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A Genome-Wide Association Study of Resistance to Stripe Rust (Puccinia striiformis f. sp. tritici) in a Worldwide Collection of Hexaploid Spring Wheat (Triticum aestivum L.)

Maccaferri, Marco, Zhang, Junli, Bulli, Peter, Abate, Zewdie, Chao, Shiaoman, Cantu, Dario, Bossolini, Eligio, Chen, Xianming, Pumphrey, Michael, Dubcovsky, Jorge
Genes, genomics, genetics 2015 v.5 no.3 pp. 449-465
Puccinia striiformis f. tritici, Triticum aestivum, disease resistance, genes, genome-wide association study, heritability, hexaploidy, loci, mature plants, models, pathogens, phenotypic variation, population structure, probability, quantitative trait loci, races, seedlings, single nucleotide polymorphism, spring wheat, stripe rust, virulence, United States
New races of Puccinia striiformis f. sp. tritici (Pst), the causal pathogen of wheat stripe rust, show high virulence to previously deployed resistance genes and are causing large yield losses worldwide. To identify new sources of resistance we performed a genome-wide association study (GWAS) using a worldwide collection of 875 spring wheat. Adult plants were evaluated under field conditions in six environments in western USA, and seedlings were tested with four Pst races. A single nucleotide polymorphism (SNP) Infinium 9K-assay provided 4,374 mapped SNPs suitable for GWAS. Population structure had a moderate effect on Pst response (R2 = 0.14-0.17). High correlations among environments and high heritabilities were observed for all Pst evaluations. GWAS identified 7 QTL (single or multiple linked SNPs) that were consistent across at least three environments and that showed an experiment-wise adjusted Bonferroni probability lower than 0.10. A second analysis excluding accessions with complete resistance identified 3 additional QTL for partial resistance. These 10 QTL explained 15% of the phenotypic variation in infection type, a percentage that increased to 19% when six significant pair-wise interactions were included in the model. A comparison with previously mapped Yr genes and Pst resistance QTL indicated that seven out of the 10 significant GWAS associations likely represent novel sources of resistance. In summary, this study provides an integrated view of stripe rust resistance resources in spring wheat and identifies new resistance loci that will be useful to diversify the current set of resistance genes deployed to control this devastating disease.