Association Mapping of Quantitative Trait Loci for Grain Color in U.S. Winter Wheat.

Red grain color of wheat cultivars is an important wheat quality trait that affects not only flour brightness but also pre-harvest sprouting (PHS) resistance. Several genes and associated markers for grain color have been reported. To determine genes to control grain color in US winter wheat, association mapping was conducted using a panel of 192 elite breeding lines and cultivars including 137 hard winter wheat (HWW) and 55 soft winter wheat (SWW) accessions. Seeds harvested from 2010 field and 2011 greenhouse experiments were evaluated for grain color intensity using a 1 (low) to 4 (high) visual score scale after soaking seeds in 1M/L sodium hydroxide (NaOH) solution for 2 h. The panel was screened using 450 simple sequence repeats (SSR), 5 primer sets for Tamyb10 genes and 9K genome-wide single nucleotide polymorphism (SNP) chips. Structure analysis generated five groups, two SWW and three HWW groups. Association analysis using Q model (q < 0.05) identified that grain color was significantly associated 7 SSRs and 4 primer sets for three Tamyb10 genes. Among them, Xwmc559 and two Tamyb10 gene markers were the most significant markers on 3A, Xbarc84 and one Tamyb10 gene marker were the most significant on 3B, and one Tamyb10 gene marker on 3D was the most significant marker on 3D. These results agree with previously reported QTLs for grain color. Significant markers were also detected on chromosome 4A and 7A. In addition, several SNPs from different chromosomes were identified to be significantly associated with grain color. The results indicate that grain color in US winter wheat mainly controlled by group 3 chromosomes, but other chromosomes such as 4A and 7A may also contribute to grain color.