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

## TL;DR

This study identifies genetic markers and candidate genes associated with flour color in winter wheat, which can help improve wheat flour quality.

## Contribution

The study reports 20 significant and stable SNP markers and develops KASP markers for improving flour color traits in wheat.

## Key findings

- Genome-wide association study identified 20 significant SNP markers across 16 loci linked to flour color traits.
- Two KASP markers for Fa* showed significant phenotypic differences among wheat materials.
- Seven candidate genes were identified that may influence flour color traits during grain development.

## Abstract

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 40 K 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 55.52% to 83.48%, 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 1 A, 5 A, 1B (2), 6B, and 4D; 6 for Fb*, located on chromosomes 2 A (2), 4 A, 4B, 6B, and 5D; and 3 for W, located on chromosomes 2 A, 4 A, 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 4 A and 6B chromosomes may affect Fb*.The results provide useful information to enhance the color quality of wheat flour in wheat.

The online version contains supplementary material available at 10.1038/s41598-025-23358-4.