Genome-Wide Identification of Loci Conferring Stem Rust Resistance in a Global Wheat Panel

Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a devastating disease that threatens wheat (Triticum aestivum L.) production worldwide. Developing resistant wheat varieties is crucial, as genetic resistance provides a more sustainable approach than chemical control. In this study, we evaluated 361 genetically diverse wheat accessions for resistance to four Pgt races, TMLKC, QFCSC, HKHJC, and LBBLC, that can overcome multiple known resistance (R) genes. Seedling responses varied widely, with most genotypes showing susceptibility. However, a subset exhibited strong resistance: 17.5% against TMLKC, 24% against QFCSC, 11.5% against HKHJC, and 23.5% against LBBLC. To identify genetic loci associated with resistance, we conducted a genome-wide association study (GWAS) using the disease phenotypic data combined with 302,524 high-quality single nucleotide polymorphisms (SNPs) data. The analysis revealed 34 significant marker-trait associations (MTAs) for stem rust resistance, distributed across 14 wheat chromosomes. Out of 34 significant MTAs, 15 were located near previously reported Sr genes, MTAs, or quantitative trait loci (QTLs) associated with stem rust resistance. The remaining 19 MTAs corresponded to the genomic regions that may contain possibly novel resistance genes. Candidate gene analysis of the significant MTAs revealed genes that may potentially play a role in disease resistance. The identified MTAs can potentially be used to transfer resistance loci to develop stem rust-resistant wheat varieties.