ARS | Publication request: DEVELOPMENT OF SSR MARKERS FOR GENOTYPING AND ASSESSING THE GENETIC DIVERSITY OF XYLELLA FASTIDIOSA IN CALIFORNIA

Submitted to: CDFA Pierce's Disease Control Program Research Symposium
Publication Type: Proceedings
Publication Acceptance Date: October 12, 2004
Publication Date: December 7, 2004
Citation: Lin, H., Civerolo, E.L., Walker, A. 2004. Development of SSR markers for genotyping and assessing the genetic diversity of Xylella fastidiosa in California. Proceedings of CDFA Pierce's Disease Control Program Research Symposium. p. 206-209.

Interpretive Summary: Recently available genomic sequences of four Xylella fastidiosa strains (PD, CVCD, ALSD and OLSD) facilitate genome wide searching to identify Simple Sequence Repeat (SSR) loci. Sixty SSR loci were selected for SSR marker development. We designed and validated 34 SSR primers with good reliability and specificity. These SSR primers showed various levels of polymorphism ranging from 3 to 23 alleles with average 11.3 alleles per locus among 43 Xylella fastidiosa strains. These multi-locus SSR markers distributed evenly across the whole genome are a useful tool for pathogen genotyping, population genetics and molecular epidemiologic study.

Technical Abstract: The availability of the complete sequences of four Xylella fastidiosa (Xf) strains (i.e., Pierce's disease of grapevine, citrus variegated chlorosis, almond leaf scorch, and oleander leaf scorch, has facilitated the identification of repeated sequence loci. A genome wide search was performed for identifying Simple Sequence Repeat (SSR) motifs among the all four strain sequence databases. A total of 34 SSR primers were designed and validated. These multi-locus DNA markers are distributed across whole genomes. We evaluated these SSR primers with 43 Xf isolates collected from four hosts; grape, citrus, almond and oleander. These SSR primers are powerful for distinguishing between and within host-associated strains with average 11.3 alleles per locus. The PCR-based SSR marker is a precise and reliable marker system for Xf identification and differentiation. This powerful of polymorphic detection system makes it a useful tool for population structure, genetic diversity and epidemiological risk assessment analysis.