Genetic dissection and stability analysis of grain protein content and thousand-grain weight in emmer wheat (Triticum turgidum subsp. dicoccum) germplasm

Emmer wheat (Triticum turgidum subsp. dicoccum), an allotetraploid species of wheat, is a rich source of nutritional as well as biotic and abiotic stress tolerance traits. It is an important genetic resource for improving grain protein content in durum and bread wheat, yet its genetic basis for protein accumulation and yield-related traits are less studied. In this study, a diverse panel of 150 emmer wheat germplasm accessions conserved in national genebank of India was evaluated for grain protein content (GPC) and thousand grain weight (TGW) across four environments (New Delhi, Pune, Karnal, and Ludhiana) during winter season 2021–2022 using an alpha lattice design. Genotypes were highly significant for GPC and TGW and substantial phenotypic variation (12.16–17.76% for GPC and 25.98 to 38.64 g for TGW) was observed based on pooled data. GPC and TGW were negatively correlated, with principal component analysis revealing opposing contributions of these traits to total phenotypic variation. We identified superior donors for GPC and TGW based on multi-environmental evaluation. Accessions EC578064, EC299074, EC577402, IC534016, and IC32513, exhibited consistently high GPC with moderate TGW across environments, while IC138455 and IC32513 were stable genotypes for GPC. Genome-wide association analysis using 6800 polymorphic SNP markers based on the 35 K Axiom Wheat Breeders’ array identified 21 significant marker–trait associations (MTAs) across environments, out of these eight markers were located on chromosome 5B. Nine stable and novel MTAs were identified, which consistently expressed across locations, highlighting genomic regions with less genotype × environment interaction. These stable MTAs were linked to genes involved in nitrate transport, stress tolerance, grain development, and yield regulation, providing biologically meaningful targets for protein improvement in emmer wheat. Overall, this study resulted in the identification of promising donor genotypes for GPC and TGW, and linked markers and candidate genes for possible deployment into breeding program for the development of high yielding and protein rich wheat cultivars.