文中出现的先后顺序排列的 ) Wang et al. 2017. Genome-wide association mapping of spot blotch resistance to three different pathotypes of Cochliobolussativus in the USDA barley core collection, Mol. Breeding Zhao K, et al. 2007. An Arabidopsis example of association mapping in structured samples. PLoS Genet. Zhao K, et al. 2011. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun. Sarah et al. 2013. Phenome-Wide Association Study (PheWAS) for Detection of Pleiotropy within the Population Architecture using Genomics and Epidemiology (PAGE) Network. PLoS Genet. Zeggini etal. 2009. Meta-analysis in genome-wide association studies. Pharmacogenomics. Lu et al. 2015. Systems Genetic Validation of the SNP-Metabolite Association in Rice Via Metabolite-Pathway-Based Phenome-Wide Association Scans. Frontiers in PlantScience. Chen et al. 2016. Comparative and parallel genome-wide association studies for metabolic and agronomic traits in cereals. NatureCommunications. Wen et al. 2017. Methodologicalimplementation of mixed linear models in multi-locus genome-wide association studies. Brief Bioinform. Tamba et al. 2017. Iterative sure independence screening EM-Bayesian LASSO algorithm for multi-locus genome-wide association studies. PLoS Comput Biol. Yang, et al. 2014. Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice. Nat. Commun. Li et al. 2012. Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets. Hum. Genet. Zhou et al. 2013. Genome-wide association mapping reveals genetic architecture of durable spot blotch resistance in US barley breeding germplasm. Mol. Breeding 欢迎关注“ 小麦研究联盟 ” ，了解小麦新进展
小麦一周文献推荐（12.17） 1、QTL analysis of falling number and seed longevity in wheat (Triticum aestivum L.) Pre-harvest sprouting (PHS) and seed longevity (SL) are complex biological processes of major importance for agricultural production. In the present study, a recombinant inbred line (RIL) population derived from a cross between the German winter wheat (Triticum aestivum L.) cultivars History and Rubens was used to identify genetic factors controlling these two physiological seed traits. A falling number (FN) test was employed to evaluate PHS, while SL was measured using a germination test (and the speed of germination) after controlled deterioration. FN of the population was assessed in four environments; SL traits were measured in one environment. Four major quantitative trait loci (QTL) for FN were detected on chromosomes 4D, 5A, 5D, and 7B, whereas for SL traits, a major QTL was found on chromosome 1A. The FN QTL on chromosome 4D that coincided with the position of the dwarfing gene Rht-D1b only had effects in environments that were free of PHS. The remaining three QTL for FN were mostly pronounced under conditions conducive to PHS. The QTL on the long arm of chromosome 7B corresponded to the major gene locus controlling late maturity α-amylase (LMA) in wheat. The severity of the LMA phenotype became truly apparent under sprouting conditions. The position on the long arm of chromosome 1A of the QTL for SL points to a new QTL for this important regenerative seed trait. 2、RNA-seq facilitates development of chromosome-specific markers and transfer of rye chromatin to wheat Transcriptome shotgun sequencing (RNA-seq) provides an abundant resource for developing molecular markers specifically related to functional genes. In this study, transcriptomes of Chinese rye cultivar Jingzhouheimai (JZHM) challenged with powdery mildew pathogen Bgt ( Blumeria graminis f. sp. tritici ) were obtained and used to develop expressed sequence tag (EST)-based simple sequence repeat (SSR) and sequence-tagged site (STS) markers. A total of 866 primer sets for EST-SSRs and STSs were designed, from which we developed 401 rye-specific markers. The highest level of polymorphism was observed in EST-SSRs (56.73%) followed by STS2 (49.07%) designed via rye-specific contigs and STS1 (35.90%) primers designed from upregulated contigs. Genotyping with newly developed markers along with cytogenetic techniques allowed us to identify nine wheat alien chromosome lines from the cross of Zhoumai 18/Jinghui 1 (Jinghui 1 is an amphiploid of wheat landrace Huixianhong and JZHM) carrying rye chromosome 6R or 6R segments of different length, which permitted preliminary location of the powdery mildew resistance gene PmJZHM6RL and 12 specific markers to 6RL FL 0.51–1.0. 5R-specific markers and genomic in situ hybridization/fluorescence in situ hybridization detected MtA5RL and T5AS·5AL-5RL chromosomes among 41 F5 plants from the cross CS ph1bph1b /MA5R, and aberrations permitted the location of the hairy peduncle gene ( Hp ) and marker XLFZ3473 to the region 5RL FL 0.78–1.0 with another nine markers locating to 5RL 0.0–0.78. The chromosome-specific markers and chromosome aberrations developed in this study will facilitate the introgression of rye chromatin into wheat. 3、Genome-wide identification and characterization of NB-ARC resistant genes in wheat (Triticum aestivum L.) and their expression during leaf rust infection Wheat ( Triticum aestivum L.) is an important cereal crop; however, its production is affected severely by numerous diseases including rusts. An efficient, cost-effective and ecologically viable approach to control pathogens is through host resistance. In wheat, high numbers of resistance loci are present but only few have been identified and cloned. A comprehensive analysis of the NB-ARC-containing genes in complete wheat genome was accomplished in this study. Complete NB-ARC encoding genes were mined from the Ensembl Plants database to predict 604 NB-ARC containing sequences using the HMM approach. Genome-wide analysis of orthologous clusters in the NB-ARC-containing sequences of wheat and other members of the Poaceae family revealed maximum homology with Oryza sativa indica and Brachypodium distachyon . The identification of overlap between orthologous clusters enabled the elucidation of the function and evolution of resistance proteins. The distributions of the NB-ARC domain-containing sequences were found to be balanced among the three wheat sub-genomes. Wheat chromosome arms 4AL and 7BL had the most NB-ARC domain-containing contigs. The spatio-temporal expression profiling studies exemplified the positive role of these genes in resistant and susceptible wheat plants during incompatible and compatible interaction in response to the leaf rust pathogen Puccinia triticina . Two NB-ARC domain-containing sequences were modelled in silico, cloned and sequenced to analyze their fine structures. The data obtained in this study will augment isolation, characterization and application NB-ARC resistance genes in marker-assisted selection based breeding programs for improving rust resistance in wheat. 