Genome-wide association mapping of leaf rust and stripe rust resistance in wheat accessions using the 90K SNP array

A genome-wide association analysis identified diverse loci for seedling and adult plant resistance to leaf rust and stripe rust. KASP markers were developed and validated for marker-assisted selection. Wheat leaf rust and stripe rust cause significant losses in many wheat producing regions worldwide. The objective of this study was to identify chromosome regions conferring resistance to both leaf rust and stripe rust at the seedling and adult plant stages. A diversity panel of 268 wheat lines, including 207 accessions from different wheat growing regions in China, and 61 accessions from foreign countries, were evaluated for leaf rust response at seedling stage using eight Chinese Puccinia triticina pathotypes, and also tested for leaf rust and stripe rust at adult plant stage in multiple field environments. The panel was genotyped with the Wheat 90 K Illumina iSelect SNP array. Genome-wide association mapping (GWAS) was performed using the mixed linear model (MLM). Twenty-two resistance loci including the known Lr genes, Lr1, Lr26, Lr3ka, LrZH22, and 18 potentially new loci were identified associated with seedling resistance, explaining 4.6 to 25.2% of the phenotypic variance. Twenty-two and 23 adult plant resistance (APR) QTL associated with leaf and stripe rust, respectively, were identified at adult stage, explaining 4.2-11.5% and 4.4-9.7% of the phenotypic variance. Among them, QLr-2BS was the potentially most valuable all-stage resistance gene. Seven and six consistent APR QTL were identified in multiple environments including best linear unbiased prediction (BLUP) data, respectively. Comparison with previously mapped resistance loci indicated that three of the seven leaf rust resistance APR QTL, and two of the six stripe rust resistance APR QTL were new. Four potentially pleiotropic APR QTL, including Lr46/Yr29, QLr-2AL.1/QYr-2AL.1, QLr-2AL.2/QYr-2AL.2, and QLr-5BL/QYr-5BL.1, were identified. Twelve associated SNPs were converted into kompetitive allele-specific PCR (KASP) markers and verified in bi-parental populations. The study reports genetic loci conferring resistance to both diseases, and the closely linked markers should be applicable for marker-assisted wheat breeding.