GWAS-Driven Identification of Genomic Regions Conferring Yield and Related Traits Under Drought Stress in Wheat

Drought stress highlights the urgent need to create drought-tolerant wheat varieties. The genome-wide association analysis was performed to identify genetic markers linked to wheat yield traits under drought stress. A diverse panel of 190 bread wheat genotypes was evaluated under both well-watered and water-limited conditions throughout three growing seasons (2021–2024) in Bahawalpur, Punjab, Pakistan using an alpha lattice design with three replications. Genotyping was performed using a 37 K SNP array. Genomic prediction models were developed using genomic best linear unbiased predictions (g-BLUPs). Heritability was the highest (0.88) for yield and the lowest (0.53) for spikes per plant. Overall stress tolerance indices ranged from 1.21 for thousand kernel weight to 0.42 for grain yield. The additive main effects and multiplicative interaction (AMMI) model and principal component analysis (PCA) identified 10 high-yielding genotypes under water-limited conditions. The 59 genomic regions were significantly associated with yield and related traits on 21 chromosomes and clustered as ten QTLs. The significant QTL for yield under drought stress on chromosomes 3A and 5B explained a phenotypic variance of 7.1% and 5.08%. The genomic best linear unbiased predictions (g-BLUP) indicated notable accuracies, for traits related to large-effect QTLs, ranging from 0.1 for flag leaf length to 0.53 for biomass. This study concluded significant variation in wheat genotypes under water-limited conditions, with moderate to high heritability. It identifies ten elite genotypes and 59 key genomic regions for drought tolerance, and the genomic prediction model, g-BLUP, aids breeding programs in developing climate-resilient wheat varieties.