Genome-wide association studies for identification of stripe rust resistance loci in diverse wheat genotypes

Introduction In North India, Puccinia striiformis f. sp. triticii (Pst), the causal agent of stripe rust, poses a significant challenge to wheat productivity. The frequent emergence of new virulent Pst strains has rendered many resistance genes ineffective. Hence, continuous identification and deployment of novel resistance genes are crucial for maintaining durable resistance and ensuring sustainable wheat cultivation. Materials and Methods A genome-wide association study (GWAS) was conducted on 652 elite, diverse wheat genotypes using 1,938 DArTseq SNP markers. Field evaluations were performed at the adult plant stage across four locations—Hisar, Karnal, Gurdaspur, and Khudwani—under natural disease conditions. Marker–trait associations were identified using General Linear Model (GLM), Mixed Linear Model (MLM), and FarmCPU approaches, considering loci with –log₁₀(p) ≥ 3 as significant. Results Analysis revealed 27 genomic regions significantly associated with stripe rust resistance across environments. Among these, four loci were located on chromosomes 2B and 6B, and three on 6A. Several loci corresponded to resistance-related genes, including NBS-LRR, F-box, LRR, protein kinase, Ser/Thr_kinase, Znf_RING-CH, E3-ubiquitin ligase, and ABC transporter genes, suggesting their potential role in rust resistance mechanisms. Discussion The study identified novel genomic regions associated with Pst resistance, providing valuable resources for wheat improvement. The functional annotation of these loci highlights their involvement in plant defense pathways. Conversion of these loci into breeder-friendly molecular markers will facilitate marker-assisted selection (MAS) and accelerate the development of durable stripe rust-resistant wheat cultivars suited to North Indian agro-ecological conditions.