Dissecting the genetic basis of grain morphology traits in Chinese wheat by genome wide association study

Grain size and shape have significant effects on grain weight and is also an important breeding target due to market and industry requirements. In this study, the genetic loci associated with six grain morphology traits including thousand grain weight, grain length (GL), grain width, grain length to width ratio (GLWR), grain area (GA) and grain perimeter (GP) in a population of 300 Chinese wheat germplasm were investigated through genome wide association mapping. A total of 189 SNPs were significantly related to the six grain traits based on the BLUP data from three environments. Of these SNPs, 24 SNPs for GA, GL, GLWR, and GP were continuously detected under all three experiments. These SNPs were distributed on chromosome 2A, 2B, 2D, 4D, 5A, and 6D, respectively. Some SNPs such as Affx-88368872 on 2A, Affx-109472887 on 6D, and Affx-108968182, Affx-111286671, Affx-110418048, Affx-109838962, Affx-88484232 on 5A were associated with multiple traits. In addition, a chromosome region tagged by 11 SNPs (585,117,524–595,658,182 bp) on chromosome 2D had significant effects on GLWR. Several genes inside the regions on chromosome 5A and 2D may play crucial roles in determining seed size and weight. We will characterize the function of these genes in grain development in our future experiments. This study provides novel insights into the genetic basis of grain morphology traits in wheat.