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Poster: Epidemiology: Population Biology Genetics


A strategy to study population variation of Xanthomonas axonopodis pv. manihotis using a new set of multiple-locus variable number tandem repeats.
L. RACHE CARDENAL (1), C. Flores (2), C. López (3), B. Szurek (2), C. Vernièr (2), R. Koebnik (2), S. Restrepo (4), A. Bernal (4) (1) Universidad de los Andes, Colombia; (2) UMR Interactions Plantes Microorganismes Environnement, IRD-Cirad-UM, Montpellier

Multiple-Locus Variable Number Tandem Repeat Analysis (MLVA) is being used to analyze genetic diversity in phytopathogenic microorganisms. One of the most important pathogens affecting Cassava crops is Xanthomonas axonopodis pv. manihotis (Xam) as its infection relates to high loses in crop productivity. Several studies have reported that Xam populations change over time. It is important to assess population diversity in this pathogen as one of the basis to develop cassava resistant varieties. Studies to typify Xam strains performed by our group showed that using Variable Number of Tandem Repeats (VNTRs) have advantages over Amplified Fragment Length Polymorphisms (AFLPs), such as low costs and high discriminatory power using small sets of markers. Consequently, in this study we standardized and tested a new scheme of VNTR loci to analyze Xam populations. First, by analyzing 12 of 65 previously sequenced genomes of Xam, which represent the worldwide variability, we selected 16 VNTR loci. We standardized four multiplex PCR to amplify four microsatellite loci in each multiplex. Finally, the 16-VNTR scheme was used to assess population diversity of Xam strains collected in four Colombian Caribbean-region localities from 2008 to 2010, 2013 and 2014. Our results show that most of Xam genetic diversity is found within populations, and that the 16-VNTR scheme is a useful tool to discriminate Xam populations up to a local scale.