Wheat (Triticum aestivum) is a major staple food crop worldwide. Genetic dissection of important agronomic traits is essential for continuous improvement of wheat yield to meet the demand of the world's growing population. We conducted a large-scale genome-wide association study (GWAS) using a panel of 768 wheat cultivars that were genotyped with 327 609 single-nucleotide polymorphisms generated by genotyping-by-sequencing and detected 395 quantitative trait loci (QTLs) for 12 traits under 7 environments. Among them, 273 QTLs were delimited to ≤1.0-Mb intervals and 7 of them are either known genes (Rht-D, Vrn-B1, and Vrn-D1) that have been cloned or known QTLs (TaGA2ox8, APO1, TaSus1-7B, and Rht12) that were previously mapped. Eight putative candidate genes were identified for three QTLs that enhance spike seed setting and grain size using gene expression data and were validated in three bi-parental populations. Protein sequence analysis identified 33 putative wheat orthologs that have high identity with rice genes in QTLs affecting similar traits. Large r² values for additive effects observed among the QTLs for most traits indicated that the phenotypes of these identified QTLs were highly predictable. Results from this study demonstrated that significantly increasing GWAS population size and marker density greatly improves detection and identification of candidate genes underlying a QTL, solidifying the foundation for large-scale QTL fine mapping, candidate gene validation, and developing functional markers for genomics-based breeding in wheat.

小麦（Triticum aestivum）是世界范围内主要的主食作物。重要的农艺性状的遗传解剖对于不断提高小麦产量以满足世界人口增长的需求至关重要。我们使用一组768个小麦品种进行了大规模的全基因组关联研究（GWAS），这些小麦品种具有通过基因分型测序产生的327609个单核苷酸多态性进行基因分型，并检测到12个性状的395个定量性状位点（QTL）在7种环境下。其中，有273个QTL被定界为≤1.0-Mb间隔，其中7个是已克隆的已知基因（Rht-D，Vrn-B1和Vrn-D1）或已知QTL（TaGA2ox8，APO1，TaSus1-7B和Rht12）。使用基因表达数据为三个QTL鉴定了八个推定的候选基因，这些QTL可增强穗粒结实和晶粒大小，并在三个双亲群体中进行了验证。蛋白质序列分析确定了33个推定的小麦直系同源物，它们与影响相似性状的QTL中的水稻基因高度同一。大r ²在大多数性状的QTL中观察到的加性效应值表明，这些鉴定出的QTL的表型是高度可预测的。这项研究的结果表明，显着增加GWAS群体的大小和标记密度大大改善了QTL潜在候选基因的检测和鉴定，为大规模QTL精细定位，候选基因验证和开发基于基因组学育种的功能标记奠定了基础在小麦中。