A novel QTL discovered for grain protein content without grain weight penalty in wheat (Triticum aestivum L.).

Wheat (Triticum aestivum L.) is a global food crop with a relatively low protein content of 9–12%. Enhancing grain protein content (GPC) without compromising grain yield remains a challenge due to the negative correlation between yield and GPC. However, recent advances in genome-wide DNA markers, high-throughput phenotyping, genome-wide association studies (GWAS), and quantitative trait loci (QTL) mapping have facilitated the identification of important QTLs. This study utilized a stable recombinant inbred line (RIL) F7 − 9 population, genotyped using high-depth genotyping-by-sequencing (GBS), and phenotyped across multi-environmental field trials to identify stable QTLs for GPC. In contrast to the often-reported negative correlation between GPC and Thousand Grain Weight (TGW), the RIL population exhibited a significant positive correlation of 0.143 (p < 0.001) between the two traits. Significant genetic variation in GPC was observed in the population, with a heritability of 0.72, indicating a strong genetic influence. Further genetic analysis revealed the presence of ten QTLs responsible for GPC variation, located on chromosomes 1D, 2B, 4B, 5 A, and 5B. Among these, QGPC.nabi-2B.2 and QGPC.nabi-5B.1 were identified in more than three environments as major QTLs. Precise mapping of QGPC.nabi-2B.2, using indigenously designed SSRs, identified potential candidate genes involved in GPC regulation. Three SNPs from this region were converted into Tetra-ARMS-PCR markers and validated in Indian wheat varieties and a genetically different RIL population. This study provides a foundation for future research into the genetic regulation of GPC in wheat, suggesting key candidate genes that could improve wheat’s nutritional quality without compromising grain weight.