MULTI-LOCUS SIMPLE SEQUENCE REPEATS AND SINGLE NUCLEOTIDE POLYMORPHISM MARKERS FOR GENOTYPING AND ASSESSING GENETIC DIVERSITY OF XYLELLA FASTIDIOSA IN CALIFORNIA

• Author(s): Lin, Hong; Civerolo, Ed; Doddapaneni, Harshavardhan; Groves, Russell; Walker, Andrew;
• Abstract: In California, information regarding the population structure and genetic diversity as well as the genetic evolutionary and epidemiological relationships among Xylella fastidiosa (Xf) strains in agricultural populations is not clear. To develop effective management strategies, we need to understand pathogen population structure and genetic diversity in the agricultural ecosystem. Here we report development and utilization of two multilocous marker systems, Simple Sequence Repeats (SSR) and single nucleotide polymorphism (SNP) for genotyping and assessing 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 strains identified 12,754 potential SNPs in coding sequences and 20,779 SNPs in non-coding regions across four Xf strains. Small scale validation (16 loci) tests showed that SNP genotype is tightly linked to the hosts from which the strains were derived. Together, SNP and SSR marker systems appear to be useful tools for pathogen detection and population genetic analyses.
• Publication Date: Nov 2006
• Journal: 2006 Pierce's Disease Research Symposium