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A VNTR tool for diagnostic and epidemiological surveillance of the plant pathogen Xanthomonas oryzae and its application to the newly reported Malagasy BLS epidemics : Session 5- Dynamique, épidémiologie et génétique des populations bactériennes

Poulin Lucie, Grygiel Pierre, Magne Maxime, Gagnevin Lionel, Vernière Christian, Rodríguez-R Luis Miguel, Forero Serna Natalia, Zhao Shuai, Rafii M., Verdier Valérie, Koebnik Ralf. 2014. A VNTR tool for diagnostic and epidemiological surveillance of the plant pathogen Xanthomonas oryzae and its application to the newly reported Malagasy BLS epidemics : Session 5- Dynamique, épidémiologie et génétique des populations bactériennes. In : 11èmes Rencontres Plantes-Bactéries, Aussois, France, 3-7 février 2014. SFP ; INRA ; CNRS ; IRD ; CIRAD. Paris : SFP, Résumé, p. 61. Rencontres plantes-bactéries. 11, Aussois, France, 3 February 2014/7 February 2014.

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Abstract : The rice pathogen Xanthomonas oryzae is responsible for Bacterial Leaf Blight (BLB), caused by the pathovar oryzae (Xoo), and Bacterial Leaf Streak (BLS), caused by the pathovar oryzicola (Xoc). These Iwo diseases cause significant crop losses in tropical rice-growing countries. We developed a Variable Number of Tandem Repeats (VNTR) typing tool for the worldwide description of these devastating pathogens. Candidate VNTR loci were selected according ta their presence and polymorphism in ten genome sequences of the three genetic Iineages described as Xoc, African Xoo and Asian Xoo. Upon testing on a panel of 3 x 20 strains, a MLVA (Multi Locus VNTR Analysis) scheme was devised and applied to 345 strains of X oryzae (Xo), representing different pathovars and geographical regions. Five out of 87 candidate loci were found to be universally present and polymorphic in all three genetic lineages. These five core loci were supplemented by three to four loci which are conserved and polymorphic in two lineages, thus constituting a 16-loci MLVA scheme with al least 12 polymorphie loci per lineage. Phylogenetic and statistic clustering analysis were performed. This scheme was able to well discriminate strains with little evidence of homoplasy. The analyses were found to be congruent with previous studies, using AFLP, RFLP, rep-PCR and MLSA. Ali three Iineages of Xo were well discriminated and two sub-lineages corresponding to African and Asian Xoc could be differentiated. Our tool is able to better distinguish strains within each cluster (Iineage, sub-lineage) than previous tools and allowed to infer hypotheses about epidemics and sources of inocula. The recently reported epidemic of BLS in Madagascar was studied in order to infer key information toward the historical invasion of Xoc strains in Africa. In conclusion, our MLVA tool serves phytosanitary measures by assisting the epidemiological surveillance of outbreaks of BLB and BLS diseases office. (Texte intégral)

Classification Agris : H20 - Plant diseases
U30 - Research methods

Auteurs et affiliations

  • Poulin Lucie, IRD (FRA)
  • Grygiel Pierre, CIRAD-BIOS-UMR PVBMT (REU)
  • Magne Maxime
  • Gagnevin Lionel, CIRAD-BIOS-UMR PVBMT (REU)
  • Vernière Christian, CIRAD-BIOS-UMR PVBMT (REU) ORCID: 0000-0002-2312-2073
  • Rodríguez-R Luis Miguel, IRD (FRA)
  • Forero Serna Natalia, IRD (FRA)
  • Zhao Shuai, IRD (FRA)
  • Rafii M., IRD (FRA)
  • Verdier Valérie, IRD (FRA)
  • Koebnik Ralf, IRD (FRA)

Source : Cirad - Agritrop (https://agritrop.cirad.fr/572837/)

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