4、High-density SNP mapping reveals closely linked QTL for resistance to Stagonospora nodorum blotch (SNB) in flag leaf and glume of hexaploid wheat The genetic control of adult plant resistance to Stagonospora nodorum blotch (SNB) is complex consisting of genes with minor effects interacting in an additive manner. Earlier studies detected quantitative trait loci (QTL) for flag leaf resistance in successive years on chromosomes 1B, 2A, 2D, 5B using SSR- and DArT-based genetic maps of progeny from the crosses EGA Blanco/Millewa, 6HRWSN125/WAWHT2074 and P92201D5/P91193D1. Similarly, QTL for glume resistance detected in successive years and multiple environments were identified on chromosomes 2D and 4B from genetic maps of P92201D5/P91193D1 and 6HRWSN125/WAWHT2074, respectively. The SSR- and DArT-based genetic maps had an average distance of 6.5, 7.8 and 9.7 cM between marker loci for populations EGA/Millewa, P92201D5/P91193D1 and 6HRWSN125/WAWHT2074, respectively. This study used single nucleotide polymorphism (SNP) markers from the iSelect Infinium 90K genotyping array to fine map genomic regions harbouring QTL for flag leaf and glume SNB resistance reducing the average distance between markers to 2.9, 3.3 and 3.4 -3.4 cM for populations P92201D5/P91193D1, EGA/Millewa and 6HRWSN125/WAWHT2074, respectively. Increasing the marker density of the genetic maps with SNPs did not identify any new QTL for SNB resistance but discriminated previously identified co-located QTL into separate but closely linked QTL. 5、Review on resistance to wheat blast disease (Magnaporthe oryzae Triticum) from the breeder point-of-view: use of the experience on resistance to rice blast disease This review on the resistance to wheat blast disease focus on the latest knowledge useful for the breeders, but also takes into account the lacks in these knowledge. To tackle this disease, it is relevant to apply a breeding strategy which has previously proven its efficacy for obtaining rice varieties with a high level of partial and durable resistance to blast. But, incomplete information is available on wheat blast resistance. Therefore, firstly, it is necessary to adjust this breeding strategy considering the worst hypothesis corresponding to every lack of knowledge. Next, the possible invalidation of every hypothesis can allow simplifying the breeding schema and its implementation. For every lack of knowledge, the practical consequences of the corresponding worst hypothesis, the study of its validity and the consequences of its possible invalidation are explained. Scientific arguments, materials and methods details are provided with the latest available references. 6、Wheat genetic resources in the post-genomics era: promise and challenges 7、B genome specific polymorphism in the TdDRF1 gene is in relationship with grain yield A and B genome copies of DRF1 gene in durum wheat were isolated and sequenced using gene variability. B genome specific polymorphism resulted, in a RIL population, in relationship with grain yield mainly in drought condition. Drought tolerance is one of the main components of yield potential and stability, and its improvement is a major challenge to breeders. Transcription factors are considered among the best candidate genes for developing functional markers, since they are components of the signal transduction pathways that coordinate the expression of several downstream genes. Polymorphisms of the Triticum durum dehydration responsive factor 1 (TdDRF1) gene that belongs to DREB2 transcription factor family were identified and specifically assigned to the A or B genome. A panel of primers was derived to selectively isolate the corresponding gene copies. These molecular information were also used to develop a new molecular marker: an allele-specific PCR assay discriminating two genotypes (Mohawk and Cocorit) was developed and used for screening a durum wheat recombinant inbred line population (RIL-pop) derived from the above genotypes. Phenotypic data from the RIL-pop grown during two seasons, under different environmental conditions, adopting an α-lattice design with two repetitions, were collected, analyzed and correlated with molecular data from the PCR assay. A significant association between a specific polymorphism in the B genome copy of the TdDRF1 gene and the grain yield in drought conditions were observed. 8、QTL for stay-green traits in wheat in well-watered and water-limited environments “Stay-green” plants retain green leaf area longer after flowering than senescent types. This can prolong carbon assimilation during grain filling, increasing yield, particularly under terminal drought stress. A population of doubled haploid wheats ( Triticum aestivum L.) derived from a cross between stay-green SeriM82 and senescent Hartog was grown in eight environments with varying degrees of water limitation. The dynamics of normalised difference vegetative index (NDVI) was followed post-flowering to evaluate change in leaf greenness. Quantitative trait loci (QTL) were identified for components of stay-green including i) maximum NDVI (Nmax), ii) an indicator of the maximum rate of senescence (SR), iii) thermal time from flowering to commencement of senescence (OnS), iv) thermal time from flowering to mid-senescence (MidS), and v) the integral of NDVI from flowering to 1500 °Cd after flowering (SGint). Genetic regions associated with QTL for stay-green traits were identified (i) in both wet and dry environments on chromosomes 4A, 4B, 4D (constitutive stay-green); (ii) primarily in wetter environments on 2A and (iii) primarily in dryer environments on 5B. Other regions associated with QTL for stay-green were identified on 3B and 7B in a mixture of environment types. In some environments, stay-green QTL co-located with QTL for seminal root angle, seedling root number and/or for yield. Other stay-green QTL were co-located with yield but not seminal root angle and seedling root number. This suggests genetic regions associated with seminal root angle and seedling root number are not solely responsible for the high yielding, stay-green phenotype. Selection for stay-green traits will increase the rate of genetic progress for adaptation of wheat to both well-watered and water-limited environments. 9、An Advanced Backcross Population through Synthetic Octaploid Wheat as a “Bridge”: Development and QTL Detection for Seed Dormancy The seed dormancy characteristic is regarded as one of the most critical factors for pre-harvest sprouting (PHS) resistance. As a wild wheat relative species, Aegilops tauschii is a potential genetic resource for improving common wheat. In this study, an advanced backcross population (201 strains) containing only Ae. tauschii segments was developed by means of synthetic octaploid wheat (hexaploid wheat Zhoumai 18 × Ae. tauschii T093). Subsequently, seed dormancy rate (Dor) in the advanced backcross population was evaluated on the day 3, 5 and 7, in which 2 major QTLs ( QDor-2D and QDor-3D ) were observed on chromosomes 2D and 3D with phenotypic variance explained values (PVEs) of 10.25 and 20.40%, respectively. Further investigation revealed significant correlation between QDor-3D and Tamyb10 gene, while no association was found between the former and TaVp1 gene, implying that QDor-3D site could be of closer position to Tamyb10 . The obtained quantitative trait locus sites (QTLs) in this work could be applied to develop wheat cultivars with PHS resistance. 