Genes & Genomics

, Volume 35, Issue 2, pp 257–264 | Cite as

Molecular cytogenetic analysis of the Vigna species distributed in Korea

  • Hae-Woon Choi
  • Min-Young Kim
  • Sang-Hoon Lee
  • Sayeda Sultana
  • Jae-Wook Bang
Research Article


Vigna plants distributed in Korea were analyzed by molecular cytogenetic fluorescence in situ hybridization (FISH), genomic in situ hybridization (GISH) and rDNA ITS/NTS sequences. FISH revealed that variable 45S rRNA gene loci (one to four) were localized on the terminal regions of chromosomes, while two conserved 5S rRNA gene loci from all species examined, except for rice bean (single locus), were detected. FISH and GISH showed the characteristic organization of rRNA gene loci and genomic homology on the chromosomes, indicating their cytogenetic relatationships. ITS sequence revealed that there was considerable variation in length (190–207 bp in ITS1, 205–221 bp in ITS2) and nucleotide composition (7–67 bp). The 5S rRNA gene unit comprised coding region (118 bp) and extensive sequence heterogeneity (97–221 bp). Phylogenetic analysis of the ITS and NTS sequences demonstrated that the Vigna species are divided into two groups: angularis (V. angularis, V. umbellata, V. nakashimae and V. nipponensis) and unguiculata (V. unguiculata, V. sesquipedalis and V. vexillata). Sequence data also showed that mung bean was closer to the angularis group.





This work was supported by the Basic Science Research Program through the National Research Foundation (NRF) funded by the Ministry of Education, Science and Technology of Korea (NRF-20110025828).


