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New multilocus variable-number tandem-repeat analysis tool for surveillance and local epidemiology of bacterial leaf blight and bacterial leaf streak of rice caused by Xanthomonas oryzae

Poulin Lucie, Grygiel Pierre, Magne Maxime, Gagnevin Lionel, Rodríguez-R Luis Miguel, Forero Serna Natalia, Zhao Shuai, El Rafil M., Dao S., Tekete C., Wonni Issa, Kolta O., Pruvost Olivier, Verdier Valérie, Vernière Christian, Koebnik Ralf. 2015. New multilocus variable-number tandem-repeat analysis tool for surveillance and local epidemiology of bacterial leaf blight and bacterial leaf streak of rice caused by Xanthomonas oryzae. Applied and Environmental Microbiology, 81 (2) : pp. 688-698.

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Quartile : Q1, Sujet : BIOTECHNOLOGY & APPLIED MICROBIOLOGY / Quartile : Q2, Sujet : MICROBIOLOGY

Abstract : Multilocus variable-number tandem-repeat analysis (MLVA) is efficient for routine typing and for investigating the genetic structures of natural microbial populations. Two distinct pathovars of Xanthomonas oryzae can cause significant crop losses in tropical and temperate rice-growing countries. Bacterial leaf streak is caused by X. oryzae pv. oryzicola, and bacterial leaf blight is caused by X. oryzae pv. oryzae. For the latter, two genetic lineages have been described in the literature. We developed a universal MLVA typing tool both for the identification of the three X. oryzae genetic lineages and for epidemiological analyses. Sixteen candidate variable-number tandem-repeat (VNTR) loci were selected according to their presence and polymorphism in 10 draft or complete genome sequences of the three X. oryzae lineages and by VNTR sequencing of a subset of loci of interest in 20 strains per lineage. The MLVA-16 scheme was then applied to 338 strains of X. oryzae representing different pathovars and geographical locations. Linkage disequilibrium between MLVA loci was calculated by index association on different scales, and the 16 loci showed linear Mantel correlation with MLSA data on 56 X. oryzae strains, suggesting that they provide a good phylogenetic signal. Furthermore, analyses of sets of strains for different lineages indicated the possibility of using the scheme for deeper epidemiological investigation on small spatial scales. (Résumé d'auteur)

Mots-clés Agrovoc : Xanthomonas oryzae, Xanthomonas oryzae pv. oryzicola, Oryza sativa, Surveillance épidémiologique, Épidémiologie, Génétique des populations, Variation génétique, Pathotype, Génome, Séquence nucléotidique, Lignée, Locus, Phylogénie, Recombinaison, Génie génétique, Distribution géographique, Provenance, Bioinformatique, Technique analytique

Mots-clés géographiques Agrovoc : Afrique, Asie, France

Mots-clés complémentaires : Séquencage

Classification Agris : H20 - Plant diseases
U30 - Research methods

Champ stratégique Cirad : Axe 4 (2014-2018) - Santé des animaux et des plantes

Auteurs et affiliations

  • Poulin Lucie, IRD (FRA)
  • Grygiel Pierre, CIRAD-BIOS-UMR PVBMT (REU)
  • Magne Maxime
  • Gagnevin Lionel, CIRAD-BIOS-UMR PVBMT (REU)
  • Rodríguez-R Luis Miguel, IRD (FRA)
  • Forero Serna Natalia, IRD (FRA)
  • Zhao Shuai, IRD (FRA)
  • El Rafil M., IRD (FRA)
  • Dao S., USTTB (FRA)
  • Tekete C., USTTB (FRA)
  • Wonni Issa, IRD (FRA)
  • Kolta O., USTTB (FRA)
  • Pruvost Olivier, CIRAD-BIOS-UMR PVBMT (REU)
  • Verdier Valérie, IRD (FRA)
  • Vernière Christian, CIRAD-BIOS-UMR PVBMT (REU) ORCID: 0000-0002-2312-2073
  • Koebnik Ralf, IRD (FRA)

Source : Cirad - Agritrop (https://agritrop.cirad.fr/575751/)

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