Deciphering the genetic architecture of stem rust resistance in a diversity panel of 1,290 Triticum aestivum germplasm

Global wheat production faces a major challenge in stem rust, caused by Puccinia graminis f. sp. tritici . The rapid evolution of the stem rust pathogen requires continuous global monitoring of its pathotypes. This surveillance is crucial for prioritizing the development of resistant cultivars and implementing other effective control measures. The predominant pathotypes in India since 2014 were selected for investigation, which includes 11 (79G31 = RRTSF), 40 A (62G29 = PTHSC), 40 − 3 (127G29 = PTTSF), and 117-6 (37G19 = KRCSC). To discover MTAs conferring stem rust resistance, an association mapping panel of ~ 1,290 bread wheat accessions was analyzed through 35 K Axiom ® Array SNP genotyping and comprehensively phenotyped at seedling stage. A multi-model GWAS approach incorporating BLINK, MLM, CMLM, MLMM, and FarmCPU models identified 14 MTAs associated with resistance across four pathotypes. 11 of the MTAs showed significant genotypic effects across the four pathotypes. Subsequent analysis of the genomic regions flanking these 14 MTAs identified 182 candidate genes with putative roles in plant defense, belonging to multiple distinct protein functional classes. Expression profiling revealed sustained expression of TraesCS6D02G397200, an L-ascorbate peroxidase (APX)-encoding gene on chromosome 6D, across stem rust-infected samples, along with elevated expression of several protein kinase- and F-box protein-encoding genes. The identified genes constitute promising candidates and valuable targets for marker-assisted breeding strategies aimed at enhancing stem rust resistance in wheat. These finding provide a useful foundation for future validation and deployment of resistance associated alleles in wheat development programs.