Genome-wide association study and KASP marker development for flour color in winter wheat

Flour color influences the quality of end-use products of common wheat ( Triticum aestivum L.). To analyze the genetic basis of flour color, the flour brightness (FL*), red-green level (Fa*), yellow-blue level (Fb*), and whiteness (W) of 341 winter wheat materials grown during the 2019-2020 years and 2020-2021 years in Emin and Qitai were measured. A genome-wide association study was conducted using a wheat 40K breeding chip with the MLM model. The coefficient of variation and generalized heritability of wheat flour color traits ranged from 0.62% to 22.23% and 0.58 to 0.83, respectively. There were strong correlations across the flour color traits. GWAS identified 20 significant and stable SNP markers distributed across 16 loci, including 1 for FL* located on chromosome 5D; 6 for Fa*, located on chromosomes 1A, 5A, 1B (2), 6B, and 4D; 6 for Fb*, located on chromosomes 2A (2), 4A, 4B, 6B, and 5D; and 3 for W, located on chromosomes 2A, 4A, and 5D. Two KASP markers were developed for Fa*, which exhibited good genotype and significant phenotypic differences among materials with different genotypes. Seven candidate genes that may affect flour color during grain development were screened, including TraesCS5D02G01340.1 , TraesCS5D02G013100 , and TraesCS5D02G014300.1 on the 5D chromosome may simultaneously influence W, FL*, and Fa*, TraesCS1B02G269100.1 and TraesCS1B02G269500.1 on the 1B chromosome may impact Fa*, while TraesCS4A02G307200 and TraesCS6B02G034100.1 on the 4A and 6B chromosomes may affect Fb*.The results provide useful information to enhance the color quality of wheat flour in wheat.