Genetic control of wheat flour end-use quality and rheology by genome-wide association studies

Improving end-use quality in bread wheat (Triticum aestivum) requires dissecting the genetic basis of complex processing traits and deploying robust prediction pipelines in breeding. We performed genome-wide association studies (GWASs) using 1767 high-quality single-nucleotide polymorphisms generated by genotyping-by-sequencing in a diverse Canada Western Red Spring panel phenotyped near Swift Current, SK, from 2009 to 2019 for grain protein content, milling yield, mixing energy, water absorption, and dough extensibility. The analysis detected significant marker-trait associations on 13 chromosomes, recovering signals at Rht-B1 and Glu-1 and revealing multiple additional signals that may represent previously unreported loci in this germplasm and environmental context, consistent with polygenic control. We then evaluated genomic selection using GBLUP (Genomic Best Linear Unbiased Predictor) and BayesB with and without including significant GWAS hits as fixed effects; gains in predictive accuracy were generally negligible, although water absorption showed modest improvement, compatible with fewer, larger effect loci. Functional annotation of genes near associated variants implicated stress responses, protein metabolism, and grain filling. Together, these results refine the genetic architecture of Canadian wheat quality and support integrating GWAS-informed biology with genome-wide prediction to accelerate quality-by-design breeding.