Identifying Loci Conferring Resistance to Leaf and Stripe Rusts in a Spring Wheat Population (Triticum aestivum) via Genome-Wide Association Mapping.

A previous genome-wide association study (GWAS) for leaf rust (caused by Puccinia triticina) resistance identified 46 resistance quantitative trait loci (QTL) in an elite spring wheat leaf rust resistance diversity panel. With the aim of characterizing the pleiotropic resistance sources to both leaf rust and stripe rust (caused by P. striiformis f. sp. tritici), stripe rust responses were tested in five U.S. environments at the adult-plant stage and to five U.S. races at the seedling stage. The data revealed balanced phenotypic distributions in this population except for the seedling response to P. striiformis f. sp. tritici race PSTv-37. GWAS for stripe rust resistance discovered a total of 21 QTL significantly associated with all-stage or field resistance on chromosomes 1B, 1D, 2B, 3B, 4A, 5A, 5B, 5D, 6A, 6B, 7A, and 7B. Previously documented pleiotropic resistance genes Yr18/Lr34 and Yr46/Lr67 and tightly linked genes Yr17-Lr37 and Yr30-Sr2-Lr27 were also detected in this population. In addition, stripe rust resistance QTL Yrswp-2B.1, Yrswp-3B, and Yrswp-7B colocated with leaf rust resistance loci 2B_3, 3B_t2, and 7B_4, respectively. Haplotype analysis uncovered that Yrswp-3B and 3B_t2 were either tightly linked genes or the same gene for resistance to both stripe and leaf rusts. Single nucleotide polymorphism markers IWB35950, IWB74350, and IWB72134 for the 3B QTL conferring resistance to both rusts should be useful in incorporating the resistance allele(s) in new cultivars.

Association mapping of leaf rust resistance loci in a spring wheat core collection.

KEY MESSAGE: We identified 15 potentially novel loci in addition to previously characterized leaf rust resistance genes from 1032 spring wheat accessions. Targeted AM subset panels were instrumental in revealing interesting loci. Leaf rust is a common disease of wheat, consistently reducing yields in many wheat-growing regions of the world. Although fungicides are commonly applied to wheat in the United States (US), genetic resistance can provide less expensive, yet effective control of the disease. Our objectives were to map leaf rust resistance genes in a large core collection of spring wheat accessions selected from the United States Department of Agriculture-Agricultural Research Service National Small Grains Collection (NSGC), determine whether previously characterized race-nonspecific resistance genes could be identified with our panel, and evaluate the use of targeted panels to identify seedling and adult plant resistance (APR) genes. Association mapping (AM) detected five potentially novel leaf rust resistance loci on chromosomes 2BL, 4AS, and 5DL at the seedling stage, and 2DL and 7AS that conditioned both seedling and adult plant resistance. In addition, ten potentially novel race-nonspecific resistance loci conditioned field resistance and lacked seedling resistance. Analyses of targeted subsets of the accessions identified additional loci not associated with resistance in the complete core panel. Using molecular markers, we also confirmed the presence and effectiveness of the race-nonspecific genes Lr34, Lr46, and Lr67 in our panel. Although most of the accessions in this study were susceptible to leaf rust in field and seedling tests, many resistance loci were identified with AM. Through the use of targeted subset panels, more loci were identified than in the larger core panels alone.

Genome Wide Association Study of Seedling and Adult Plant Leaf Rust Resistance in Elite Spring Wheat Breeding Lines.

Leaf rust is an important disease, threatening wheat production annually. Identification of resistance genes or QTLs for effective field resistance could greatly enhance our ability to breed durably resistant varieties. We applied a genome wide association study (GWAS) approach to identify resistance genes or QTLs in 338 spring wheat breeding lines from public and private sectors that were predominately developed in the Americas. A total of 46 QTLs were identified for field and seedling traits and approximately 20-30 confer field resistance in varying degrees. The 10 QTLs accounting for the most variation in field resistance explained 26-30% of the total variation (depending on traits: percent severity, coefficient of infection or response type). Similarly, the 10 QTLs accounting for most of the variation in seedling resistance to different races explained 24-34% of the variation, after correcting for population structure. Two potentially novel QTLs (QLr.umn-1AL, QLr.umn-4AS) were identified. Identification of novel genes or QTLs and validation of previously identified genes or QTLs for seedling and especially adult plant resistance will enhance understanding of leaf rust resistance and assist breeding for resistant wheat varieties. We also developed computer programs to automate field and seedling rust phenotype data conversions. This is the first GWAS study of leaf rust resistance in elite wheat breeding lines genotyped with high density 90K SNP arrays.