Identifying Loci Associated with Grain Quality Traits of Landraces and Modern Varieties of Spring Bread Wheat under Conditions of Western Siberia

Landraces of wheat represent valuable genetic resources for enhancing the grain quality of modern wheat varieties. In this study, a panel comprising 94 landraces sourced from the VIR collection (Russia) and 142 wheat varieties from breeding programs of Russia and Kazakhstan was subjected to genome-wide association study (GWAS) to pinpoint genomic regions and identify candidate genes associated with grain quality traits in wheat breeding. Genotyping of the germplasm panel was conducted using the Affymetrix 25K platform, while phenotypic data for agronomic traits were collected over two growing seasons (2022 and 2023) in Western Siberia. Investigation of the genotypic structure revealed seven distinct clusters within the landraces and breeding varieties population, indicating a clear genetic differentiation among the landraces. Notably, the В genome of the landrace germplasm exhibited the highest proportion of SNP markers (41%). Based on experiment data among 294 MTAs seven unique loci were identified with a −log10(p) value >6 in the landrace collection that had significant associations with grain protein content, grain gluten, strong gluten content, gluten index, and vitreousness (AX-158572632, wsnp_Ex_c10084_16572374, BobWhite_c31129_60, AX-158586137, AX-94949506, BobWhite_c46257_130, wsnp_JG_c5646_2148382). These markers were distributed on chromosomes A, 2B, 5B, 6B, and 6D with ranged of phenotypic variation 9–26%.