Hierarchical Analysis and Diversity Studies of Xylella fastidiosa Populations in California by Multi-locus Simple Sequence Repeat Markers

Authors: Lin, Hong; THAMMIRAJU,, SYAMALA RANI - UC DAVIS; WALKER,, ANDREW - UC DAVIS; Stenger, Drake; Civerolo, Edwin

Submitted to: CDFA Pierce's Disease Control Program Research Symposium
Publication Type: Proceedings
Publication Acceptance Date: 10/9/2007
Publication Date: 12/12/2007
Citation: Lin, H., Thammiraju,, S., Walker,, A.M., Stenger, D.C., Civerolo, E.L. 2007. Hierarchical Analysis and Diversity Studies of Xylella fastidiosa Populations in California by Multi-locus Simple Sequence Repeat Markers. In: Proceedings of CDFA Pierce's Disease Control Program Research Symposium, December 12-14, 2007, San Diego, California. p. 144-147.

Interpretive Summary: Limited genetic variation within crop hosts may influence pathogen population structure by imposing strong directional selection which may lead to breakdown of resistance. Pierce’s Disease (PD) of grapevine is caused by the bacterium Xylella fastidiosa. To define genetic diversity and population structure of this pathogen in Californian vineyards, we used multilocus simple sequence repeat (SSR) marker analysis as a tool. Eighteen SSR markers were used on 83 X. fastidiosa strains isolated from 15 grape populations in Sonoma, Napa, Kern and Temecula regions of California. Average genetic diversity observed was relatively high (H = 0.807, I=0.5385) across the 18 loci examined but diversity was not correlated with grape cultivar. No evidence for hierarchical population structure was found as nearly all of the variation (98%) was due to diversity within, not between, populations. This result may be explained by a high level of gene flow among X. fastidiosa populations resident in Californian vineyards. The data also suggests dominance of selection pressure over other forces in structuring X. fastidiosa populations. These finding indicate that disease management of PD in individual vineyards or growing regions must account for all diversity resident in the state, not merely variation within a specific region or grape cultivar. We also initiated similar studies for almond specific Xf strains to better understand host specific diversity patterns and specific population structure, if any, for the almond Xf strains.

Technical Abstract: Xylella fastidiosa is the causative agent of Pierce’s Disease (PD) in grapevine. Using 18 simple sequence repeat (SSR) markers, we assessed variation within and between populations of X. fastidiosa isolated from grapevine in California. Eighty-three X. fastidiosa isolates from 15 populations present in four regions of California were evaluated for sequence variation. Average genetic diversity was substantial (H = 0.807, I=0.5385) across the 18 loci examined. Diversity within populations varied from 0.227±0.058 (population Sangiacom) to 0.583±0.63 (population Temecula) but was not dependent upon with the grape cultivar serving as host. Analysis of Molecular Variance (AMOVA) indicated no hierarchical population structure, as 98% of the variation was attributed to within population diversity. Higher order variation was minor; diversity among populations or among regions each accounted for only 1% of the variation observed. Principal component analysis (PCA) indicated that only ~53% of the variation was explained by the first three components, further suggesting a lack of hierarchical population structure in X. fastidosa infecting grape in California. Collectively, these results indicate high levels of gene flow between populations and further suggests that strong selection may dominate other population genetic forces responsible for structuring X. fastidiosa populations resident in Californian grapes. We also initiated similar studies for almond specific Xf strains to better understand host specific diversity patterns and specific population structure for the almond Xf strains.