  1. Adetula OA, Fatokun CA, Obigbesan G (2005) Centromeric banding pattern of mitotic chromosomes in V. vexillata (TVnu 73). Afr J Biotechnol 5:400–402Google Scholar
  2. Ba FS, Pasquet RS, Gepts P (2004) Genetic diversity in cowpea (V. unguiculata (L.) Walp.) as revealed by RAPD markers. Genet Resour Crop Evol 51:539–550CrossRefGoogle Scholar
  3. Choi HW, Kim JS, Lee SH, Bang JW (2008) Physical mapping by FISH and GISH of rDNA loci and discrimination of genomes A and B in Scilla scilloides complex distributed in Korea. J Plant Biol 51:408–412CrossRefGoogle Scholar
  4. Choi HW, Koo DH, Bang KH, Paek KY, Seong NS, Bang JW (2009) FISH and GISH analysis of the genomic relationships among Panax species. Genes Genom 31:99–105CrossRefGoogle Scholar
  5. de Jong H (2003) Visualizing DNA domains and sequences by microscopy: a fifty-year history of molecular cytogenetics. Genome 46:943–946PubMedCrossRefGoogle Scholar
  6. Diouf D, Hilu KW (2005) Microsatellites and RAPD markers to study genetic relationships among cowpea breeding lines and local varieties in Senegal. Genet Resour Crop Evol 52:1057–1067CrossRefGoogle Scholar
  7. Doi K, Kaga A, Tomooka N, Vaughan DA (2002) Molecular phylogeny of genus Vigna subgenus Ceratotropis based on rDNA ITS and atpB-rbcL intergenic spacer of cpDNA sequences. Genetica 114:129–145PubMedCrossRefGoogle Scholar
  8. Dover G (1982) Molecular drive: cohesive mode of species evolution. Nature 9:111–116CrossRefGoogle Scholar
  9. Ellis THN, Lee D, Thomas CM, Simpson PR, Cleary WG, Newman MA, Burchan KWG (1988) 5S rRNA genes in Pisum: sequence, long range and chromosomal organization. Mol Genet 214:333–342CrossRefGoogle Scholar
  10. Fukui K, Kamisugi Y, Sakai F (1994) Physical mapping of 5S rDNA loci by direct-cloned biotinylated probes in barley chromosomes. Genome 37:105–111PubMedCrossRefGoogle Scholar
  11. Galasso I, Pignone D, Perrino P (1992) Cytotaxonomic studies in Vigna I. General techniques and V. unguiculata C-banding. Caryologia 45:155–161Google Scholar
  12. Galasso I, Schumidt T, Pignone D, Heslop-Harrison JS (1995) The molecular cytogenetics of V. unguiculata (L.) Walp: the physical organization and characterization of 18S-5.8S-25S rRNA genes, 5S rRNA genes, telomere-like sequences, and a family of centromeric repetitive DNA sequences. Theor Appl Genet 91:928–935CrossRefGoogle Scholar
  13. Galasso I, Harrison GE, Pignone D, Brandes A, Heslop-Harrison JS (1997) The distribution and organization of Ty1-copia-like reteotransposable elements in the genome of V. unguiculata (L.) Walp. (cowpea) and its relatives. Ann Bot 80:327–333CrossRefGoogle Scholar
  14. Ge XH, Li ZY (2007) Intra- and intergenomic homology of B-genome chromosomes in trigenomic combinations of the cultivated Brassica species revealed by GISH analysis. Chromosome Res 15:849–861PubMedCrossRefGoogle Scholar
  15. Goel S, Raina SN, Ogihara (2002) Molecular evolution and phylogenetic implications of internal transcribed spacer sequences of nuclear ribosomal DNA in the Phaseolus-Vigna complex. Mol Phylogen Evol 22:1–19CrossRefGoogle Scholar
  16. Gottlob-McHugh SG, Levesque M, MacKenzie K, Oslon M, Yarosh O, Johnson DA (1990) Organization of the 5S rRNA genes in the soybean Glycine max (L.) Merrill and conservation of the 5S rDNA repeat structure in higher plant. Genome 33:486–494PubMedCrossRefGoogle Scholar
  17. Gründler P, Unfried I, Pascher K, Schweizer D (1991) rDNA intergenic region from Arabidopsis thaliana: structural analysis, intraspecific variation and functional implications. J Mol Biol 221:1209–1222CrossRefGoogle Scholar
  18. Guerra M, Kenton A, Bennett MD (1996) rDNA sites in mitotic and polytene chromosomes of V. unguiculata (L.) Walp. and Phaseolus coccineus L. revealed by in situ hybridization. Ann Bot 78:157–161CrossRefGoogle Scholar
  19. Jiang J, Gill BS (2006) Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research. Genome 49:1057–1068PubMedCrossRefGoogle Scholar
  20. Kenicer GJ, Kajita T, Pennington RT, Murata J (2005) Systematics and biogeography of Lathyrus (Leguminosae) based on internal transcribed spacer and cpDNA sequence data. Am J Bot 92:1199–1209PubMedCrossRefGoogle Scholar
  21. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparable studies of nucleotide sequences. J Mol Evol 16:111–120PubMedCrossRefGoogle Scholar
  22. Kollipara KP, Singh RJ, Hymowitz T (1997) Phylogenetic and genomic relationship in the genus Glycine wild based on sequences from ITS region of nuclear rDNA. Genome 40:57–68PubMedCrossRefGoogle Scholar
  23. Koo DH, Plaha P, Lim YP, Hur Y, Bang JW (2004) A high resolution karyotype of Brassica rapa ssp. pekinensis revealed by pachytene analysis and multicolor fluorescence in situ hybridization. Theor Appl Genet 109:1346–1352PubMedCrossRefGoogle Scholar
  24. Koo DH, Choi HW, Cho JK, Hur Y, Bang JW (2005) A high-resolution karyotype of cucumber (C. sativus L. ‘Winter Long’) revealed by C-banding, pachytene analysis, and RAPD-aided fluorescence in situ hybridization. Genome 48:534–540PubMedCrossRefGoogle Scholar
  25. Lapitan NLV (1992) Organization and evolution of higher plant genomes. Genome 35:171–181CrossRefGoogle Scholar
  26. Lee SH, Choi HW, Sung JS, Bang JW (2010) Inter-genomic relationships among three medicinal herbs: cnidium officinale, Ligusticum chuanxiong and Angelica polymorpha. Genes Genom 32:95–101CrossRefGoogle Scholar
  27. Lim KY, Matyasek R, Kovarik A, Fulnecek J, Leitch AR (2005) Molecular cytogenetics and tandem repeat sequence evolution in the allopolyploid Nicotiana rustica compared with diploid progenitors N. paniculata and N. undulata. Cytogenet Genome Res 109:298–309PubMedCrossRefGoogle Scholar
  28. Ngan F, Shaw P, But P, Wang J (1999) Molecular authentication of Panax species. Phytochemistry 50:787–791PubMedCrossRefGoogle Scholar
  29. Saini A, Jawali N (2009) Molecular evolution of 5S rDNA region in Vigna subgenus Ceratotropis and its phylogenetic implications. Plant Syst Evol 280:187–206CrossRefGoogle Scholar
  30. Sastri DC, Hilu K, Appels R, Lagudah ES, Playford J, Baum BR (1992) An overview of evolution in plant 5S rDNA. Plant Syst Evol 183:169–181CrossRefGoogle Scholar
  31. Schwarzacher T, Leitch AR, Bennett MD, Heslop-Harrison JS (1989) In situ localization of parental genomes in a wide hybrid. Ann Bot 64:315–324Google Scholar
  32. Sen NK, Bhowal JG (1960) Cytotaxonomy studies on Vigna. Cytologia 25:195–207CrossRefGoogle Scholar
  33. Sultana S, Lee SH, Bang JW, Choi HW (2010) Physical mapping of rRNA gene loci and inter-specific relationships in wild Lilium distributed in Korea. J Plant Biol 53:433–443CrossRefGoogle Scholar
  34. Taketa S, Harrison GE, Heslop-Harrison JS (1999) Comparative physical mapping of the 5S and 18S-25S rDNA in nine wild Hordeum species and cytotypes. Theor Appl Genet 98:1–9CrossRefGoogle Scholar
  35. Verdcourt B (1970) Studies in the Leguminosae-Papilionoideae for the ‘Flora of Tropical East Africa’ IV. Kew Bull 24:507–569CrossRefGoogle Scholar
  36. Vijaykumar A, Saini A, Jawali N (2011) Molecular characterization of intergenic spacer region of 5S ribosomal RNA genes in subgenus Vigna: extensive hybridization among V. unguiculata subspecies. Plant Syst Evol 294:38–55CrossRefGoogle Scholar
  37. Xu P, Wu X, Wang B, Liu Y, Qin D, Ehler JD, Close TJ, Hu T, Lu Z, Li G (2010) Development and polymorphism of V. unguiculata ssp. unguiculata microsatellite markers used for phylogenetic analysis in asparagus bean (V. unguiculata ssp. sesquipedalis (L.) Verdc.). Mol Breed 25:675–684CrossRefGoogle Scholar
  38. Yoon MS, Lee J, Kim CY, Baek HJ (2007) Genetic relationships among cultivated and wild V. angularis (Willd.) Ohwi et Ohashi and relatives from Korea based on AFLP markers. Genet Resour Crop Evol 54:875–883CrossRefGoogle Scholar

Copyright information

© The Genetics Society of Korea 2013

Authors and Affiliations

  1. 1.Department of Biological SciencesCollege of Biological Science and Biotechnology, Chungnam National UniversityDaejeonSouth Korea

Personalised recommendations