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
2015
Poulin, L. | Grygiel, P. | Magne, M. | Gagnevin, L. | Rodriguez-R, L. M. | Forero Serna, N. | Zhao, S. | El Rafii, M. | Dao, S. | Tekete, C. | Wonni, I. | Koita, O. | Pruvost, O. | Verdier, V. | Vernière, C. | Koebnik, R. | Résistance des plantes aux bio-agresseurs (UMR RPB) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 2 - Sciences et Techniques (UM2) | UMR - Interactions Plantes Microorganismes Environnement (UMR IPME) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [Occitanie]) | Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR) | Département Systèmes Biologiques (Cirad-BIOS) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad) | Université des Sciences, des Techniques et des Technologies de Bamako (USTTB) | Institut de l'Environnement et Recherches Agricoles [Ouagadougou] (INERA) ; Centre national de la recherche scientifique et technologique [Ouagadougou] (CNRST) | This work was supported by the French Agence Nationale de la Recherche (ANR-10-BLAN-1723) and the French Direction Generale de l'Armement (DGA) (2010 34 0006). Lucie Poulin is grateful to DGA for her Ph.D. fellowship (2011 60 091). Shuai Zhao is grateful to the Bourses Doctorales en Alternance from the French Embassy in China, the program of postgraduate education and research of Guangxi (T31036), and the plans for joint training of doctoral students and academic visiting of postgraduates of Guangxi University (L300278) for support. | ANR-10-BLAN-1723,XANTHracing,Nouvelles méthodes de traçage appliquées aux Xanthomonas pathogènes du riz et des citrus(2010)
International audience
Afficher plus [+] Moins [-]anglais. 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.
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