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ARS Home » Pacific West Area » Pullman, Washington » WHGQ » Research » Publications at this Location » Publication #317411
Title: Secreted protein gene derived-single nucleotide polymorphisms (SP-SNPs) reveal population diversity and differentiation of Puccinia striiformis f. sp. tritici in the United States

Author
item XIA, C - Washington State University
item WANG, M - Washington State University
item WAN, A - Washington State University
item JIWAN, D - Washington State University
item See, Deven
item Chen, Xianming

Submitted to: Fungal Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/24/2016
Publication Date: 3/4/2016
Citation: Xia, C.J., Wang, M.N., Wan, A.M., Jiwan, D.A., See, D.R., Chen, X. 2016. Secreted protein gene derived-single nucleotide polymorphisms (SP-SNPs) reveal population diversity and differentiation of Puccinia striiformis f. sp. tritici in the United States. Fungal Biology. 120(5):729-744.

Interpretive Summary: In population genetic studies, growing awareness has been raised on non-neutral markers which can provide more estimates of evolutionary differentiation caused by different selections among populations, even though neutral genetic markers have provided unbiased estimates of divergence time and the amount of genetic drift. In the present study, we developed over a hundred potentially non-neutral secreted protein gene-derived single nucleotide polymorphism (SP-SNP) markers for the causal fungus of stripe rust, one of the most destructive pathogens in wheat production worldwide. A total of 352 isolates collected over all stripe rust epidemiological regions in the United States were genotyped using 92 SP-SNP markers to study the population diversity and differentiation, revealing 242 unique genotypes. A moderate, but significant correlation between the SP-SNP data and virulence data was found, and clustering of the 242 multi-locus genotypes was consistent by various clustering analyses. Significant differences between the eastern and western U.S. stripe rust fungal populations. High heterogeneity was found in the national population with significant differences identified among epidemiological regions. Analysis of population differentiation among epidemiological regions revealed isolates from the western US were more diverse than isolates from the eastern US. Isolates from the western US were more diverse than isolates from the eastern US. These newly developed, potentially non-neutral SP-SNP markers could be useful in identifying genomic regions or genes under selection in the stripe rust fungal populations.

Technical Abstract: In population genetic studies, growing awareness has been raised on non-neutral markers which can provide more estimates of evolutionary differentiation caused by different selections among populations, even though neutral genetic markers have provided unbiased estimates of divergence time and the amount of genetic drift. In the present study, we developed over a hundred potentially non-neutral secreted protein gene-derived single nucleotide polymorphism (SP-SNP) markers for Puccinia striiformis f. sp. tritici (Pst), the causal agent of stripe rust, one of the most destructive pathogens in wheat production worldwide. A total of 352 Pst isolates collected over all stripe rust epidemiological regions in the United States (US) were genotyped at 92 SP-SNP loci to study the population diversity and differentiation, revealing 242 multi-locus genotypes. A moderate, but significant correlation (r = 0.43; P = 0.01) between the SP-SNP data and virulence data was found. Clustering of all 242 multi-locus genotypes was consistent by multivariate discriminant analysis of principal components, neighbor-joining method and Bayesian clustering algorithm. Analysis of molecular variance (AMOVA) detected significant differences between the eastern and western US Pst populations. High heterogeneity was found in the national population with significant differences identified among epidemiological regions. Analysis of population differentiation among epidemiological regions revealed isolates from the western US were more diverse than isolates from the eastern US. Isolates from the western US were more diverse than isolates from the eastern US. These newly developed potentially non-neutral SP-SNP markers could be useful in identifying genomic regions or genes under selections in Pst populations.