ARS | Publication request: Genotyping and Assessing Genetic Diversity in Pd Strain Xylella Fastidiosa by Simple Sequence Repeat (Ssr) DNA Markers

Submitted to: American Phytopathological Society Annual Meeting
Publication Acceptance Date: March 15, 2004
Publication Date: July 31, 2004
Citation: Lin, H., Civerolo, E.L., Barros, S., Hu, R., Francis, M., Walker, A. 2004. Genotyping And Assessing Genetic Diversity In Pd Strain Xylella Fastidiosa By Simple Sequence Repeat (Ssr) DNA Markers [abstract]. Phytopathology. 94:s61.

Technical Abstract: The insect-transmitted bacterium, Xylella fastidiosa (Xf), causes diseases in many economically important plants, including Pierce's disease in grape. Understanding the genetic diversity and population structure of the pathogen are critical steps in managing disease outbreaks. With the recent availability of the sequencing of the genomes of four Xf strains, Pierce's disease of grapevine (PD), citrus variegated chlorosis (CVC), almond leaf scorch (ALS), and oleander leaf scorch (OLS), identification of repeated sequence loci is facilitated. A genome wide search was performed for identifying Simple Sequence Repeat (SSR) motifs among the all four strain sequence databases, and 60 SSR loci were selected for primer design. These simple repeat motifs consist of 2-8 bp repeat units and were distributed across the whole genome. We evaluated these SSR primers with 21 Xf isolates collected from Napa Valley, San Joaquin Valley and southern California vineyards. Seventy percent of these SSR primers were highly polymorphic and distinguished genetically close strains. This PCR-based SSR marker is a precise and repeatable marker system. The power of this polymorphic detection system makes it a useful tool for population structure, genetic diversity and epidemiological risk assessment analyses.