GWAS on yield-related traits of Pakistani wheat under post-anthesis heat stress

Heat stress is a major threat to spring wheat (Triticum aestivum) production in the Indo-Gangetic plains of South Asia, particularly in India and Pakistan. Breeding for heat-tolerant cultivars is an effective strategy to improve wheat productivity in stressed environments. To identify quantitative trait loci (QTL) for heat tolerance, we conducted a genome-wide association study (GWAS) to identify marker-trait associations (MTAs) using single-nucleotide polymorphism (SNP) markers generated via genotyping-by-sequencing (GBS). We evaluated a panel of 184 Pakistani spring wheat accessions for 13 yield-related agronomic traits under induced terminal heat stress. GWAS using the Bayesian information and linkage disequilibrium iteratively nested keyway (BLINK) model identified 295 significant MTAs on all 21 wheat chromosomes. Notably, two QTL intervals (QTL), on chromosomes 3D (5 SNPs) and 5B (3 SNPs), exhibited pleiotropic effects on grain weight (GW) and grain per spike (GPS). In addition, three QTL intervals comprising 9 SNPs on chromosome 7 A, 7 SNPs on 3B, and 4 SNPs on 5 A were significantly associated with the heat susceptibility index (HSI). Furthermore, clusters on chromosome 2B (5 SNPs) and 6B (4 SNPs) were linked to kernel weight reduction (KWR). The identified QTLs and candidate genes associated with HSI and KWR provide valuable genetic resources for fine-mapping and the development of breeder-friendly markers for selecting heat-tolerant wheat cultivars.