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Comparative efficacy of four candidate DNA barcode regions for identification of Vicia species

Published online by Cambridge University Press:  11 December 2015

Sebastin Raveendar
Affiliation:
National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Republic of Korea
Jung-Ro Lee
Affiliation:
National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Republic of Korea
Donghwan Shim
Affiliation:
Department of Forest Genetic Resources, Korea Forest Research Institute, Suwon 441-350, Republic of Korea
Gi-An Lee
Affiliation:
National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Republic of Korea
Young-Ah Jeon
Affiliation:
National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Republic of Korea
Gyu-Taek Cho
Affiliation:
National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Republic of Korea
Kyung-Ho Ma
Affiliation:
National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Republic of Korea
Sok-Young Lee
Affiliation:
National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Republic of Korea
Gi-Ho Sung
Affiliation:
Institute for Bio-medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung 210-701, Republic of Korea Catholic Kwandong University, International St. Mary's Hospital, Incheon Metropolitan City 404-834, Republic of Korea
Jong-Wook Chung
Affiliation:
National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Republic of Korea
Corresponding

Abstract

The genus Vicia L., one of the earliest domesticated plant genera, is a member of the legume tribe Fabeae of the subfamily Papilionoideae (Fabaceae). The taxonomic history of this genus is extensive and controversial, which has hindered the development of taxonomic procedures and made it difficult to identify and share these economically important crop resources. Species identification through DNA barcoding is a valuable taxonomic classification tool. In this study, four DNA barcodes (ITS2, matK, rbcL and psbA-trnH) were evaluated on 110 samples that represented 34 taxonomically best-known species in the Vicia genus. Topologies of the phylogenetic trees based on an individual locus were similar. Individual locus-based analyses could not discriminate closely related Vicia species. We proposed a concatenated data approach to increase the resolving power of ITS2. The DNA barcodes matK, psbA-trnH and rbcL were used as an additional tool for phylogenetic analysis. Among the four barcodes, three-barcode combinations that included psbA-trnH with any two of the other barcodes (ITS2, matK or rbcL) provided the best discrimination among Vicia species. Species discrimination was assessed with bootstrap values and considered successful only when all the conspecific individuals formed a single clade. Through sequencing of these barcodes from additional Vicia accessions, 17 of the 34 known Vicia species could be identified with varying levels of confidence. From our analyses, the combined barcoding markers are useful in the early diagnosis of targeted Vicia species and can provide essential baseline data for conservation strategies, as well as guidance in assembling germplasm collections.

Type
Research Article
Copyright
Copyright © NIAB 2015 

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Comparative efficacy of four candidate DNA barcode regions for identification of Vicia species
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