High-quality bonds: serine acetyltransferase 2 gene revealed by GWAS is associated with grain protein content in spring durum wheat

Grain protein content (GPC) is a critical determinant of durum wheat quality, with cysteine playing a pivotal role in gluten strength. This study aimed to develop genetic markers associated with GPC through a genome-wide association study (GWAS) and validate their utility for breeding programs. A panel of 190 durum wheat accessions was phenotyped for GPC across multiple environments and genotyped using 4927 high-quality SNPs. GWAS identified a significant SNP on chromosome 4B, located in an intergenic region. Through the analysis of linkage disequilibrium decay rate, and functional gene ontology annotation, the <i>serine acetyltransferase 2</i> gene involved in cysteine biosynthesis was identified as a candidate gene for GPC. A missense mutation (Gly325Ser) in the ninth exon of <i>sat2</i> was associated with a 1.33% GPC increase in spring durum wheat recombinant inbred lines. Structural analysis indicated that the Gly325Ser mutation alters the SAT2 protein's C-terminal <i>α</i>-helix, potentially influencing enzyme activity. Additionally, an intronic SNP showed association with multi-year average GPC increase of 0.92% in spring durum wheat. Despite the intronic SNP's lack of direct amino acid impact, its high phenotypic variance explained (40.23% in spring wheat) suggests regulatory roles in gene expression. Expression profiling of <i>TAsat2</i> homologous from bread wheat revealed peak transcription during grain filling stages, aligning with grain protein accumulation dynamics. The developed KASP markers demonstrated robust allelic discrimination, offering practical tools for marker-assisted selection. This study provides actionable genetic resources for breeding high-protein spring durum wheat genotypes.