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Population typing of the causal agent of cassava bacterial blight in the Eastern Plains of Colombia using two types of molecular markers

Molecular typing of pathogen populations is an important tool for the development of effective strategies for disease control. Diverse molecular markers have been used to characterize populations of Xanthomonas axonopodis pv. manihotis (Xam), the main bacterial pathogen of cassava. Recently, diversity and population dynamics of Xam in the Colombian Caribbean coast were estimated using AFLPs, where populations were found to be dynamic, diverse and with haplotypes unstable across time.

Trujillo CA, Arias-Rojas N, Poulin L, Medina CA, Tapiero A, Restrepo S, Koebnik R, Bernal AJ1.

 

 BMC Microbiol. 2014 Jun 19;14:161. doi: 10.1186/1471-2180-14-161.

http://www.ncbi.nlm.nih.gov/pubmed/24946775

 

Abstract

 

BACKGROUND:

 

Molecular typing of pathogen populations is an important tool for the development of effective strategies for disease control. Diverse molecular markers have been used to characterize populations of Xanthomonas axonopodis pv. manihotis (Xam), the main bacterial pathogen of cassava. Recently, diversity and population dynamics of Xam in the Colombian Caribbean coast were estimated using AFLPs, where populations were found to be dynamic, diverse and with haplotypes unstable across time. Aiming to examine the current state of pathogen populations located in the Colombian Eastern Plains, we also used AFLP markers and we evaluated the usefulness of Variable Number Tandem Repeats (VNTRs) as new molecular markers for the study of Xam populations.

 

RESULTS:

 

The population analyses showed that AFLP and VNTR provide a detailed and congruent description of Xam populations from the Colombian Eastern Plains. These two typing strategies clearly separated strains from the Colombian Eastern Plains into distinct populations probably because of geographical distance. Although the majority of analyses were congruent between typing markers, fewer VNTRs were needed to detect a higher number of genetic populations of the pathogen as well as a higher genetic flow among sampled locations than those detected by AFLPs.

 

CONCLUSIONS:

 

This study shows the advantages of VNTRs over AFLPs in the surveillance of pathogen populations and suggests the implementation of VNTRs in studies that involve large numbers of Xam isolates in order to obtain a more detailed overview of the pathogen to improve the strategies for disease control.

 

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Figure 4: Estimation of genetic populations of Xam in the Eastern Plains using AFLP and VNTR markers.Xam isolates were assigned to the optimal number of clusters (K) estimated using STRUCTURE 2.3.3. A) Two genetic clusters estimated using AFLP data. B) Five genetic clusters estimated among isolates using VNTR data. Each isolate is represented by a single vertical line broken into K-colored segments. Color length in vertical lines represents the proportion of each inferred K clusters for each isolate. Color code of isolates labels represent the geographical origin of isolate: La Libertad: black; Granada: blue; Fuente de Oro: red and Orocué: green. Lines at the bottom delimit each estimated genetic population (K). Fixation index (FST) is indicated for each population.

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