Identification and Validation of SNP Markers Linked to the Stripe Rust Resistance Gene Yr5 in Wheat

Abstract

Stripe rust (Puccinia striiformis Westend f. sp. tritici) is a devastating disease for wheat (Triticum aestivum L.) production worldwide. Yr5 is a race‐specific resistance gene, effective to all races that have been identified in the United States. Therefore, it has been increasingly used for US cultivar development. The goal of this study was to identify and validate single‐nucleotide polymorphism (SNP) markers tightly linked with Yr5, evaluate their usefulness with a diverse set of wheat materials, and dissect the Yr5 region to search for candidate genes using a comparative genomic approach. Competitive allele‐specific polymerase chain reaction (KASP) markers based on Illumina iSelect 9000 SNP loci IWA6121 and IWA4096 were identified as flanking markers for Yr5 in two spring wheat recombinant inbred line populations that were developed from crosses between moderately susceptible line ‘WA8149’ and Yr5 donors ‘S0900317’ and ‘S0900163.’ These markers were closer to the gene than previously reported markers. Haplotype analysis based on loci of these KASP markers in a set of the Pacific Northwest spring and winter wheat lines and a worldwide spring wheat core collection showed that the combined haplotype for these markers is nearly diagnostic for the presence of Yr5. The Yr5‐syntenic regions in Brachypodium and rice (Oryza sativa L.) contained a putative gene encoding a nucleotide binding site–leucine‐rich repeat disease resistance protein. Wheat gene Traes_2BL_B5FC3BC9E showed high similarity with these Brachypodium and rice genes, and a marker designed from this gene was mapped closest to Yr5 in the recombinant inbred line populations. This study provides useful SNP markers for Yr5 in wheat breeding programs and resources for potential map‐based cloning of Yr5.