10、miR430: the novel heat-responsive microRNA identified from miRNome analysis in wheat (Triticum aestivum L.) 11、Genetic and Molecular Characterization of Leaf Rust Resistance in Two Durum Wheat Landraces Leaf rust, caused by Puccinia triticina, is a constraint to durum wheat (Triticum turgidum subsp. durum) production, and landraces are reported to be an important source of resistance. Two Portuguese landraces (Aus26582 and Aus26579) showed resistance against durum-specific P. triticina races and were crossed with a susceptible landrace (Bansi) to develop recombinant inbred line (RIL) populations. Monogenic segregation for leaf rust resistance was observed among both RIL populations. The underlying locus, temporarily named LrAW2, was mapped to the short arm of chromosome 6B in the Aus26582/Bansi population and five DArTseq markers cosegregated with LrAW2. Simple sequence repeat markers sun683 and sun684, developed from the chromosome survey sequence (CSS) contig 6BS 2963854, identified through BlastN search of cosegregating DArTseq markers in the International Wheat Genome Sequencing Consortium database, cosegregated with LrAW2. Comparison of the CSS contig 6BS 2963854-based sequences amplified from parental genotypes led to the development of marker sunKASP 60, which also showed close linkage with LrAW2. Markers sun684 and sunKASP 60 showed close association with LrAW2 in both RIL populations. The amplification of LrAW2-specific products by linked markers in Aus26582, Aus26579, and Guayacan (Lr61) indicated that LrAW2 may be Lr61. The alternate amplicon or haplotype produced with LrAW2-linked markers in Australian durum cultivars demonstrated their effectiveness in marker-assisted selection. 12 Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat Since the introduction of wheat into Australia by the First Fleet settlers, germplasm from different geographical origins has been used to adapt wheat to the Australian climate through selection and breeding. In this paper, we used 482 cultivars, representing the breeding history of bread wheat in Australia since 1840, to characterize their diversity and population structure and to define the geographical ancestral background of Australian wheat germplasm. This was achieved by comparing them to a global wheat collection using in-silico chromosome painting based on SNP genotyping. The global collection involved 2,335 wheat accessions which was divided into 23 different geographical subpopulations. However, the whole set was reduced to 1,544 accessions to increase the differentiation and decrease the admixture among different global subpopulations to increase the power of the painting analysis. Our analysis revealed that the structure of Australian wheat germplasm and its geographic ancestors have changed significantly through time, especially after the Green Revolution. Before 1920, breeders used cultivars from around the world, but mainly Europe and Africa, to select potential cultivars that could tolerate Australian growing conditions. Between 1921 and 1970, a dependence on African wheat germplasm became more prevalent. Since 1970, a heavy reliance on International Maize and Wheat Improvement Center (CIMMYT) germplasm has persisted. Combining the results from linkage disequilibrium, population structure and in-silico painting revealed that the dependence on CIMMYT materials has varied among different Australian States, has shrunken the germplasm effective population size and produced larger linkage disequilibrium blocks. This study documents the evolutionary history of wheat breeding in Australia and provides an understanding for how the wheat genome has been adapted to local growing conditions. This information provides a guide for industry to assist with maintaining genetic diversity for long-term selection gains and to plan future breeding programs. 13 Natural variation in photoperiodic flowering pathway and identification of photoperiod-insensitive accessions in wild wheat, Aegilops tauschii The D-genome progenitor of hexaploid wheat, Aegilops tauschii Coss., has a wide natural species range in central Eurasia and possesses wide natural variation in heading and flowering time. Here, we report identification of two Ae. tauschii accessions insensitive to short day length. Similarly to a loss or reduced degree of vernalization requirement, the photoperiod-insensitive mutations were found only in the early flowering sublineage (TauL1b) of Ae. tauschii . Quantitative trait locus (QTL) analyses using two F2 mapping populations showed that a QTL for heading time on the long arm of chromosome 5D was related to the early heading phenotype of the photoperiod-insensitive accessions under short-day conditions. In the photoperiod-insensitive accession, expression patterns of two flowering-related genes were altered under short-day conditions compared with the patterns in photoperiod-sensitive accessions. This study indicates that analysis of natural variations in the Ae. tauschii population is useful to find novel genetic loci controlling agronomically important traits. 14 Genetic and physical mapping of a putative Leymus mollis-derived stripe rust resistance gene on wheat chromosome 4A | Plant Disease Wheat stripe rust is one of the most damaging diseases of wheat worldwide. The wheat–Leymus mollis introgression line M8664-3 exhibits all-stage resistance to Chinese stripe rust races. Genetic analysis of stripe rust resistance was performed by crossing M8664-3 with the susceptible line Mingxian169. Analysis of the disease resistance of F2 and F2:3 populations revealed that its resistance to Chinese stripe rust race 33(CYR33) is controlled by a single dominant gene, temporarily designated as YrM8664-3. Genetic and physical mapping showed that YrM8664-3 is located in bin 4AL13-0.59-0.66 close to 4AL12-0.43-0.59 on chromosome 4AL and is flanked by SNP markers AX111655681 and AX109496237 with genetic distances of 5.3 and 2.3 cM, respectively. Resistance spectrum and position analyses indicated that YrM8664-3 may be a novel gene. Molecular detection using the markers linked to YrM8664-3 with wheat varieties which commonly cultivated and wheat–L. mollis derived lines showed that YrM8664-3 is also present in other wheat–L. mollis introgression lines, but absent in commercial common wheat cultivars. YrM8664-3 is thus a potentially valuable source of stripe rust resistance for breeding. 