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

• DOI: 10.1128/aem.02768-14
• Publication Date: 2014-11-15T04:45:14Z
• Authors: L. Poulin; P. Grygiel; M. Magne; L. Gagnevin; L. M. Rodriguez-R; N. Forero Serna; S. Zhao; M. El Rafii; S. Dao; C. Tekete; I. Wonni; O. Koita; O. Pruvost; V. Verdier; C. Vernière; R. Koebnik
• Keywords: 0301 basic medicine; http://aims.fao.org/aos/agrovoc/c_2615; [SDV]Life Sciences [q-bio]; Minisatellite Repeats; Xanthomonas oryzae; http://aims.fao.org/aos/agrovoc/c_16411; Xanthomonas oryzae pv. oryzicola; http://aims.fao.org/aos/agrovoc/c_330601; http://aims.fao.org/aos/agrovoc/c_5083; http://aims.fao.org/aos/agrovoc/c_37958; http://aims.fao.org/aos/agrovoc/c_3224; bioinformatique; surveillance épidémiologique; http://aims.fao.org/aos/agrovoc/c_34326; 2. Zero hunger; Molecular Epidemiology; http://aims.fao.org/aos/agrovoc/c_1513; http://aims.fao.org/aos/agrovoc/c_27583; http://aims.fao.org/aos/agrovoc/c_165; génétique des populations; http://aims.fao.org/aos/agrovoc/c_5438; http://aims.fao.org/aos/agrovoc/c_16022; Epidemiological Monitoring; épidémiologie; http://aims.fao.org/aos/agrovoc/c_15975; http://aims.fao.org/aos/agrovoc/c_15974; 570; Xanthomonas; provenance; http://aims.fao.org/aos/agrovoc/c_24383; Oryza sativa; http://aims.fao.org/aos/agrovoc/c_24869; 03 medical and health sciences; lignée; phylogénie; http://aims.fao.org/aos/agrovoc/c_3081; http://aims.fao.org/aos/agrovoc/c_13325; http://aims.fao.org/aos/agrovoc/c_6475; H20 - Maladies des plantes; Plant Diseases; locus; http://aims.fao.org/aos/agrovoc/c_29225; génome; pathotype; Oryza; séquence nucléotidique; http://aims.fao.org/aos/agrovoc/c_24059; http://aims.fao.org/aos/agrovoc/c_666; variation génétique; Molecular Typing; recombinaison; génie génétique; technique analytique; U30 - Méthodes de recherche; distribution géographique

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.