Genome-wide association analysis identifies seven loci conferring resistance to multiple wheat foliar diseases, including brown and yellow rust resistance originating from Aegilops ventricosa

We assembled a European bread wheat (Triticum aestivum L.) association mapping panel (n = 480) genotyped using a 90,000 feature single nucleotide polymorphism array, with the aim of identifying genetic loci controlling resistance to four fungal diseases: yellow (stripe) rust (YR), brown (leaf) rust (BR), Septoria tritici blotch (ST) and powdery mildew (PM). Simulations showed our panel to have good power to detect genetic loci, with > 50% probability of identifying loci controlling as little as 5% of the variance when heritability was 0.6 or more. Using disease infection data collected across 31 trials undertaken in five European countries, genome-wide association studies (GWAS) identified 34 replicated genetic loci (20 for YR, 12 for BR, two for PM, 0 for ST), with seven loci associated with resistance to two or more diseases. Construction and analysis of eight bi-parental populations enabled two selected genetic loci, yellow rust resistance locus YR_2A010 (chromosome 2A) and YR_6A610 (6A), to be independently cross-validated, along with the development of genetic markers to track resistance alleles at these loci. Notably, the chromosome 2A yellow and brown rust resistance locus corresponds to the 2N^vS introgression from the wild wheat species, Aegilops ventricosa. We found evidence of strong selection for 2N^vS over recent breeding history, being present in 48% of the most recent cultivars in our panel. Collectively, we define the genetic architectures controlling resistance to major fungal diseases of wheat under European field environments, and provide resources to exploit these for the development of new wheat cultivars with improved disease resistance.