GWAS Reveals Stable Genetic Loci and Candidate Genes for Grain Protein Content in Wheat

Grain protein content (GPC) is a key quality trait in wheat, determining both nutritional value and end-use functionality, yet its genetic architecture is complex and highly influenced by the environment. In this study, a diverse panel of 327 wheat accessions was evaluated for GPC across multiple environments. Significant phenotypic variation was observed, with best linear unbiased estimates (BLUEs) ranging from 12.80% to 18.79%, and a moderate broad-sense heritability (<i>h</i>² = 0.52) was estimated. Genotype-by-environment interactions were highly significant. Genome-wide association analysis using the FarmCPU model identified seven stable quantitative trait nucleotides (QTNs) associated with GPC on chromosomes 1A, 1B, 2A, 2D, 3B, 5A, and 6A. Among these, <i>QGpc.yzu-2A</i> was consistently detected in three environments. Further analysis of the <i>QGpc.yzu-2A</i> region identified 26 annotated genes, 8 of which were expressed in grains. One gene, <i>TraesCS2A02G473000</i> (RNA-binding protein), exhibited high nucleotide diversity and is a strong candidate for functional validation. Additionally, <i>QGpc.yzu-6A</i> co-localized with the known <i>TaNAM-6A</i> gene, reinforcing the role of this region in GPC regulation. This study provides valuable insights into the genetic basis of GPC in wheat and offers molecular markers and candidate genes for marker-assisted selection to improve grain protein content in breeding programs.