title: 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.).
abstract: 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 responsible for large yield losses worldwide. To identify new sources of resistance we performed a genome-wide association study (GWAS) using a worldwide collection of 1000 spring wheat accessions. Adult plants were evaluated under field conditions in six environments in the western United States, and seedlings were tested with four Pst races. A single-nucleotide polymorphism (SNP) Infinium 9K-assay provided 4585 SNPs suitable for GWAS. High correlations among environments and high heritabilities were observed for stripe rust infection type and severity. Greater levels of Pst resistance were observed in a subpopulation from Southern Asia than in other groups. GWAS identified 97 loci that were significant for at least three environments, including 10 with an experiment-wise adjusted Bonferroni probability < 0.10. These 10 quantitative trait loci (QTL) explained 15% of the phenotypic variation in infection type, a percentage that increased to 45% when all QTL were considered. Three of these 10 QTL were mapped far from previously identified Pst resistance genes and QTL, and likely represent new resistance loci. The other seven QTL mapped close to known resistance genes and allelism tests will be required to test their relationships. 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.
authors.affiliation: Department of Plant Sciences, University of California, Davis, California 95616 Department of Agricultural Sciences (DipSA), University of Bologna, Bologna 40127, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Maccaferri
authors.affiliation: Department of Plant Sciences, University of California, Davis, California 95616.
authors.forename: Junli
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420.
authors.forename: Peter
authors.initials: P
authors.lastname: Bulli
authors.affiliation: Department of Plant Sciences, University of California, Davis, California 95616.
authors.forename: Zewdie
authors.initials: Z
authors.lastname: Abate
authors.affiliation: USDA-ARS, 1605 Albrecht Blvd, Fargo, North Dakota 58105.
authors.forename: Shiaoman
authors.initials: S
authors.lastname: Chao
authors.affiliation: Department of Viticulture and Enology, University of California, Davis, California 95616.
authors.forename: Dario
authors.initials: D
authors.lastname: Cantu
authors.affiliation: Department of Plant Sciences, University of California, Davis, California 95616.
authors.forename: Eligio
authors.initials: E
authors.lastname: Bossolini
authors.affiliation: USDA-ARS, Wheat Genetics, Quality Physiology, and Disease Research Unit, and Department of Plant Pathology, Washington State University, Pullman, Washington 99164.
authors.forename: Xianming
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420.
authors.forename: Michael
authors.initials: M
authors.lastname: Pumphrey
authors.affiliation: Department of Plant Sciences, University of California, Davis, California 95616 Howard Hughes Medical Institute, Chevy Chase, Maryland 20815 Jdubcovsky@ucdavis.edu.
authors.forename: Jorge
authors.identifier: http://orcid.org/0000-0002-7571-4345
authors.initials: J
authors.lastname: Dubcovsky
mesh_terms: D001487:Basidiomycota / Q000472:pathogenicity*; D060467:Disease Resistance / Q000235:genetics*; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D020641:Polymorphism, Single Nucleotide; D011123:Polyploidy; D040641:Quantitative Trait Loci; D014908:Triticum / Q000235:genetics* / Q000276:immunology / Q000382:microbiology
keywords: association mapping; bread wheat; disease resistance; genetic map; yellow rust