Genomic and physiological insights into heat–drought tolerance in wheat through GWAS and phenotypic evaluation

Climate change-driven heat and drought stresses during reproductive stages significantly threaten wheat productivity. To investigate the genetic and physiological basis of combined heat–drought (HD) tolerance, we evaluated 345 wheat genotypes under three environments of HD stresses, non-stress glasshouse conditions and a late-sowing field trial. HD stresses caused significant reductions in chlorophyll content, flag leaf area, biomass, seed-setting rate and grain weight-related traits. Notably, HD-tolerant lines maintained higher grain weight, grain number and chlorophyll retention, with less than half the reductions observed in sensitive genotypes. A genome-wide association study using a 40K single-nucleotide polymorphism (SNP) array identified 124 candidate SNPs (cSNPs) associated with 51 traits across three environments with 78 cSNPs associated with HD tolerance. In total, 24 cSNP blocks exhibited pleiotropic associations with multiple traits under those three environments. Tight genomic co-localisations were detected between chlorophyll content (SPAD or CCM200 values), flag leaf width, seed-setting rate and grain yield components (thousand grain weight, grain number per spike), with superior haplotypes identified, supporting their utility in selections. Stay-green traits appeared to contribute significantly to yield stability under HD stresses. Those results provide valuable genomic and physiological insights into wheat HD tolerance for future targeted wheat breeding.