An optimized microsatellite scheme for assessing populations of Xanthomonas phaseoli pv. manihotis

Rache Leidy, Blondin Laurence, Flores Carolina, Trujillo Cesar, Szurek Boris, Restrepo Silvia, Koebnik Ralf, Bernal Adriana Jimena, Vernière Christian. 2019. An optimized microsatellite scheme for assessing populations of Xanthomonas phaseoli pv. manihotis. Phytopathology, 109 (5) : 859-869.

https://doi.org/10.1094/PHYTO-06-18-0210-R

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Quartile : Q1, Sujet : PLANT SCIENCES

Liste HCERES des revues (en SHS) : oui

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

Résumé : Diverse molecular markers have been used to analyze the genetic diversity of plant pathogens. Compared with traditional fingerprinting methods, multiple loci variable number of tandem repeat analyses (MLVAs) have gained importance recently due to their reproducibility, high discriminatory power, ease of performance, low cost, and throughput potential. These characteristics are desirable for continuous pathogen monitoring, especially for pathogens with relatively low genetic diversity, and for disease epidemiology studies. Genetic diversity studies of Xanthomonas phaseoli pv. manihotis, which is the causal agent of cassava bacterial blight, have shown variability and changes in the bacterial population over time. Thus, an easy and fast method needs to be developed to type populations of this pathogen in different countries of the world, especially on small scales. In this study, we developed an MLVA scheme to analyze X. phaseoli pv. manihotis variability on a local scale. The MLVA-15 scheme comprises 15 variable number of tandem repeat loci grouped into four multiplex polymerase chain reaction pools. We showed that the MLVA-15 scheme had slightly higher discriminatory ability at the locality level when compared with amplified fragment length polymorphisms. The MLVA-15 scheme allowed for an accurate determination of the number of genotypes in the sample and showed reproducibility and portability. Additionally, this scheme could be used to analyze numerous strains in a reasonable timeframe. The MLVA-15 scheme was highly specific to X. phaseoli but up to eight tandem repeat loci could be amplified from other Xanthomonas spp. Finally, we assessed the utility of the scheme for analyses of X. phaseoli pv. manihotis genetic variability in the Colombian Caribbean region. MLVA-15 distinguished 88.9% of the haplotypes in our sample. Strains originating from the same field and isolated at the same time could be discriminated. In this study, the advantages of the MLVA-15 scheme targeting 6- or 7-bp repeats were demonstrated. Moreover, this scheme was a fast method that was appropriate for routine monitoring of X. phaseoli pv. manihotis populations on a local scale and, thus, was useful for addressing epidemiological questions.

Mots-clés Agrovoc : épidémiologie, agent pathogène, marqueur génétique, Xanthomonas campestris phaseoli, maladie des plantes, pathologie végétale, variation génétique

Mots-clés libres : Epidemiology, Molecular marker, Pathogen diversity, Tandem repeat, Xanthomonas

Classification Agris : H20 - Maladies des plantes
H50 - Troubles divers des plantes

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

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