15 A novel wheat cysteine-rich receptor-like kinase gene CRK41 is involved in the regulation of seed germination under osmotic stress in Arabidopsis thaliana The bread wheat gene TaCRK41 encodes a cysteine-rich receptor kinase. It is down-regulated by various abiotic stresses and by exposure to abscisic acid. A transient expression experiment in Arabidopsis thaliana protoplasts involving a fusion between the sequence encoding green fluorescence protein and the TaCRK41 allele from either the salinity tolerant bread wheat cultivar Shanrong No. 3 (SR3) or its salinity sensitive progenitor cultivar Jinan 177 (JN177) showed that the TaCRK41 product is deposited in the cytoplasm. Recombinant TaCRK41 originating from both SR3 and JN177 displayed no kinase activity in vitro . The constitutive expression of TaCRK41 in A. thaliana resulted in a marked reduction in the plants’ sensitivity to both exogenous abscisic acid and to salinity during germination. The level of ABA-induced transcription of ABI3 , ABI5 and the ABI5 -controlled genes EM1 and EM6 was significantly reduced in plants subjected to stress. The data support the idea that TaCRK41 is involved in the regulation of ABA-dependent germination under conditions of osmotic stress. 16 Characterization of QTLs for Root Traits of Wheat Grown under Different Nitrogen and Phosphorus Supply Levels Root is important in acquiring nutrients from soils. Developing marker-assisted selection for wheat root traits can help wheat breeders to select roots desirable for efficient acquisition of nutrients. A recombinant inbred line (RIL) population derived from wheat varieties Xiaoyan 54 and Jing 411 was used to detect QTLs for maximum root length and root dry weight (RDW) under control, low nitrogen and low phosphorus conditions in hydrophobic culture (HC). We totally detected 17 QTLs for the investigated root traits located at 13 loci on 11 chromosomes. These loci differentially expressed under different nutrient supplying levels. The RILs simultaneously harboring positive alleles or negative alleles of the most significant three QTLs for RDW, qRDW.CK-2A, qRDW.CK-2D , and qRDW.CK-3B , were selected for soil column culture (SC) trial to verify the effects of these QTLs under soil conditions. The RILs pyramiding the positive alleles not only had significantly higher shoot dry weight, RDW, nitrogen and phosphorus uptake in all the three treatments of the HC trial, but also had significantly higher RDW distribution in both the top- and sub-soils in the SC trial than those pyramiding the negative alleles. These results suggested that QTL analysis based on hydroponic culture can provide useful information for molecular design of wheat with large and deep root system. 17 A wheat MYB transcriptional repressor TaMyb1D regulates phenylpropanoid metabolism and enhances tolerance to drought and oxidative stresses in transgenic tobacco plants MYB transcription factors are involved in the regulation of plant development and response to biotic and abiotic stress. In this study, TaMyb1D, a novel subgroup 4 gene of the R2R3-MYB subfamily, was cloned from wheat (Triticum aestivum L.). TaMyb1D was localized in the nucleus and functioned as a transcriptional repressor. The overexpression of TaMyb1D in tobacco (Nicotiana tabacum) plants repressed the expression of genes related to phenylpropanoid metabolism and down-regulated the accumulation of lignin in stems and flavonoids in leaves. These changes affected plant development under normal conditions. The expression of TaMyb1D was ubiquitous and up-regulated by PEG6000 and H2O2 treatments in wheat. TaMyb1D-overexpressing transgenic tobacco plants exhibited higher relative water content and lower water loss rate during drought stress, as well as higher chlorophyll content in leaves during oxidative stress. The transgenic plants showed a lower leakage of ions as well as reduced malondialdehyde and H2O2 levels during conditions of drought and oxidative stresses. In addition, TaMyb1D up-regulated the expression levels of ROS- and stress-related genes in response to drought stress. Therefore, the overexpression of TaMyb1D enhanced tolerance to drought and oxidative stresses in tobacco plants. Our study demonstrates that TaMyb1D functions as a negative regulator of phenylpropanoid metabolism and a positive regulator of plant tolerance to drought and oxidative stresses. 18 Characterization of the CCT family and analysis of gene expression in Aegilops tauschii Flowering is crucial for reproductive success in flowering plant. The CCT domain-containing genes widely participate in the regulation of flowering process in various plant species. So far, the CCT family in common wheat is largely unknown. Here, we characterized the structure, organization, molecular evolution and expression of the CCT genes in Aegilops tauschii , which is the D genome donor of hexaploid wheat. Twenty-six CCT genes ( AetCCT ) were identified from the full genome of A . tauschii and these genes were distributed on all 7 chromosomes. Phylogenetic analysis classified these AetCCT genes into 10 subgroups. Thirteen AetCCT members in group A, C, H and G achieved rapid evolution based on evolutionary rate analysis. The AetCCT genes respond to different exogenous hormones and abiotic treatments, the expression of AetCCT4 , 7 , 8 , 11 , 12 , 16 , 17 , 19 , 21 and 22 showed a significant 24 h rhythm. This study may provide a reference for common wheat's evolution, domestication and evolvement rules, and also help us to understand the ecological adaptability of A . tauschii . 欢迎关注 小麦研究联盟 ，了解小麦新进展
VRN1的多重效应---兼论分子育种 作者：麦萌 群里今天说到分子育种的问题，有的小伙伴抛出下面一张图。 图里的观点我是一半赞同一半不赞同。不赞同的是分子育种的精华是将DNA带进田间。我倒是认为恰好相反，未来应该是田间的育种材料必须经过实验室DNA检验才能种到田里。现在还有一种说法叫做分子设计育种，这个叫法很贴切。也许初期经验不足，设计出的材料在田间不是最好的，但是一旦经验上升为科学，育种是一门艺术的说法也许终将会消失 。 群里后来又有小伙伴抛出“从头驯化”的观点。我很崇拜这个观点，有的时候我就想，小麦的穗子为啥不能长得像水稻像谷子像狗尾草？如果将来有一天会有这样一个项目，我都给他起好名字了，叫逆天改命。所谓我命由我不由天，大自然的馈赠不够完美，就想改改而已 。 扯远了，回到今天推送的主题 VRN1 ，提到 VRN1 就不得不提 严六零 教授，为啥呢？因为这个人低调奢华有内涵，高端大气上档次 ，说笑的 ，那主要是因为VRN1是人家克隆的，现在这篇PNAS上的文章引用已经上千次了（下图）。 找到了VRN1是不是就心满意足了，然而并没有，严老师在接下来的3年时间里又接连把VRN2以及VRN3给克隆了。 就问服不服！？话说十几年前小麦里图位克隆就玩的这么溜的也没谁了，当然这里还要提一下严老师当时所在的实验室，加州大学戴维斯分校的Jorge Dubcovsky实验室（见下图）。刚入门的新研究生可以翻翻他实验室发的文章，如果能信手拈来，你离大神也不远了 。 好了，人物介绍到这。我们来看今天的这篇研究，题目是“ Nitrogen use efficiencyis regulated by interacting proteins relevant to development in wheat ”，发表在plant biotechnology journal上，通讯作者是 严六零 教授。