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Development of SP-SNP markers and use them to characterize populations of the stripe rust pathogen and identify markers associated to avirulence genes
C. XIA (1), M. Wang (1), A. Wan (1), X. Chen (2). (1) Washington State University, Pullman, WA, U.S.A.; (2) Washington State University; USDA-ARS, Wheat Genetics, Quality, Physiology, and Disease Research Unit, Pullman, WA, U.S.A.

<i>Puccinia striiformis</i> f. sp. <i>tritici</i> is a basidiomycete fungus causing of stripe rust, one of the most important diseases of wheat, but not many markers are available for determining the population structures and studying virulence. We developed 92 secreted protein derived-single nucleotide polymorphism (SP-SNP) markers and used them, together with virulence tests, to characterize the pathogen populations in various stripe rust epidemiological regions in the US. The SP-SNP data had a moderate, but significant correlation (<i>r</i>=0.43; <i>P</i>=0.01) with the virulence data. Bayesian clustering algorithm, neighbor-joining method, and principal component analysis clustered the 242 multi-locus genotypes obtained from 352 isolates into two genetic lineages and an admix group with different levels of heterozygosity. Analysis of molecular variance detected significant differences between eastern and western US populations and among some populations of the epidemiological regions. The western US isolates were more diverse than the eastern US isolates, and the isolates from southwestern US were more related those in the eastern than to those in the other western regions. Significantly associated SP-SNPs were detected for nine avirulence genes. The results indicated that SP-SNPs are useful in characterizing the pathogen populations, determining evolutionary mechanisms, and identifying markers associated to avirulence genes.

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