Watkins wheat landraces: a treasure of stripe rust resistance alleles identified using multi-model association...

Genome-wide association mapping of 297 Watkins wheat landraces across diverse stripe rust races & genetic lineages identified 87 QTL. However, only 29 high-confidence loci were detected across multiple stripe rust isolates, identified by both GWAS models, and/or co-localizing with previously designated Yr genes, highlighting Watkins landraces as valuable pre-breeding donors for stripe rust resistance. Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), remains a major global constraint to wheat production. Rapid pathogen evolution, exemplified by the recent breakdown of Yr15 in Europe, underscores the need to identify diverse and durable resistance loci. The A.E. Watkins landrace collection represents a globally diverse pre-breeding resource with substantial untapped variation for stripe rust resistance. In this study, 297 Watkins landraces were evaluated against six diverse Pst isolates (representing five races and three North American lineages) at the seedling stage and subjected to genome-wide association analysis using high-density whole-genome resequencing data. Continuous phenotypic variation was observed across isolates, with several accessions displaying stable resistance across all pathogen lineages. Across the six isolate-specific GWAS analyses, a total of 87 QTL were identified. Seven loci co-localized with designated or cloned Yr genes and an additional 34 loci overlapped previously reported stripe rust QTL, whereas the majority did not coincide with known loci, suggesting potential novel resistance regions. Only 29 high-confidence QTL (including some previously cloned/mapped QTL) conferred resistance to two or more isolates, multiple statistical models and/or co-localizing with previously designated Yr genes, indicating robust genomic signals. Several Watkins accessions carried favorable alleles for multiple Yr resistance loci, identifying promising donor candidates for validation and pre-breeding.