Marker–trait association analysis of kernel hardness and related agronomic traits in a core collection of wheat lines

Identification of marker–trait associations is the first step towards marker-assisted selection in plant breeding. Here we assess genetic diversity and population structure of 94 diverse wheat elite lines and use genome-wide association mapping to identify marker–trait associations for five important traits: kernel hardness (KHA), thousand-kernel weight, grain protein content, test weight (TWT), and plant height (PHT). The 94 accessions employed in this study were grouped into three subpopulations based on the first three principal components, which accounted for 51.5 % of the variations. A mixed linear model was used to detect marker–trait associations incorporating covariance of population structure and relative kinship. A total of six marker loci was significantly associated with KHA, TWT, and PHT after the correction of false discovery rate (αc = 0.05). The gene pinB was found to be highly associated with KHA, and is reported to be a major determinant of KHA together with the gene pinA at the Ha locus on chromosome 5D. Marker XwPt-7187 on chromosome 2A was also significantly associated with KHA, two Diversity Arrays Technology markers XwPt-1250 and XwPt-4628 with TWT, and marker Xgwm512 with PHT, making the first report of marker–trait associations in these genomic regions.