High-Density Genetic Linkage Map Construction and QTL Mapping of Grain Shape and Size in the Wheat Population Yanda1817 × Beinong6

High-density genetic linkage maps are necessary for precisely mapping quantitative trait loci (QTLs) controlling grain shape and size in wheat. By applying the Infinium iSelect 9K SNP assay, we have constructed a high-density genetic linkage map with 269 F 8 recombinant inbred lines (RILs) developed between a Chinese cornerstone wheat breeding parental line Yanda1817 and a high-yielding line Beinong6. The map contains 2431 SNPs and 128 SSR & EST-SSR markers in a total coverage of 3213.2 cM with an average interval of 1.26 cM per marker. Eighty-eight QTLs for thousand-grain weight (TGW), grain length (GL), grain width (GW) and grain thickness (GT) were detected in nine ecological environments (Beijing, Shijiazhuang and Kaifeng) during five years between 2010–2014 by inclusive composite interval mapping (ICIM) (LOD≥2.5). Among which, 17 QTLs for TGW were mapped on chromosomes 1A, 1B, 2A, 2B, 3A, 3B, 3D, 4A, 4D, 5A, 5B and 6B with phenotypic variations ranging from 2.62% to 12.08%. Four stable QTLs for TGW could be detected in five and seven environments, respectively. Thirty-two QTLs for GL were mapped on chromosomes 1B, 1D, 2A, 2B, 2D, 3B, 3D, 4A, 4B, 4D, 5A, 5B, 6B, 7A and 7B, with phenotypic variations ranging from 2.62% to 44.39%. QGl.cau-2A.2 can be detected in all the environments with the largest phenotypic variations, indicating that it is a major and stable QTL. For GW, 12 QTLs were identified with phenotypic variations range from 3.69% to 12.30%. We found 27 QTLs for GT with phenotypic variations ranged from 2.55% to 36.42%. In particular, QTL QGt.cau-5A.1 with phenotypic variations of 6.82–23.59% was detected in all the nine environments. Moreover, pleiotropic effects were detected for several QTL loci responsible for grain shape and size that could serve as target regions for fine mapping and marker assisted selection in wheat breeding programs.

高密度遗传连锁图谱是精准定位调控小麦粒形与粒重的数量性状基因座（quantitative trait loci, QTLs）的必要工具。本研究通过应用Infinium iSelect 9K单核苷酸多态性（Single Nucleotide Polymorphism, SNP）分型检测技术，以中国核心小麦育种亲本烟农1817（Yanda1817）与高产品系北农6（Beinong6）杂交衍生的269个F₈代重组自交系（recombinant inbred lines, RILs）为材料，构建了一张高密度遗传连锁图谱。该图谱包含2431个SNP标记以及128个SSR与EST-SSR标记，总覆盖长度达3213.2厘摩（cM），标记间平均间距为1.26 cM。在2010至2014年五年间的9个生态环境（北京、石家庄、开封）中，本研究采用完备复合区间作图法（inclusive composite interval mapping, ICIM）（LOD≥2.5），共检测到88个与千粒重（thousand-grain weight, TGW）、粒长（grain length, GL）、粒宽（grain width, GW）及粒厚（grain thickness, GT）相关的QTLs。其中，调控千粒重的17个QTLs被定位在1A、1B、2A、2B、3A、3B、3D、4A、4D、5A、5B及6B染色体上，表型变异贡献率介于2.62%至12.08%之间；另有4个千粒重相关稳定QTL，可分别在5个和7个环境中被检测到。调控粒长的32个QTLs被定位在1B、1D、2A、2B、2D、3B、3D、4A、4B、4D、5A、5B、6B、7A及7B染色体上，表型变异贡献率介于2.62%至44.39%之间；其中QGl.cau-2A.2可在所有环境中被检测到，且表型变异贡献率最高，表明其为一个主效且稳定的QTL。针对粒宽，本研究共鉴定到12个QTLs，表型变异贡献率介于3.69%至12.30%之间。本研究还检测到27个调控粒厚的QTLs，表型变异贡献率介于2.55%至36.42%之间；尤为值得关注的是，表型变异贡献率为6.82%~23.59%的QGt.cau-5A.1可在全部9个环境中被检测到。此外，本研究发现多个调控粒形与粒重的QTL位点存在多效性，这些位点可作为小麦育种中精细定位与标记辅助选择的靶标区域。