GWAS With a Global Population of Wheat Stripe Rust Identified High-Confidence Avirulence Gene Candidates

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a globally destructive disease characterised by rapid virulence evolution. Despite its significance, the genetic basis of avirulence variation at a global scale remains poorly understood. In this study, we integrated virulence phenotypes against 18 Yr resistance genes with genome-wide variation from a worldwide collection of Pst isolates to resolve the population-genomic architecture of avirulence. We identified multiple avirulence-associated genomic regions and defined 69 candidate effectors, with 11 high-confidence candidates meeting five stringent criteria based on effector properties and association significance. Allele frequency analyses revealed striking geographic differentiation; many variants showed high or near-fixation in specific regions, notably East Africa, South America and inland China, while remaining rare elsewhere. This pattern indicates a strong population structure driven by regionally confined polymorphisms in host-recognition genes. Furthermore, structural modelling supported direct molecular recognition between the resistance protein Yr9 and multiple candidate AvYr9 effectors, providing mechanistic insights into specificity. Together, this study establishes a global population-genomic framework for effector discovery and elucidates virulence evolution in Pst. These candidates represent valuable resources for understanding rust pathogenicity and developing durable resistance in wheat.