Hostname: page-component-848d4c4894-75dct Total loading time: 0 Render date: 2024-05-23T08:54:05.629Z Has data issue: false hasContentIssue false

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 authors. E-mail: sung97330@gmail.com; jwchung73@korea.kr
*Corresponding authors. E-mail: sung97330@gmail.com; jwchung73@korea.kr

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 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Bailey, CD, Carr, TG, Harris, SA and Hughes, CE (2003) Characterization of angiosperm nrDNA polymorphism, paralogy, and pseudogenes. Molecular Phylogenetics and Evolution 29: 435455.CrossRefGoogle ScholarPubMed
Caputo, P, Frediani, M, Gelati, MT, Venora, G, Cremonini, R and Ruffini Castiglione, M (2013) Karyological and molecular characterisation of subgenus Vicia (Fabaceae). Plant Biosystems 147: 12421252.Google Scholar
CBOL Plant Working Group: Hollingsworth PM, Forrest, LL, Spouge, JL, Hajibabaei, M, Ratnasingham, S, van der Bank, M, Chase, MW, Cowan, RS, Erickson, DL, Fazekas, AJ, Graham, SW, James, KE, Kim, KJ, Kress, WJ, Schneider, H, van AlphenStahl, J, Barrett, SCH, van den Berg, C, Bogarin, D, Burgess, KS, Cameron, KM, Carine, M, Chacón, J, Clark, A, Clarkson, JJ, Conrad, F, Devey, DS, Ford, CS, Hedderson, TAJ, Hollingsworth, ML, Husband, BC, Kelly, LJ, Kesanakurti, PR, Kim, JS, Kim, YD, Lahaye, R, Lee, HL, Long, DG, Madriñn, S, Maurin, O, Meusnier, I, Newmaster, SG, Park, CW, Percy, DM, Petersen, G, Richardson, JE, Salazar, GA, Savolainen, V, Seberg, O, Wilkinson, MJ, Yi, DK and Little, DP (2009) A DNA barcode for land plants. Proceedings of the National Academy of Sciences 106: 1279412797.Google Scholar
Chase, MW, Salamin, N, Wilkinson, M, Dunwell, JM, Kesanakurthi, RP, Haidar, N and Savolainen, V (2005) Land plants and DNA barcodes: short-term and long-term goals. Philosophical Transactions of the Royal Society B: Biological Sciences 360: 18891895.Google Scholar
Chase, MW, Cowan, RS, Hollingsworth, PM, van den Berg, C, Madrinan, S, Petersen, G, Seberg, O, Jorgsensen, T, Cameron, KM, Carine, M, Pedersen, N, Hedderson, TAJ, Conrad, F, Salazar, GA, Richardson, JE, Hollingsworth, ML, Barraclough, TG, Kelly, L and Wilkinson, M (2007) A proposal for a standardised protocol to barcode all land plants. Taxon 56: 295299.CrossRefGoogle Scholar
Chen, SL, Yao, H, Han, JP, Liu, C, Song, JY, Shi, LC, Zhu, YJ, Ma, XY, Gao, T, Pang, XH, Luo, K, Li, Y, Li, XW, Jia, XC, Lin, YL and Leon, C (2010) Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS ONE 5: e8613.Google Scholar
Endo, Y, Choi, BH, Ohashi, H and Delgado-Salinas, A (2008) Phylogenetic relationships of new world Vicia (Leguminosae) inferred from nrDNA internal transcribed spacer sequences and floral characters. Systematic Botany 33: 356363.Google Scholar
Felsenstein, J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783791.Google Scholar
Frediani, M, Maggini, F, Gelati, MT and Cremonini, R (2004) Repetitive DNA sequences as probes for phylogenetic analysis in Vicia genus. Caryologia 57: 379386.Google Scholar
Gao, T and Chen, SL (2009) Authentication of the medicinal plants in Fabaceae by DNA barcoding technique. Planta Medica 75: 417.Google Scholar
Gao, T, Yao, H, Song, J, Liu, C, Zhu, Y, Ma, X, Pang, X, Xu, H and Chen, S (2010) Identification of medicinal plants in the family Fabaceae using a potential DNA barcode ITS2. Journal of Ethnopharmacology 130: 116121.Google Scholar
