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ARS Home » Pacific West Area » Parlier, California » San Joaquin Valley Agricultural Sciences Center » Crop Diseases, Pests and Genetics Research » Research » Publications at this Location » Publication #161353
Title: DEVELOPMENT OF SSR MARKERS FOR GENOTYPING AND ASSESSING GENETIC DIVERSITY OF XYLELLA FASTIDIOSA

Author
item Lin, Hong
item Civerolo, Edwin
item BARROS, SAMUEL - UNIV OF CA, DAVIS
item WALKER, ANDREW - UNIV OF CA, DAVIS

Submitted to: American Society of Enology and Viticulture Annual Meeting Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 2/17/2004
Publication Date: 6/21/2004
Citation: Lin, H., Civerolo, E.L., Barros, S., Walker, A. 2004. Development of ssr markers for genotyping and assessing genetic diversity of Xylella fastidiosa [Abstract]. American Society of Enology and Viticulture. p. 162.

Interpretive Summary:

Technical Abstract: The objective of this work is to develop a DNA based marker system for unambiguous differentiation and identification of Xylella fastidiosa (Xf) strains. Simple Sequence Repeat (SSR) marker is a precise and repeatable marker system. With the completion of the genomic sequencing of four Xf strains (PD, CVC, ALS and OLS), the identification of repeated sequence loci is facilitated. A genome wide search was performed for SSR loci among the sequence databases of all four strains and 400-500 various repetitive types of SSR loci were identified from each strain. These loci are evenly distributed across whole genome and are potentially useful for SSR marker design. Based on the repeat length and types, 60 SSR loci were selected for primer design. We evaluated these SSR primers with 5 PD Xf collections; four from Napa vineyards and one from the Temecula (the one used for whole genome sequence). Results indicated that 70% of SSR primers were able to detect various degrees of polymorphisms among the 5 isolates. These PCR-based SSR markers provide an excellent tool for research in epidemiological analysis, genetic structure of microbial populations, and fingerprinting isolated colonies.