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United States Department of Agriculture

Agricultural Research Service

Title: Multilocus Simple Sequence Repeats and Single Nucleotide Polymorphism Markers for Genotyping and Assessing Genetic Diversity of Xylella Fastidiosa in California

Authors
item Lin, Hong
item Civerolo, Edwin
item Doddapaneni, Harshavardhan - UC, DAVIS
item Groves, Russell - UNIVERSITY OF WISCONSIN
item Walker, Andrew - UC, DAVIS

Submitted to: CDFA Pierce's Disease Control Program Research Symposium
Publication Type: Proceedings
Publication Acceptance Date: September 25, 2006
Publication Date: November 27, 2006
Citation: Lin, H., Civerolo, E.L., Doddapaneni, H., Groves, R., Walker, A. 2006. Multilocus simple sequence repeats and single nucleotide polymorphism markers for genotyping and assessing genetic diversity fo xylella fastidiosa in california. Proceedings of CDFA Pierce's Disease Control Program Research Symposium, November 27-29, 2006, San Diego, California. p.160-163.

Interpretive Summary: Understanding of pathogen population structure and diversity is crucial for development of effective disease management strategies. DNA-based methodologies are ideally suited for this purpose. Here we report development and utilization of two DNA detection systems, Simple Sequence Repeats (SSR) and single nucleotide polymorphism (SNP) for assessment of population structure and genetic diversity of Xylella fastidiosa (Xf) in California. Strain diversity studies using SSRs on Xf samples from different geographic populations and/or from different hosts demonstrated that host selection plays an important role in genetic differentiation of Xf populations in California. Whole-genome comparison of four sequenced strains identified 12,754 potential SNPs in gene sequences and 20,779 SNPs in non-gene regions across the four Xf strains. Small scale validation (16 locations) tests showed that SNP patterns are correlated with hosts from which the Xf strains were isolated. Together, SNP and SSR marker systems are useful tools for pathogen detection and population genetic analyses.

Technical Abstract: To develop effective disease management strategies, we need to understand population structure and genetic diversity of pathogens in agricultural ecosystems. Current information regarding population structure and genetic diversity of Xylella fastidiosa (Xf) in California is insufficient to adequately describe genetic, evolutionary, and epidemiological relationships of Xf strains in crops. Here we report development and utilization of two multi-locus genetic marker systems, Simple Sequence Repeats (SSR) and Single Nucleotide Polymorphism (SNP) for genotype identification and assessment of genetic diversity of Xf in California. Strain diversity studies using SSRs on samples from different geographic populations and/or from different hosts demonstrated that host selection plays an important role in Xf genetic differentiation among agricultural populations in California. Whole-genome comparison of four sequenced Xf strains identified 12,754 potential SNPs in coding sequences and 20,779 SNPs in non-coding regions among the four Xf strains. Small scale validation tests (16 loci) showed that SNP genotype is tightly linked to the host from which a strain was recovered. Together, SNP and SSR marker systems appear to be useful tools for pathogen detection and population genetic analyses.

Last Modified: 10/22/2014
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