Gregory, TR (2005) DNA barcoding does not compete with taxonomy. Nature 434: 1067.Google Scholar
Haider, A, Hassanin, BR, Mahmoud, N and Madkour, M (2000) Molecular Characterization of Some Species of the Genus Vicia . Cairo: Arab Council for Graduate Studies and Scientific Research.Google Scholar
Haider, N, Nabulsi, I and MirAli, N (2012) Identification of species of Vicia subgenus Vicia (Fabaceae) using chloroplast DNA data. Turkish Journal of Agriculture and Forestry 36: 297308.Google Scholar
Hollingsworth, PM, Graham, SW and Little, DP (2011) Choosing and using a plant DNA barcode. PLoS ONE 6: e19254.Google Scholar
Hosseinzadeh, Z, Pakravan, M and Tavassoli, A (2008) Micromorphology of seed in some Vicia species from Iran. Rostaniha 9: 96107.Google Scholar
Jaaska, V (2005) Isozyme variation and phylogenetic relationships in Vicia subgenus Cracca (Fabaceae). Annals of Botany 96: 10851096.CrossRefGoogle ScholarPubMed
Kimura, M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16: 111120.Google Scholar
King, MG and Roalson, EH (2008) Exploring evolutionary dynamics of nrDNA in Carex subgenus Vignea (Cyperaceae). Systematic Botany 33: 514524.CrossRefGoogle Scholar
Kress, WJ and Erickson, DL (2007) A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS ONE 2: e508.Google Scholar
Kress, WJ, Wurdack, KJ, Zimmer, EA, Weigt, LA and Janzen, DH (2005) Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences 102: 83698374.Google Scholar
Liu, J, Moller, M, Gao, LM, Zhang, DQ and Li, DZ (2011) DNA barcoding for the discrimination of Eurasian yews (Taxus L., Taxaceae) and the discovery of cryptic species. Molecular Ecology Resources 11: 89100.Google Scholar
Ma, KH, Kim, NS, Lee, GA, Lee, SY, Lee, JK, Yi, JY, Park, YJ, Kim, TS, Gwag, JG and Kwon, SJ (2009) Development of SSR markers for studies of diversity in the genus Fagopyrum . Theoretical and Applied Genetics. 119: 12471254.CrossRefGoogle ScholarPubMed
Maxted, N (1993) A phenetic investigation of Vicia L. subgenus Vicia (Leguminosae, Vicieae). Botanical Journal of the Linnean Society 111: 155182.Google Scholar
Maxted, N (1995) An Ecogeographic Study of Vicia Subgenus Vicia. Systematic and Ecogeographic Studies in Crop Genepools 8 . Rome, Italy: IBPGR.Google Scholar
Maxted, N, Callimassia, MA and Bennett, MD (1991) Cytotaxonomic studies of eastern Mediterranean Vicia species (Leguminosae). Plant Systematics and Evolution 177: 221234.Google Scholar
Meier, R, Shiyang, K, Vaidya, G and Ng, PKL (2006) DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Systematic Biology 55: 715728.Google Scholar
Meyer, CP and Paulay, G (2005) DNA barcoding: error rates based on comprehensive sampling. PLoS Biology 3: e422.Google Scholar
MirAli, N, El-Khouri, S and Rizq, F (2007) Genetic diversity and relationships in some Vicia species as determined by SDS-PAGE of seed proteins. Biologia Plantarum 51: 660666.Google Scholar
Naranjo, CA, Ferrari, MR, Palermo, AM and Poggio, L (1998) Karyotype, DNA content and meiotic behaviour in five South American species of Vicia (Fabaceae). Annals of Botany 82: 757764.Google Scholar
Navratilova, A, Neumann, P and Macas, J (2003) Karyotype analysis of four Vicia species using in situ hybridization with repetitive sequences. Annals of Botany 91: 921926.Google Scholar
