Wheat Genetic Loci Conferring Resistance to Yellow Rust in the Face of Recent Epidemics of Genetically Diverse Races of the Fungus Puccinia Striiformis F. Sp. Tritici

Abstract Yellow rust (YR), or stripe rust, is a major fungal disease of wheat (Triticum aestivum) caused by Puccinia striiformis f. sp. tritici (Pst). Since 2011, the historically clonal European Pst races have been superseded by the rapid incursion of genetically diverse lineages, reducing the resistance of varieties that previously showed durable resistance. Identification of sources of genetic resistance to such races is a high priority for wheat breeding. Here we use a wheat eight-founder multi-parent population genotyped with a 90,000 feature single nucleotide polymorphism array to genetically map adult plant YR resistance to such new Pst races. Analysis of five trials, at three sites in the UK, consistently identified four highly significant quantitative trait loci (QTL) across all test environments, located on chromosomes 1A (QYr.niab-1A.1), 2A (QYr.niab-2A.1), 2B (QYr.niab-2B.1) and 2D (QYr.niab-2D.1). Together these explained ~ 50% of the phenotypic variation, and genetic markers were developed that distinguished resistant and susceptible alleles. Analysis of these QTL in two-way and three-way combinations showed combinations conferred greater resistance than single QTL. Four additional major-effect QTL were detected in two or more trials, together explaining 15–20% of the phenotypic variation, as well as six minor QTL. Genomic analysis found the median physical interval size of these eight QTL to be 19.8 Mbp, and QYr.niab-2A.1 and QYr.niab-2D.1 to be at homoeologous locations on the group-2 chromosomes. Notably, the QYr.niab-2B.1 physical interval contained five nucleotide-binding leucine-rich repeat (NLR) candidate genes with integrated BED domains, of which two corresponded to the cloned resistance genes Yr7 and Yr5/YrSp.