摘要如下， Wheat (Triticum aestivum) has low nitrogen use efficiency (NUE). The genetic mechanisms controlling NUE are unknown. Positional cloning of a major quantitative trait locus (QTL) for N-related agronomic traits showed that the vernalization gene TaVRN-A1 was tightly linked with TaNUE1, the gene shown to influence NUE in wheat . Because of an Ala 180 /Val 180 substitution, TaVRN-A1a and TaVRN-A1b proteins interact differentially with TaANR1, a protein encoded by a wheat orthologue of Arabidopsis nitrate regulated 1 (ANR1). The transcripts of both TaVRN-A1 and TaANR1 were down-regulated by nitrogen. TaANR1 was functionally characterized in TaANR1::RNAi transgenic wheat, and in a natural mutant with a 23-bp deletion including 10 bp at the 5' end of intron 5 and 13 bp exon 6 in gDNA sequence in its gDNA sequence, which produced transcript that lacked the full 84-bp exon 6. Both TaANR1 and TaHOX1 bound to the Ala 180 /Val 180 position of TaVRN-A1 . Genetically incorporating favorable alleles from TaVRN-A1 , TaANR1 , and TaHOX1 increased grain yield from 9.84% to 11.58% in the field. Molecular markers for allelic variation of the genes that regulate nitrogen can be used in breeding programs aimed at improving NUE and yield in novel wheat cultivars. 在一个双亲群体中检测到5A长臂上有一个氮相关的QTL，并且该QTL也与开花期，叶绿素含量，每穗粒数，单株产量以及收获指数显著相关，所以推测该这些性状都受该QTL调控。随后将QTL对应的基因命名为 TaNUE1 。 为了进一步克隆该基因，15个重组体用来进一步缩小区间，经过筛选6410个BC1F3株系，最终最小物理区间内有3个基因，分别是 TaCYB5 ， TaAGLG1 以及 TaVRN-A1 （下图）。 （其实我对这图里的QTL峰顶为啥没与VRN1对应有一种执念） 接下来就是要看看这个区间的序列在两个材料中的差异。最后发现T aVRN-A1 的启动子区以及内含子上有差异。但是TaVRN-A1的表达并没有受氮水平的影响，所以推测可能是在蛋白水平上起作用。 在蛋白水平上， TaAGLG1 有一个蛋白替换， TaVRN-A1 有两个。然后就检测这两个MADS蛋白是否与 ANR1 基因互作。 ANR1 基因在拟南芥里调控侧根生长并且响应硝酸根处理， ANR1 也编码一个MADS蛋白。蛋白互作实验发现，只有 TaVRN-A1 的一个等位变异能与 ANR1 基因互作。进一步通过序列比对，确定蛋白互作的关键位点，而此关键位点正好位于氨基酸有差异的地方（下图）。 至此，本文的关键打通，下面是一些验证性的实验，包括转基因，突变体等。另外也发现 TaVRN-A1a 也能与 TaHOX1 互作， TaHOX1 在小麦的抽穗期中具有重要功能。这个结果说明 TaVRN-A1 ， ANR1 和 TaHOX1 ，这三个基因间的互作关系影响了氮相关的性状。 这篇文章到此结束，细节的地方还请参考原文。接下来介绍另外一篇与VRN1有关的文章。其实这篇文章在其刚刚在线的时候我们简单的介绍过（ 原文中此处为链接，暂不支持采集 ），最近又正式在线，正式在线的排版很好，索性就看了一遍，在育种上比较重要，感觉有必要给大家再说一说。这篇说到 VRN1还与根的发育有关 。 首先在219份小麦里做关联分析，发现5B上的一个QTL与根的伸展角度有关（nodal root angle index）。这个QTL包含6个连锁的SNP，同时发现 VRN-B1 也位于这个区间里（下图）。 VRN1冬性的等位基因存在的话会减少根生长的夹角（见下图），冬性的等位基因在苗期降低根长，而在开花期则会使根长增加。 在大麦里也观察到这一现象。不同的一点是，在苗期冬性等位基因并没有明显的影响根长。 VRN-H1 既能够促进开花也能让根扎得更深（steep, cheap, and deep）。而对 VRN-H2 的分析（ VRN-H1 的靶基因）发现， VRN-H2 的一个缺失变异能够打破这种双重作用，该缺失变异能够促进开花但不影响根的生长。 为了进一步确定是 VRN-B1 控制根型而不是因为与其他基因连锁导致的，作者安排了转基因实验，实验结果证明了是VRN-B1基因。后面作者又进一步分析了表达以及在自然群体中的效应。 这篇文章给我们一个启示，开花早，可能根扎的不深，扎的不深就不容易抗旱。毕竟干旱节水也是育种的一个重要方面。文中在大麦里已经发现可以打破这种连锁，在小麦里还需要进一步挖掘。 结合第一篇文章提到的关于N吸收与利用的问题来看，这个问题还挺复杂。有的时候我们想要早熟的，结果导进去其他性状又不好了。既然明白了VRN1的多重作用，后面就有机会改造它。 其实回头再看看我们讨论的分子育种问题，不是分子育种（分子设计育种）不行，而是我们才刚刚开始。正如早期的计算机干不了多少活，现在呢？离了它，那将是多么麻烦的一件事 。 欢迎关注“小麦生信联盟”，了解小麦新进展 请点击此处输入图片描述
美国人口占世界总人口的百分之五，但其农业却生产了世界粮食总量的五分之一。这还没完全反映美国的农业生产力水平，根据政府计划，美国每年为水土保持或其他目的，要休耕大量土地，产量因此受到限制。若取消这些限制，粮食产量还可以大幅度增加。美国是世界上城市化程度最高的国家，农业人口小于人口总数的百分之一。美国农业人口一直在减少，生产率却不断提高。近几十年来，美国的农业劳动生产率超过欧盟各国，居世界首位。它是世界上玉米、小麦、稻米、大豆、棉花等主要作物单位面积产量最高的国家之一。从统计资料上看，一九五零到二零零零年，世界粮农组织常规统计的十种主要农作物中，美国有五种居于第一位，另外五种交替排在首位。二零零一年，玉米、小麦、大豆、稻谷和花生等五种主要农作物中，美国的单位面积产量高于世界平均水平，其中大豆和花生高出一倍以上。在世界各国农产品总产量的排位中，美国的玉米、大豆和奶类总产量在世界上连续几十年遥遥领先居首位，棉花和肉类等一般在前两位之内。按照主要农产品人均占有水平，多年来一直在世界的前三位之内。 从十九世纪起，美国农业不但使美国人民摆脱了饥饿，还孕育了现代化的美国。美国的农业为其工业提供了大量的原料，同时在机械化和种子改良的推动下，解放了大量劳动力，为城市和工业提供了大量的人力资源。美国的农业现代化主要是从三个方面展开的：首先是农业机械化，惠特尼的轧棉机和麦考尼克的收割机为代表，仅农业机械化一项就把劳动效率提高了几十倍，使美国农业走向了工业化；第二是种子改良，本文主人公马克·卡尔顿 就是其中最重要的人物，这些无名英雄被美国老百姓称为反饥饿斗士，因为他们使得美国的大部分农作物的单位面积产量一直高居世界前矛；第三是化肥的广泛使用，使得美国农业产量进一步提高。所有这一切主要是在美国内战后的几十年内完成的。这一切使的美国稳稳地进入了现代工业化，也使美国成了世界第一强国。要是少了马克·卡尔顿的工作，美国的农业现代化就会晚好多年才能实现，因此卡尔顿对美国农业的贡献不可估量。 一八六六年三月七日，马克·卡尔顿出生于俄亥俄（ Ohio）州门罗（Monroe）县接近耶露沙冷（Jerusalem）的地方。父亲，路易·卡尔顿（LouisD Carleton）有英国血统，来自宾夕法尼亚。母亲，丽缔亚·曼（Lydia J Mann）有荷兰血统。 一八七六年，卡尔顿十岁时，他们一家搬到了堪萨斯（ Kansas）州的克劳德县（Cloud）。他的早期教育来自俄亥俄和堪萨斯的农村小学（Rural School）。一八八四年，卡尔顿进入了曼哈顿（Manhattan KS）的堪萨斯农学院（Kansas Agricultural College）的二年级学习植物学和化学。一八八七年，卡尔顿从堪萨斯农学院毕业并获得学士学位。一八八八年至一八九一年，卡尔顿出任位于堪萨斯维契塔（Whichita）市的加菲尔德大学（Garfield University）的自然史教授。在此期间，卡尔顿学会了拉丁语和希腊语，同时在田间收集到了大量的植物真菌。一八八九年，卡尔顿带了一队学生，来到了科罗拉多（Colorado）、犹他（Utah）、怀俄明（Wyoming）、蒙他那（Montana）的落基山脉（Rocky Mountains）中采集植物标本。一八九一年夏天，卡尔顿和他的学生来到了堪萨斯西南部、科罗拉多东南部、印地安人的保留区（位于现在的俄荷拉荷马（Oklahoma）州）、德克萨斯（Texas）州，采集植物标本。卡尔顿把这一期间的研究成果，发表在《国家植物标本图集》（NationalHerbarium）上，卡尔顿发现了按地区分布的植物群，这给他后来的农学（Agronomy）研究带来了很大的启发。一八九二年至一八九三年，卡尔顿在堪萨斯农学院读研究生，并获得硕士学位。 一八九三年，卡尔顿来到堪萨斯州农业试验站任助理研究员。在那里，卡尔顿加入了 A·S·希区克科（A·S·Hitchcock）教授的研究团队，研究美国小麦的黑锈病（Blackrust）。卡尔顿和希区克科仔细地观察了小麦的各类真菌，同时还到农民那里进行实地考察。他们试制了几种杀真菌的药，但效果很差。他们发现了一系列真菌研究实验方法。这一时期，他们最重要的成果是发现了不同种类的小麦长有不同种类的真菌，没有一种真菌能存于所有的小麦中。 因为卡尔顿在农业试验站的杰出工作，卡尔顿被任命为美国农业部植物病理生理处（ Vegetable Physiology and Pathology of the United States Department of Agriculture）的助理病理学家。一八九四年三月，卡尔顿来到了华盛顿。希区克科这样评价他：“一个卓越的、值得信赖的人。”卡尔顿身高超过一米九，极为严肃，精力充沛，满面胡须，从没有人听到他说过一句笑话。同事说“卡尔顿能做任何事情，就象是一头牛。” 在他的新职位上，卡尔顿继续着他的小麦黑锈病研究，他放弃了书桌和图表来到了大平原地区的农场。一位住在萨林那（ Salina）的农民，B·B·斯蒂密尔（B·B·Stimmel），给了卡尔顿一片试验田。经过一段时间的研究，卡尔顿发现与流行的观点相反，对小麦危害最大的是黑锈秆菌，而不是桔锈叶菌。大量的早期研究走错了方向。卡尔顿和瑞士科学家杰柯布·艾里克森（JakobEriksson），同时发现小麦的黑锈病是无法痊愈的，只有缩短小麦生长期来避免它。这项研究成果使得卡尔顿开始了对抗黑锈病的小麦新品种研究。卡尔顿很快就收集到了上千种的小麦品种，他发现只有几种小麦能在干旱、寒冷和黑锈病的情况下存活。卡尔顿从实验和观察中得出了一个极为重要的结论：适合大平原种植的小麦必须是能抗旱、抗寒、抗黑锈病、早熟的小颗粒小麦。卡尔顿还敏锐地察觉到农业中的技术、环境、和经济问题。这些成果集中发表在卡尔顿的一篇早期的重要论文“论美国小麦的改良”中。在这篇论文中，卡尔顿明确指出。美国需要的是硬小麦而不是软小麦。卡尔顿预见到了美国将会大面积地种植小麦，并且主要在大平原地区，卡尔顿要为大面积地种植小麦打下一个坚实的基因基础。 几年后，卡尔顿发现堪萨斯州中部俄罗斯和德国移民的小麦收成很好，很少欠收。甚至在大平原地区绝大部分地区的小麦颗粒无收的情况下，他们的收成依然很好。一八九六年，卡尔顿来到这些地区，这些小麦给他留下了深刻的印象。在得知俄罗斯和德国移民的小麦的习性后，卡尔顿进行了大量的试验。最后，卡尔顿得出了一个改变美国农业史的结论：俄罗斯小麦最适合在美国大平原地区种植。 一八九七年，卡尔顿和阿曼达·伊利莎白·富特成婚。婚后，卡尔顿来到了内布拉斯加（ Nebraska）州林肯（Lincoln）市的内布拉斯加州农业试验站工作。在林肯市的这一时期，卡尔顿开始研究俄罗斯的气侯、农业、和语言。他比较了俄罗斯高原与美国大平原的各种条件，更让他坚信，俄罗斯小麦经过数代的自然选择，更适合于美国大平原地区。卡尔顿写到：“经过四年的研究，我的结论是俄罗斯和西伯利亚小麦最适合在大平原地区种植。”后来，他又写到：“我越来越觉得，土壤和气侯对于小麦品种的影响，将对美国的农业产生巨大的影响。”这时，卡尔顿已经有了一个至关重要的理念：俄罗斯高原与美国大平原在土壤和气侯上很相似，而这一相似性将对美国的小麦生产产生深远影响。 卡尔顿开始说服他的上司，让他到俄罗斯去证实他的理论。当时的农业部外国种子和植物引进处处长，戴维· A·菲尔蔡德是（David A Fairchild）堪萨斯农学院院长的儿子，他派了很多人到世界各地收集各种植物种子，来改良美国植物。菲尔蔡德派尼尔斯·E·汉森（Niels E Hansen）去俄罗斯收集能在北部大平原生长的草种。汉森碰巧带回来了一些小麦种子，菲尔蔡德和卡尔顿试种了这些种子之后，菲尔蔡德说服了农业部部长詹姆斯·威尔逊（James Wilson）让卡尔顿去俄罗斯考察小麦。 一八九八年六月二十四日，菲尔蔡德给在林肯市的卡尔顿发了一封电报，告知农业部批了一笔特别基金，专门给卡尔顿用于去俄罗斯收集各类小颗粒小麦种子。卡尔顿在回电中说：“对我来说，这是一个很大的惊喜。这是我多年前就想做的事。”卡尔顿满怀热情地接受了这个任务，他不仅要收集种子，他还要研究小麦与环境的关系。农业部部长威尔逊给了卡尔顿一封信，信中考虑到了卡尔顿可能遇到的各种情况，最后威尔逊写到：“卡尔顿先生此行是为了提高美国的农业生产来考察欧洲和西亚的农业的。” 卡尔顿交待完他在林肯市的工作一个月后，来到了英格兰。观察了几天麦种孵化，卡尔顿又去了法国、比利时、德国、丹麦、瑞士、奥地利、匈牙利、和俄罗斯的主要大城市。俄罗斯之行始于黑海，他去了奥德萨这个红冬麦的中心产地，去了乌克兰、伏尔加河谷、巴库、最后从奥德萨离开了俄罗斯经波兰、法国、英国回国。 卡尔顿在俄罗斯和农民们在交谈 卡尔顿俄罗斯之行只有几封信可以参考，大多数人是从他的公告版上间接了解的。卡尔顿在俄罗斯要用他那蹩脚的俄语去和那些富有的农场主打交道，还要和那些贫穷的农民们交流，最难的是要求那些政府官员帮他去找他想要的麦种。卡尔顿从俄罗斯带回了二十三种不同的小麦种子、一种荞麦种子、两种饲料种子、及很多种不同的园林植物。卡尔顿带回美国的古班加（ Kubanka）麦种适合于从德克萨斯到科罗拉多的高原地带，还有一种适合于达科达地区的春麦种。卡尔顿从伏尔加河谷，带回来了很多适合于美国北方的春麦种。他还找到了几种燕麦和其它有用的农产品种子。因为严重干旱，卡尔顿没有在俄罗斯的冬麦产区停留。他要求当地官员把种子寄给他，直到一八九九年二月，他在去华盛顿的路上才收到。卡尔顿把他对俄罗斯谷物的研究成果写进了题目为“俄罗斯谷物在美国的移植”的报告中。 一八九九年秋，卡尔顿接受了一九零零年巴黎谷物展览会上监管美国谷物的职位。一九零零年，卡尔顿去了巴黎。同年六月，他从巴黎再次来到俄罗斯。这次，他是为了冬小麦。七月，卡尔顿到达了奥德萨开始对高加索和克里门的小麦进行调查。这一次，卡尔顿的俄语有了很大的长进，他说：“因为我过了语言关，我很快就取得了上次来俄罗斯时的那些成果。”他为农业部收集了大量的冬小麦，种种迹象表明，其中有一种叫卡尔科夫（ Kharkov）的冬小麦，最适合大平原地区种植。同时，他还给堪萨斯的一位农民寄去了不少麦种。卡尔顿还拍了数百张照片。九月，卡尔顿结束了这次俄罗斯之行。在布达佩斯特（Budapest），卡尔顿写道：“我获得了所有我想要的东西，还有几百幅照片和很多有价值的资料。 卡尔顿的论文和 旅 行很快得到了认可。改组后的农业部，任命他为植物工业局（ Bureau of Plant Industry）谷物专家。卡尔顿最重要的工作就是引进俄罗斯谷物，他与大平原各州的农业试验站建立了合作关系，把种子发放给各州的农业试验站。试验毫无偏见，卡尔顿并不只想推广俄罗斯麦种。 一九零一年，卡尔顿开始推广古班加小麦，这是一种能在美国生长的抗旱性极好的硬粒小麦。