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

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 six races and three North American lineages) 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 lineages. A total of 87 QTLs were identified across all 21 wheat chromosomes. Ten loci co-localized with designated or cloned Yr genes, including Yr84, Yr85, Yrq1, Yr71, Yr60, Yr62, Yr50, Yr68, Yr34, and Lr34/Yr18/Sr57. An additional 34 loci overlapped previously reported stripe rust QTL, whereas the majority did not coincide with known loci, suggesting potential novel resistance regions. Eighteen QTLs were supported by multiple isolates, and fourteen showed supports across statistical models, indicating robust genomic signals. Several Watkins accessions carried favorable alleles that co-localized with multiple Yr-aligned loci, identifying promising donor candidates for validation and pre-breeding. Key MessageGenome-wide association mapping of 297 Watkins wheat landraces across diverse stripe rust races & genetic lineages identified 87 QTL, including 10 formally designated Yr genes and 46 novel loci, highlighting Watkins landraces as valuable pre-breeding donors for novel all-stage stripe rust resistance.