Genome-wide association mapping and haplotype analysis reveal the genetic architecture of sodicity tolerance in bread wheat (Triticum aestivum L.)

Sodicity stress is a major abiotic constraint limiting bread wheat (Triticum aestivum L.) productivity worldwide. To dissect its genetic basis, a diverse panel of 158 wheat accessions was evaluated under normal and sodic conditions across 2 years, revealing substantial phenotypic variation and trait-dependent heritability ranging from low (biomass) to high (Na⁺/K⁺ ratio). Genome-wide association analysis identified 56 significant (P < 0.00001) marker–trait associations (MTAs) linked to sodicity tolerance, including loci that were stable across environments. A total of 96 putative candidate genes associated with MTAs were identified and were primarily involved in ion transport, cell signaling, redox regulation, and transcriptional control. The analysis of superior haplotypes revealed significant associations with key agronomic traits. Haplotype H001 (TraesCS5A02G521600) and H004 (TraesCS6B02G031300) were associated with higher ear weight, showing increases of 15.93% and 54.37%, respectively. Similarly, haplotype H003 (TraesCS5B02G422400) was associated with a 27.27% improvement in the Na⁺/K⁺ ratio, while haplotype H004 (TraesCS5A02G366900) was associated with a 3.47% reduction in days to maturity. Furthermore, the accumulation of favorable alleles was associated with enhanced sodicity tolerance and improved yield performance. Of the 56 MTAs, five were successfully validated using KASP markers in an independent population, confirming their robustness and potential for deployment. Multi-trait genotype–ideotype distance index (MGIDI) analysis identified elite genotypes (IC416408, IC0296308, and IC532238) with superior performance under sodic conditions. Overall, this study provides 56 robust genomic loci, 5 validated markers, and 4 superior haplotypes that can be directly utilized in marker-assisted and haplotype-based breeding for developing sodicity-tolerant wheat cultivars.