A minisatellite-based MLVA for deciphering the global epidemiology of the bacterial cassava pathogen Xanthomonas phaseoli pv. manihotis

Rache Leidy, Blondin Laurence, Diaz Tatis Paula, Flores Carolina, Camargo Andrea, Kanté Moussa, Wonni Issa, López Camilo, Szurek Boris, Dupas Stéphane, Pruvost Olivier, Koebnik Ralf, Restrepo Silvia, Bernal Adriana Jimena, Vernière Christian. 2023. A minisatellite-based MLVA for deciphering the global epidemiology of the bacterial cassava pathogen Xanthomonas phaseoli pv. manihotis. PloS One, 18 (5):e0285491, 16 p.

Liste HCERES des revues (en SHS) : oui

Thème(s) HCERES des revues (en SHS) : Psychologie-éthologie-ergonomie; Staps

Résumé : Cassava Bacterial Blight (CBB) is a destructive disease widely distributed in the different areas where this crop is grown. Populations studies have been performed at local and national scales revealing a geographical genetic structure with temporal variations. A global epidemiology analysis of its causal agent Xanthomonas phaseoli pv. manihotis (Xpm) is needed to better understand the expansion of the disease for improving the monitoring of CBB. We targeted new tandem repeat (TR) loci with large repeat units, i.e. minisatellites, that we multiplexed in a scheme of Multi-Locus Variable number of TR Analysis (MLVA-8). This genotyping scheme separated 31 multilocus haplotypes in three clusters of single-locus variants and a singleton within a worldwide collection of 93 Xpm strains isolated over a period of fifty years. The major MLVA-8 cluster 1 grouped strains originating from all countries, except the unique Chinese strain. On the contrary, all the Xpm strains genotyped using the previously developed MLVA-14 microsatellite scheme were separated as unique haplotypes. We further propose an MLVA-12 scheme which takes advantage of combining TR loci with different mutation rates: the eight minisatellites and four faster evolving microsatellite markers, for global epidemiological surveillance. This MLVA-12 scheme identified 78 haplotypes and separated most of the strains in groups of double-locus variants (DLV) supporting some phylogenetic relationships. DLV groups were subdivided into closely related clusters of strains most often sharing the same geographical origin and isolated over a short period, supporting epidemiological relationships. The main MLVA-12 DLV group#1 was composed by strains from South America and all the African strains. The MLVA-12 scheme combining both minisatellite and microsatellite loci with different discriminatory power is expected to increase the accuracy of the phylogenetic signal and to minimize the homoplasy effects. Further investigation of the global epidemiology of Xpm will be helpful for a better control of CBB worldwide.

Mots-clés Agrovoc : épidémiologie, variation génétique, marqueur génétique, génétique des populations, surveillance épidémiologique, génotype, Xanthomonas campestris phaseoli, phylogénie, microsatellite, polymorphisme génétique, Xanthomonas

Mots-clés géographiques Agrovoc : Viet Nam, France, Burkina Faso, Afrique

Mots-clés libres : Haplotypes, Genetic epidemiology, Cassava, Genetic loci, Colombia, Polymerase chain reaction, Genotyping, Population genetics

Classification Agris : H20 - Maladies des plantes

Champ stratégique Cirad : CTS 4 (2019-) - Santé des plantes, des animaux et des écosystèmes

Agences de financement hors UE : Universidad de los Andes, Agropolis Fondation

Projets sur financement : (FRA) PAIX

Auteurs et affiliations

• Rache Leidy, Universidad de los Andes (COL)
• Blondin Laurence, CIRAD-BIOS-UMR PHIM (FRA)
• Diaz Tatis Paula, Universidad Antonio Nariño (COL)
• Flores Carolina, IRD (FRA)
• Camargo Andrea, Universidad Antonio Nariño (COL)
• Kanté Moussa, Université de Montpellier (FRA)
• Wonni Issa, INERA (BFA)
• López Camilo, Universidad Nacional de Colombia (COL)
• Szurek Boris, IRD (FRA)
• Dupas Stéphane, Universidad de los Andes (COL)
• Pruvost Olivier, CIRAD-BIOS-UMR PVBMT (REU)
• Koebnik Ralf, IRD (FRA)
• Restrepo Silvia, Universidad de los Andes (COL)
• Bernal Adriana Jimena, Universidad de los Andes (COL) - auteur correspondant
• Vernière Christian, Université de Montpellier (FRA) ORCID: 0000-0002-2312-2073 - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/604667/)

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