但是，因其加工不易，美国的食物加工厂，不愿意用它做通心粉原料。他们用的是软春小麦。为了推广古班加小麦，卡尔顿用试验和化学分析证明了古班加小麦的优越性。他给很多食物加工厂作了演示。卡尔顿为了推广古班加小麦甚至收集了很多欧洲的古班加小麦通心粉食谱。一九零四年，这一年的春小麦遭到了历史上最严重的黑秆锈病。于是，红河谷一带的农民，象卡尔顿期待的那样开始种植古班加小麦了。同时，北达科达州的农业试验站开始让食物加工厂漂白加工古班加小麦。最后，食物加工厂开始接受古班加小麦了。卡尔顿胜利了。 推广俄罗斯红冬麦就容易多了。农民们早已接受了土尔其冬麦了，而俄罗斯红冬麦卡尔科夫和它很相似，但远好过土尔其冬麦。很快，俄罗斯红冬麦就在中部大平原大面积种植了。 在其它农产品的推广上，卡尔顿取得了参差不齐的成果。 进入二十世纪后，在两篇著名的论文中，卡尔顿论证了美国有能力让本国人民长期吃饱，并能应付全世界的谷物需求。当时有一个流行观点，土地的粮食产量在逐年下降，而人口则在逐年增长，人类的食物短缺是无法避免的。卡尔顿指出，单位土地的粮食产量正在增加，尤其是在改良品种中，种植面积也在增长，他准确地预言到小麦将不再短缺。 卡尔顿很快就有了反饥饿斗士的称号，同时他也成了美国农业的顶尖人物。一九零八年，卡尔顿当选为美国农学会（ American Society of Agronomy）主席。在他的就职演说中，卡尔顿是这样定义农业科学的：“农业科学是对田野中所有物种进行研究的科学，并对其每一科目进行专业化研究，这也是农学家的使命。”一九一六年，卡尔顿发表了他的经典著作《The Small Grains》。这时，卡尔顿到了他荣誉的顶峰。 一九一六年，给卡尔顿加薪的推荐信被打了回来，尽管经过努力后，农业部还是给他加了薪。但是，这一事件预示了卡尔顿的职业生涯将过早地结束。就是在这一时期，卡尔顿的个人财政状况陷入了危机。卡尔顿有四个孩子，三千美元的年薪，使他没有多少积蓄。当他的一个女儿患了小儿麻痹症之后，卡尔顿开始四处借钱，为女儿到处求医。为了德克萨斯州的农场和佛罗里达果园的经营，卡尔顿常常不去上班。一九一七年农业部的调查结果，证明卡尔顿的问题很严重，但因其名声太大，而没有采取行动。卡尔顿的儿子因病需要手术，另一个女儿又因病早逝，这一切造成了他的破产。卡尔顿先向同事借钱，再向谷物商借钱，这与他的职务有利益冲突。一九一八年，农业部长戴维·休斯顿（ David Houston）让卡尔顿辞职。卡尔顿的朋友为他上诉过，但没有结果。 后来的日子里，卡尔顿为美国谷物公司（ United States Grain Corporation）做了两年的研究工作。一九二零年到一九二四年，卡尔顿来到巴那马和洪都拉斯为美国水果公司（American Fruit Company）研究香蕉疾病。一九二四年，卡尔顿应一位富有的秘鲁棉花种植商的请求，来到秘鲁工作。一九二五年，卡尔顿在秘鲁死于 疟疾。 卡尔顿被安葬在秘鲁的派塔（ Paita）。 学者们认为：“从一八六零年到一九一零年这半个世纪内，美国经历了一次农业革命，其中包括农业机械的发明应用和科学耕种方法的推广，政府迅速和不断地对农业加以注意和协助，以及农业教育的广泛开展。”这次农业革命的最大成果是加快了垦殖西部土地的进程，使美国的耕地面积迅速扩大，农产品数量急剧增长。据统计，十九世纪七十年代美国增加了一点五亿英亩耕地。一八八零年到一九零零年的二十年间又增加耕地三点零三亿英亩。农产品数量的增长从出口粮食的增长中可以看出：一八八三年以前的五十八年间美国共出口二十点六四亿蒲式尔小麦，但一半以上是在一八七四年后出口的。也就是说最后十年的出口量超过了前四十八年出口量的总和。这次农业革命使美国的农业获得了长足的进步，一跃而跻身于世界先进农业国之林。这次农业革命主要是农业机械的广泛应用、种子的改良、和化学肥料的大量使用，其中对种子改良贡献最大的人就是马克·卡尔顿。
小麦B基因组的起源 做小麦研究的基本都知道小麦B基因组之间相对A/D基因组要具有更高的基因组多样性，也即B基因组相对不保守。已经有不少研究探究B基因组的起源问题，当然都是在分子标记基础之上，这里有个别研究认为B基因组是多起源的。随着小麦基因组参考序列的公布以及测序技术的进一步发展，在序列水平上解析B基因起源已不是问题，14年science上的那篇文章虽然已经报道过，但我认为所采集物种较少，六倍体也只有中国春。 鉴于我最近接触的六倍体小麦重测序数据，我更倾向于小麦Ｂ基因组是多起源的。由于数据量较少和缺少Ｂ基因组的祖先种序列，也不排除Ｂ基因组在自然进化和人工选择上经历了剧烈的选择从而导致这种Ｂ基因组见巨大的差异。 说完这个说说刚刚看到的这篇文章吧，同样和B基因组有关。 Transposon insertion resulted in the silencing of Wx-B1n in Chinese wheat landraces . 文章很简单，就是发现TE插入Wx-B1之后，导致功能丧失。这个TE是从3B染色体上剪切过来的，不是复制哟。还算是比较简单的一篇文章，让我想起了TaGS5-B1的情况，B1基因内部有两处TE插入，从表达水平来看，相比A1和D1，B1基因表达水平剧烈下降。也许补一些实验，也可以发发文章。 小麦基因组巨大，在生物信息学分析时，眼光不要紧盯着基因区，绝大部分的非基因区藏着很多宝贝。这样巨大的异源多倍体是一个很好的研究研究基因组形成与进化的案例。当然，以目前的Illumina短测序来分析TE的变异情况还是有一定难度的。
The pangenome of hexaploid bread wheat 今天看到这样一篇文章，着实高兴了一番。在小麦参考基因组刚刚公布，文章还未发表的情况下，突然跳出了一篇小麦宏基因组的文章，让人不得不得感叹，这都是什么世道。匆匆看过一遍之后，有点失望，这分析也太简单了，怪不得只发在了The plant journal上，需要挖掘的信息很多。 文章一共使用了18个小麦品种，其中就包括中国春，还有其他16个澳大利亚的小麦品种。分析的内容都很初级，这里不再详谈了。说点和它的原始数据有关的事。看完文章之后，竟然没说原始数据在哪里可以下载。于是匆忙给 David Edwards 教授发邮件询问。发完之后我就下载附件信息再看，结果竟然有说在什么地方下载原始数据。看到这，我寻思大事不好，人家提供了我竟然发邮件说没有，闹了国际大笑话。我于是赶紧看看是否发出去了。结果又让我大吃了一惊，David教授竟然回我邮件了。大意就是说我们提供了，只不过文章还未正式上线，数据还未整理好。我看看了时间，可能恰好是David教授刚刚上班，正在收邮件呢。我看了下原始数据从2011年就有了一部分数据，后面陆陆续续又补充了很多。也难怪，写文章时小麦还没有一个像样的参考基因组，de novo组装也不太现实。 在这里还是感谢David教授，非常及时又爽快的给我回邮件。貌似和老外邮件交流很少碰到有去无回的。这让我想起了给国内的一些老板发邮件请教问题的时候，绝大部分老板不会回我。印象中老师华中农大研究玉米的严建兵老师给我回过几次，还有凌宏清老师给我回过一次。
【明辨是非】从生态学专业角度出发，我在转基因应用对粮食安全、生态环境保护与健康安全方面的本能判断为：一是不能直接增产，不可能转一两个基因就增加产量，没有这样的增产基因（育种专家佟屏亚先生在这方面更有发言权）；二是农药与除草剂使用量增加而不是减少，转基因控制了主要害虫后，次要害虫还要借助农药；抗除草剂转基因作物释放会鼓励农民使用更多除草剂，看看全球转基因技术应用后的农药与除草剂用量就知道，尤其美国的例子更具说服力；三是健康安全方面目前还没有安全定论，安全证书不能证明安全，还需要进行更多的独立第三方实验，如果不能做人体实验，也需要对实验动物尤其灵长类动物做超越90天的长期实验，从而确保安全。下面刊登自然杂志评论转基因小麦失败的报道，所报道的一些迹象证明我们前面的判断，这对国内的转基因大跃进或许是个降温的提醒。老外是客观的认真的，这种态度值得我们学习。国内转基因学家也应当认真做一些类似大田实验，对转基因水稻、小麦、玉米、棉花、花生等都认真设计长期实验，看看产量、农药、除草剂用量的变化，不要看一两季，要看三五年甚至十年以上，用科学事实说话，强于做无休止的争论一百辈。如果我们成功了，英国人失败了，那是中国人的骄傲啊。同时转载著名生物学家留实先生的评论，从他的评论来看，目前的转基因科技，政治的成分已经大于科学的成分了，这是全球资本市场化造成的苦果，科学研究也难保净土。。。 本文链接：http://blog.sina.com.cn/s/blog_502041670102w1t5.html “失败中成功 ” ？《自然》如此评价转基因小麦试验田失败 今日出版的国际顶奸杂志《自然》针对不久前报道的 英国转基因小麦田间试验完全失败 的消息，发表了题为“ 失败中成功 ” 的社论。 2012 年开始在英国伦敦北部进行的转基因小麦田间试验不仅没有达到预期的增产，甚至于连应当有的驱虫效果也没见到。该失败的试验 结果发表在自然出版集团旗下的《科学报告》 上。 面对如此现实，老奸巨滑的挺转杂志《自然》尽发表社论称 “ A failed crop trial of genetically modified wheat still provides crucial lessons for those battling to provide the planet’s growing population with a sustainable food supply ” （一个失败的转基因小麦田间试验仍然为要为星球增长人口提供可持续食物供给的人提供关键教训）。真是见过无耻的，没见过这么无耻的。 在这篇社论里，《自然》还不忘讥讽那些反转人士，称 “ The crop failed , but so did the protests. The research was done; a useful result was obtained. Ironically, had the protests succeeded and the trial been abandoned, the protesters would be unable to crow about the crop’s failure. ” （转基因作物失败了，但它的反对者也同样失败。研究完成了并获得了有用的结果。如果反对者成功地迫使该试验放弃，那反对者就不可能拿转基因作物失败说事了）。真是见过混蛋的，没见过这么混蛋的。 《自然》社论 最后说 “ All who care about evidence-based policy-making should thank those who continue to struggle against both the difficulties of doing science and the added difficulties caused by people who would see science abandoned. We will all need the fruits — and the cereals — of their labours. ” （所有关心以证据为基础制定政策的人都应当感谢那些与科学的艰难以及由于那些希望科学被放弃而增加的困难继续斗争的人。我们都需要他们辛劳的“水果”及 “ 谷物食品 ” ）可《自然》别忘了，它对中国科学家蒋高明等的的 增加粮食作物产量 又 增加经济财政收入 的 环保生态农业 的硕果是个什么态度 ？ 《今日中国》以 9 种语言报道了弘毅生态农场的成功实践 ，但这样好的研究结果试图 “ 登顶《自然》 ” 却不能成功。 《自然》，你是不是被转基因转昏了头，不知啥叫失败？啥叫成功？ 附： http://www.nature.com/news/success-in-failure-1.17855 Nature | Editorial Success in failure A failed crop trial of genetically modified wheat still provides crucial lessons for those battling to provide the planet’s growing population with a sustainable food supply. 25 June 2015 Updated: 1. 01 July 2015 It is rare for failures to be lauded in science. History, as it is often said, is written by the winner. The history of research is no different. Related stories · GM wheat that emits pest alarm signals fails in field trials · Departing head of biotech institute defends GM field trials · Misplaced protest More related stories But failure in science is vital. Another cliché about history is equally applicable to scientific flops: people who are ignorant of them are doomed to repeat them. Which brings us to a green — and to some, an unpleasant — field in England. In 2012, a team based at Rothamsted Research, an agricultural-science institute a short train ride north of London, planted wheat that they had genetically modified to emit a chemical used by aphids as a warning that they are under attack. The researchers wanted to see whether this would give the crops a way of repelling the damaging pests. They thought that the chemical might also attract insect parasites alerted to the promised presence of aphids. Before they got the chance, the crops attracted a swarm of protesters. Opponents of genetic modification (GM) technology mounted an imaginative, if sometimes bizarre, campaign against the trial, complete with dubious scientific claims, loaves of bread adorned with cartoon cow heads, and videos promising to ‘Take the Flour Back’ complete with rock-music soundtrack. The research itself cost ￡732,000 (US$1.2 million) over five years. Securing the site from those who threatened to tear it up cost nearly ￡1.8 million. The idea behind what has, rather unfortunately, become