Piergiovanni, AR and Taranto, G (2005) Specific differentiation in Vicia genus by means of capillary electrophoresis. Journal of Chromatography A 1069: 253260.Google Scholar
Raina, SN and Ogihara, Y (1995) Ribosomal DNA repeat unit polymorphism in 49 Vicia species. Theoretical and Applied Genetics 90: 477486.Google Scholar
Raveendar, S, Lee, JR, Park, JW, Lee, GA, Jeon, YA, Lee, YJ, Cho, GT, Ma, KH, Lee, SY and Chung, JW (2015) Potential use of ITS2 and matK as a two-locus DNA barcode for identification of Vicia species. Plant Breeding and Biotechnology 3: 5866.Google Scholar
Ruffini Castiglione, MR, Frediani, M, Gelati, MT, Ravalli, C, Venora, G, Caputo, P and Cremonini, R (2011) Cytology of Vicia species. X. Karyotype evolution and phylogenetic implication in Vicia species of the sections Atossa, Microcarinae, Wiggersia and Vicia . Protoplasma 248: 707716.Google Scholar
Ruffini Castiglione, MR, Frediani, M, Gelati, MT, Venora, G, Giorgetti, L, Caputo, P and Cremonini, R (2012) Cytological and molecular characterization of Vicia barbazitae Ten. & Guss. Protoplasma 249: 779788.Google Scholar
Sakowicz, T and Cieslikowski, T (2006) Phylogenetic analyses within three sections of the genus Vicia . Cellular & Molecular Biology Letters 11: 594615.Google Scholar
Schaefer, H, Hechenleitner, P, Santos-Guerra, A, de Sequeira, MM, Pennington, RT, Kenicer, G and Carine, MA (2012) Systematics, biogeography, and character evolution of the legume tribe Fabeae with special focus on the middle-Atlantic island lineages. BMC Evolutionary Biology 12: 250.Google Scholar
Shiran, B, Kiani, S, Sehgal, D, Hafizi, A, ul-Hassan, T, Chaudhary, M and Raina, SN (2014) Internal transcribed spacer sequences of nuclear ribosomal DNA resolving complex taxonomic history in the genus Vicia L. Genetic Resources and Crop Evolution 61: 909925.Google Scholar
Starr, JR, Naczi, RF and Chouinard, BN (2009) Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae). Molecular Ecology Resources 9: 151163.Google Scholar
Steinke, D, Zemlak, TS, Boutillier, JA and Hebert, PDN (2009) DNA barcoding of Pacific Canada's fishes. Marine Biology 156: 26412647.Google Scholar
Tamura, K, Stecher, G, Peterson, D, Filipski, A and Kumar, S (2013) MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Molecular Biology and Evolution 30: 27252729.Google Scholar
Vencovsky, R and Crossa, J (1999) Variance effective population size under mixed self and random mating with applications to genetic conservation of species. Crop Science 39: 12821294.Google Scholar
Vijayan, K and Tsou, CH (2010) DNA barcoding in plants: taxonomy in a new perspective. Current Science 99: 15301541.Google Scholar
Zhang, AB, He, LJ, Crozier, RH, Muster, C and Zhu, CD (2010) Estimating sample sizes for DNA barcoding. Molecular Phylogenetics and Evolution 54: 10351039.Google Scholar
Supplementary material: File

Raveendar supplementary material

Table S1

Download Raveendar supplementary material(File)
File 19.3 KB
Supplementary material: File

Raveendar supplementary material

Table S2

Download Raveendar supplementary material(File)
File 12.3 KB
Supplementary material: File

Raveendar supplementary material

Figures S1-S14

Download Raveendar supplementary material(File)
File 396.7 KB