Characterization of stable grain protein content loci on chromosome 6D without adverse effect on yield traits in bread wheat.

This study identified and validated novel QTL controlling GPC, predicted the underlying candidate genes, and provides valuable insights for improving wheat nutritional quality while minimizing yield penalties. Grain protein content (GPC) is a key determinant of wheat quality, but its improvement is often limited by a negative correlation with yield. To elucidate the genetic architecture of GPC, a genome-wide association study was conducted on 224 wheat cultivars genotyped with a 120 K SNP array and phenotyped across three environments. We identified three stable quantitative trait loci (QTL) on chromosome 6D, QGPC.sau-SCV-6D.1, QGPC.sau-SCV-6D.2, and QGPC.sau-SCV-6D.3 which were consistently detected across environments and in best linear unbiased prediction analyses. These loci explained 4.94-9.12% of the phenotypic variance. Notably, the GPC increasing alleles exhibited no adverse effect on major yield components, including thousand-grain weight and grain number per spike. Validation in two independent recombinant inbred line populations confirmed the stable effects of these three QTL. Candidate gene analysis within the QTL intervals highlighted five genes with putative roles in regulating GPC. These findings establish chromosome 6D as a valuable genomic region for breeding high-protein wheat and provide practical markers for marker-assisted selection with minimal yield penalties.