known as ‘whiffy wheat’ showed promise in the laboratory. Yet in field trials the crop is an unquestionable failure. A paper published on 25 June in the journal Scientific Reports notes that the GM crops “showed no reduction in aphids or increase in parasitism” compared with controls ( T. J. A. Bruce et al. Sci. Rep. http://doi.org/5sr; 2015 ). This is disappointing on many levels. First, because of the effort — and money — that has gone into the concept. Second, because GM crops will surely have a major role in providing a future sustainable food supply. As Earth’s population grows, so does its appetite. Work aimed at increasing crop yields, by both GM and non-GM methods, is among the most crucial research being conducted on the planet. So hostility towards GM research — one reason why it is rare for such crop trials to reach field-scale studies in Europe — is still among the most important societal issues for science to address. Some opponents of GM crops have reacted with predictable claims: that the trial was a waste of money, that investment in GM science should therefore be cut off, and that this one set-back means the entire concept is flawed. Hardly. “Considering all GM crops as a single case is increasingly problematic.” As with most negative results in research, things can still be learnt from this trial. The team might yet modify the way their crop emits the alarm pheromone and may experiment in areas with higher densities of parasites. The crop failed , but so did the protests. The research was done; a useful result was obtained. Ironically, had the protests succeeded and the trial been abandoned, the protesters would be unable to crow about the crop’s failure. GM research continues at Rothamsted, as it does around the world. Some of it will work and some will not. Those who wish to make an argument against GM crops face major problems. The rise of new techniques such as CRISPR means that what is and is not a GM organism is an increasingly grey area, both scientifically and for regulators. And these crops, with all the controversy that comes with them, are no longer the sole preserve of huge agri-businesses. The use of GM technology is increasingly being passed to the people who really need it — those in developing countries who are trying to improve the agriculture of their nations. Considering all GM crops as a single case is increasingly problematic. Consumer-friendly traits, such as apples that do not turn brown, now vie with nutritional enhancement for developing nations and drought resistance. Small academic groups around the world are producing locally tailored varieties alongside the engineered staples that major companies sell in huge quantities to farmers in the developed world. And the debate is no longer limited to crops — on page 13 , we report on GM pigs that could soon make their way into the human food chain. All who care about evidence-based policy-making should thank those who continue to struggle against both the difficulties of doing science and the added difficulties caused by people who would see science abandoned. We will all need the fruits — and the cereals — of their labours. Journal name: Nature Volume: 523, Pages: 5 Date published: (02 July 2015) DOI: doi:10.1038/nature.2015.17855 Nature20150625_GM wheat that emits pest alarm signals fails in field trials http://www.nature.com/news/gm-wheat-that-emits-pest-alarm-signals-fails-in-field-trials-1.17854 Nature | News GM wheat that emits pest alarm signals fails in field trials Wheat modified to send out insect pheromones does not repel aphids. · Daniel Cressey 25 June 2015 A pioneering genetically modified (GM) wheat crop that emits an insect alarm pheromone to ward off pests has not worked in field trials, disappointed researchers say. Scientists at Rothamsted Research, an agricultural science institute north of London, had hoped that promising experiments in the laboratory 1 — where the wheat did repel damaging aphids — would translate into the field, and would mean that crops could be grown using less insecticide. “The disappointing thing was when we tested it in the field we didn’t find any significant reduction . We didn’t get the result that would have been useful in taking this forward,” says Toby Bruce, a chemical ecologist at Rothamsted. “It was quite sad.” Related stories · Departing head of biotech institute defends GM field trials · Misplaced protest · Nature news blog: Rothamsted trial attacked More related stories The field trials, whch started in 2012, attracted notoriety when anti-GM protestors threatened to destroy the crop and staged protests at the Rothamsted site. The protests did not disrupt the research, but making the site secure added around ￡1.8 million (US$2.8 million) to the study's research cost of ￡732,000. The levels of aphids seen in the field trials were low — so low that the wheat might not have needed to be sprayed with pesticides had it been a commercially planted field, the Rothamsted team says in a paper published today in Scientific Reports 2 . But compared to a control crop of wheat, the GM crops showed no improved yields, no reduction in aphids and no increase in attacks by aphid predators (such as parasitic wasps and ladybirds). “The field is the ultimate arbiter,” says John Pickett, a chemical ecologist who led the work. “This hypothesis was tested false.” Try, try again Pickett says that the researchers are not abandoning the pheromone idea altogether, because there are reasons to believe that it might work if the field trial is modified. François Verheggen, who works on insect pheromones and pest management at the University of Liège in Belgium, says that it takes high levels of alarm pheromones to attract aphid predators. The pheromones emitted by the wheat in the Rothamsted trial would have reached sufficient levels only after around 71 days, leaving crops unprotected before then, he says. And, he adds, because the wheat in the trial released pheromones continually, the aphids might have become used to the signal. Aphids are repelled when they sense strong differences in pheromone emissions between one area and the next, he says. The Rothamsted team plans to modify their crop to emit the pheromone in a burst — simulating natural release — rather than continuously. They may also try to test the crop in areas that have much higher concentrations of parasitic wasps, Pickett says. Jonathan Gershenzon, who studies plant chemistry at the Max Planck Institute for Chemical Ecology in Jena, Germany, says that he would not have expected continuous emission of a pheromone to work. His team has previously shown that a transgenic version of the flowering plant Arabidopsis thaliana , which emits an alarm pheromone, is not protected against aphids 3 . “It was good that they tried. It’s a different system with wheat, it’s a different aphid,” and they did it in field conditions, he says. “I give them lots of points for trying and even more points for being willing to publish negative data. It shows how science can work.” Journal name: Nature DOI: doi:10.1038/nature.2015.17854 References 1. Beale, M. H. et al . Proc. Natl Acad. Sci. USA 103 , 10509 – 10513 ( 2006 ). 1. Article 2. PubMed 3. ChemPort Show context 2. Bruce, T. J. A. et al . Sci. Rep. http://dx.doi.org/10.1038/srep11183 ( 2015 ). 0. PubMed Show context 3. Kunert, G. , Reinhold C. Gershenzon, J. et al . BMC Ecol. 10 , 23 ( 2010 ). 0. Article 1. PubMed 2. ChemPort 本文地址: http://www.sciencenets.com/home.php?mod=spaceuid=38do=blogquickforward=1id=6236 本文发表在《 华人科学网 》 博客 ，转载请注明出处并署上作者姓名，商业用途须获得作者和本站授权。。。。
