An optimized microsatellite scheme for assessing populations of Xanthomonas phaseoli pv. manihotis
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.
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Subjects: | H20 - Maladies des plantes, H50 - Troubles divers des plantes, épidémiologie, agent pathogène, marqueur génétique, Xanthomonas campestris phaseoli, maladie des plantes, pathologie végétale, variation génétique, http://aims.fao.org/aos/agrovoc/c_2615, http://aims.fao.org/aos/agrovoc/c_5630, http://aims.fao.org/aos/agrovoc/c_24030, http://aims.fao.org/aos/agrovoc/c_36124, http://aims.fao.org/aos/agrovoc/c_5962, http://aims.fao.org/aos/agrovoc/c_5974, http://aims.fao.org/aos/agrovoc/c_15975, |
Online Access: | http://agritrop.cirad.fr/592075/ http://agritrop.cirad.fr/592075/7/phyto-06-18-0210-r.pdf |
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dig-cirad-fr-5920752024-01-29T01:51:31Z http://agritrop.cirad.fr/592075/ http://agritrop.cirad.fr/592075/ 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. Phytopathology, 109 (5) : 859-869.https://doi.org/10.1094/PHYTO-06-18-0210-R <https://doi.org/10.1094/PHYTO-06-18-0210-R> 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 eng 2019 Phytopathology H20 - Maladies des plantes H50 - Troubles divers des plantes épidémiologie agent pathogène marqueur génétique Xanthomonas campestris phaseoli maladie des plantes pathologie végétale variation génétique http://aims.fao.org/aos/agrovoc/c_2615 http://aims.fao.org/aos/agrovoc/c_5630 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_36124 http://aims.fao.org/aos/agrovoc/c_5962 http://aims.fao.org/aos/agrovoc/c_5974 http://aims.fao.org/aos/agrovoc/c_15975 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/592075/7/phyto-06-18-0210-r.pdf text Cirad license info:eu-repo/semantics/restrictedAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1094/PHYTO-06-18-0210-R 10.1094/PHYTO-06-18-0210-R info:eu-repo/semantics/altIdentifier/doi/10.1094/PHYTO-06-18-0210-R info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1094/PHYTO-06-18-0210-R |
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H20 - Maladies des plantes H50 - Troubles divers des plantes épidémiologie agent pathogène marqueur génétique Xanthomonas campestris phaseoli maladie des plantes pathologie végétale variation génétique http://aims.fao.org/aos/agrovoc/c_2615 http://aims.fao.org/aos/agrovoc/c_5630 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_36124 http://aims.fao.org/aos/agrovoc/c_5962 http://aims.fao.org/aos/agrovoc/c_5974 http://aims.fao.org/aos/agrovoc/c_15975 H20 - Maladies des plantes H50 - Troubles divers des plantes épidémiologie agent pathogène marqueur génétique Xanthomonas campestris phaseoli maladie des plantes pathologie végétale variation génétique http://aims.fao.org/aos/agrovoc/c_2615 http://aims.fao.org/aos/agrovoc/c_5630 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_36124 http://aims.fao.org/aos/agrovoc/c_5962 http://aims.fao.org/aos/agrovoc/c_5974 http://aims.fao.org/aos/agrovoc/c_15975 |
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H20 - Maladies des plantes H50 - Troubles divers des plantes épidémiologie agent pathogène marqueur génétique Xanthomonas campestris phaseoli maladie des plantes pathologie végétale variation génétique http://aims.fao.org/aos/agrovoc/c_2615 http://aims.fao.org/aos/agrovoc/c_5630 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_36124 http://aims.fao.org/aos/agrovoc/c_5962 http://aims.fao.org/aos/agrovoc/c_5974 http://aims.fao.org/aos/agrovoc/c_15975 H20 - Maladies des plantes H50 - Troubles divers des plantes épidémiologie agent pathogène marqueur génétique Xanthomonas campestris phaseoli maladie des plantes pathologie végétale variation génétique http://aims.fao.org/aos/agrovoc/c_2615 http://aims.fao.org/aos/agrovoc/c_5630 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_36124 http://aims.fao.org/aos/agrovoc/c_5962 http://aims.fao.org/aos/agrovoc/c_5974 http://aims.fao.org/aos/agrovoc/c_15975 Rache, Leidy Blondin, Laurence Flores, Carolina Trujillo, Cesar Szurek, Boris Restrepo, Silvia Koebnik, Ralf Bernal, Adriana Jimena Vernière, Christian An optimized microsatellite scheme for assessing populations of Xanthomonas phaseoli pv. manihotis |
description |
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. |
format |
article |
topic_facet |
H20 - Maladies des plantes H50 - Troubles divers des plantes épidémiologie agent pathogène marqueur génétique Xanthomonas campestris phaseoli maladie des plantes pathologie végétale variation génétique http://aims.fao.org/aos/agrovoc/c_2615 http://aims.fao.org/aos/agrovoc/c_5630 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_36124 http://aims.fao.org/aos/agrovoc/c_5962 http://aims.fao.org/aos/agrovoc/c_5974 http://aims.fao.org/aos/agrovoc/c_15975 |
author |
Rache, Leidy Blondin, Laurence Flores, Carolina Trujillo, Cesar Szurek, Boris Restrepo, Silvia Koebnik, Ralf Bernal, Adriana Jimena Vernière, Christian |
author_facet |
Rache, Leidy Blondin, Laurence Flores, Carolina Trujillo, Cesar Szurek, Boris Restrepo, Silvia Koebnik, Ralf Bernal, Adriana Jimena Vernière, Christian |
author_sort |
Rache, Leidy |
title |
An optimized microsatellite scheme for assessing populations of Xanthomonas phaseoli pv. manihotis |
title_short |
An optimized microsatellite scheme for assessing populations of Xanthomonas phaseoli pv. manihotis |
title_full |
An optimized microsatellite scheme for assessing populations of Xanthomonas phaseoli pv. manihotis |
title_fullStr |
An optimized microsatellite scheme for assessing populations of Xanthomonas phaseoli pv. manihotis |
title_full_unstemmed |
An optimized microsatellite scheme for assessing populations of Xanthomonas phaseoli pv. manihotis |
title_sort |
optimized microsatellite scheme for assessing populations of xanthomonas phaseoli pv. manihotis |
url |
http://agritrop.cirad.fr/592075/ http://agritrop.cirad.fr/592075/7/phyto-06-18-0210-r.pdf |
work_keys_str_mv |
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