A Genome-Wide Association Study of Resistance to Stripe Rust (Puccinia striiformis f. sp. tritici) in a Worldwide Collection of Hexaploid Spring Wheat (Triticum aestivum L.)

New races of Puccinia striiformis f. sp. tritici (Pst), the causal pathogen of wheat stripe rust, show high virulence to previously deployed resistance genes and are responsible for large yield losses worldwide. To identify new sources of resistance we performed a genome-wide association study (GWAS) using a worldwide collection of 1,000 spring wheat. Adult plants were evaluated under field conditions in six environments in the western USA, and seedlings were tested with four Pst races. A single nucleotide polymorphism (SNP) Infinium 9K-assay provided 4,585 SNPs suitable for GWAS. High correlations among environments and high heritabilities were observed for stripe rust infection type and severity, and population structure had a moderate effect on these traits (R² = 0.14-0.17). GWAS identified seven QTL that were consistent across at least three environments and that showed an experiment-wise adjusted Bonferroni probability lower than 0.10. A second analysis excluding accessions with near-immune resistance identified 3 additional QTL for partial resistance. These 10 QTL explained 15% of the phenotypic variation in infection type, a percentage that increased to 19% when six significant pair-wise interactions were included in the model. A comparison with previously mapped Pst resistance genes and QTL suggests that seven out of the ten significant GWAS associations represent novel sources of resistance. In summary, this study provides an integrated view of stripe rust resistance resources in spring wheat and identifies new resistance loci that will be useful to diversify the current set of resistance genes deployed to control this devastating disease.