Flanking sequence determination and event-specific detection of genetically modified wheat B73-6-1 Junyi Xu, Jijuan Cao, Dongmei Cao, Tongtong Zhao, Xin Huang, Piqiao Zhang and Fengxia Luan Acta Biochim Biophys Sin 2013, 45: 416–421; doi: 10.1093/abbs/gmt016 Food Inspection Center, Liaoning Entry-Exit Inspection and Quarantine Bureau, Dalian 116001, China In order to establish a specific identification method for genetically modified (GM) wheat, exogenous insert DNA and flanking sequence between exogenous fragment and recombinant chromosome of GM wheat B73-6-1 were successfully acquired by means of conventional polymerase chain reaction (PCR) and thermal asymmetric interlaced (TAIL)-PCR strategies. Newly acquired exogenous fragment covered the full-length sequence of transformed genes such as transformed plasmid and corresponding functional genes including marker uidA, herbicide-resistant bar, ubiquitin promoter, and high-molecular-weight gluten subunit. The flanking sequence between insert DNA revealed high similarity with Triticum turgidum A gene (GenBank: AY494981.1). A specific PCR detection method for GM wheat B73-6-1 was established on the basis of primers designed according to the flanking sequence. This specific PCR method was validated by GM wheat, GM corn, GM soybean, GM rice, and non-GM wheat. The specifically amplified target band was observed only in GM wheat B73-6-1. This method is of high specificity, high reproducibility, rapid identification, and excellent accuracy for the identification of GM wheat B73-6-1. 图例: 小麦B73-6-1基因组分析 全文: http://abbs.oxfordjournals.org/content/45/5/416.full 引用此文的文献: 1 Transgenic cereals: Current status and future prospects 2 Loop-Mediated Isothermal Amplification for the Event-Specific Detection of Wheat B73-6-1 3 Event-Specific Qualitative and Quantitative Detection in Transgenic Soybean OsDREB3 Based on the 5 ' Flanking Sequence
今天不少网站有一条英国用传统育种技术培养出“超级小麦”的新闻，这一新闻的要点是“产量增加了 30% ”而且“没有用基因修饰（ genetic modification ）或转基因技术”，如《 英国科学家研制超级小麦 - 超级小麦 》、《 英国科学家研发超级小麦 产量增 3 成 》，但这些新闻多来源于英国 BBC 的消息（ BBC News: Cambridge-based scientists develop 'super-whea t' ），因此，技术上细节不够清楚，各新闻译的也不够到位，如有的译为“研究人员将 杂交样品 和使用 胚胎移植技术（ embryo transfer techniques ） 带来一个全新的小麦品系”，也有的编译为“科学家利用 异花传粉 ，和 种子胚胎转移科技 ，将部分远古大麦品种的强韧特性，重新注入现代英国小麦品种，制造出这款 “ 超级小麦 ” 。”或“英国科学家使用的是 交叉授粉 和 种子胚胎移植技术 ，将原始小麦品种中的一些优势基因转移到现代小麦品种上”。 为了了解技术细节，我找到更详细的一篇英文报道： AllAboutFeed - UK scientist develop new 'super' wheat breed 。“ The result is a ‘synthetic’ wheat which, when crossed with modern UK varieties, could offer new sources of yield improvement, drought tolerance, disease resistance and input use efficiency. The synthetic wheat programme involves crossing durum pasta wheat with wild goat-grass using traditional crossing techniques in the glasshouse combined with t issue culture in the research laboratory to guarantee seed germination . The process required no genetic modification of the crops. The resulting hybrid plants produce the ‘synthetic’ seed which is then used in crossing programmes with current varieties. ”从这篇新闻来看，最重要的技术要点是“ 传统的（远缘）杂交技术 ”和“ 胚胎培养技术（属于植物组织培养技术的一种，胚培养用于挽救杂种胚的败育） ”。所以，上述新闻中的翻译不够精确。照字面翻译会造成误导。 另外，从这篇新闻也可以看出，由于反对转基因的势力在欧洲实在太大，以至于植物育种又有向传统育种技术回归的趋势。
A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii , the wheat D-genome progenitor http://www.pnas.org/content/early/2013/04/18/1219082110.abstract wheat D-genome progenitor.pdf Abstract The current limitations in genome sequencing technology require the construction of physical maps for high-quality draft sequences of large plant genomes, such as that of Aegilops tauschii , the wheat D-genome progenitor. To construct a physical map of the Ae. tauschii genome, we fingerprinted 461,706 bacterial artificial chromosome clones, assembled contigs, designed a 10K Ae. tauschii Infinium SNP array, constructed a 7,185-marker genetic map, and anchored on the map contigs totaling 4.03 Gb. Using whole genome shotgun reads, we extended the SNP marker sequences and found 17,093 genes and gene fragments. We showed that collinearity of the Ae. tauschii genes with Brachypodium distachyon , rice, and sorghum decreased with phylogenetic distance and that structural genome evolution rates have been high across all investigated lineages in subfamily Pooideae, including that of Brachypodieae. We obtained additional information about the evolution of the seven Triticeae chromosomes from 12 ancestral chromosomes and uncovered a pattern of centromere inactivation accompanying nested chromosome insertions in grasses. We showed that the density of noncollinear genes along the Ae. tauschii chromosomes positively correlates with recombination rates, suggested a cause, and showed that new genes, exemplified by disease resistance genes, are preferentially located in high-recombination chromosome regions.
国家已禁止向小麦粉中添加过氧化苯甲酰(BPO)，快速检测小麦粉中BPO添加量对于保障食品安全非常重要。BPO在添入小麦粉中后部分会被还原成为苯甲酸，使得对其原始添加量的检测非常繁琐。本文探讨了利用近红外漫反射光谱法进行小麦粉中BPO添加当量检测的可行性。通过向无添加剂小麦粉中添加不同量的过氧化苯甲酰粉末，制备小麦粉样本133个。样本在实验室放置一段时间后，采集光谱数据，通过小波变换滤除光谱噪声。用偏最小二乘法建立光谱数据与BPO原始添加当量之间的模型，模型校正集决定系数 R 2 cal 是0.890 1，校正标准偏差RMSEC是40.85 mg·kg -1 ，预测决定系数 R 2 pred 为0.886 5，预测标准偏差RMSEP为44.69 mg·kg -1 。结果表明：基于近红外光谱的小麦粉BPO添加当量检测具有较高的可行性，该方法有望为食品中某些添加物的快速检测提供新的途径。 近红外漫反射光谱法检测小麦粉过氧苯甲酰.pdf
和植物CNV相关研究: http://blog.sciencenet.cn/home.php?mod=spaceuid=479743do=blogid=394965 这是我一直比较困惑的领域:人类遗传学对这东西比较关注,而植物学里研究很少,所以当看到这类文章会比较留意.今天又增加了一个例子:Copy Number Variation Affecting the Photoperiod-B1 and Vernalization-A1 Genes Is Associated with Altered Flowering Time in Wheat ( Triticum aestivum ) http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033234 知到了,未必会去研究,精力有限;但如果一点都不了解,有时会直接导致对有些东西的判断失误.什么东西是最重要的,常常是不可预测的.所以古人云:山穷水复疑无路,柳暗花明有一村. 看到好文章,略书几笔,有用之时能忆之,此大妙也!
近日，多国科学家在Journal of Experimental Botany连续发表3篇小麦增产的综述文章，由于我是吃面长大的，现在分享这三篇文章，希望科学家能早日实现小麦的 质高优产 。 1.如何通过提高太阳能利用率(RUE)来提高小麦产量？ Raising yield potential of wheat. I. Overview of a consortium.pdf 2.如何通过提高净光合速率(PN)提高产量？ Raising yield potential of wheat. II. Increasing photosynthetic.pdf 3.如何权衡增产与抗倒伏的关系(trade-offs)？ Raising yield potential of wheat. III. Optimizing partitioning to.pdf
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