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Genetic differentiation of Vigna species by RAPD, URP and SSR markers

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Biologia Plantarum

Abstract

Seventy genotypes belonging to 7 wild and cultivated Vigna species were genetically differentiated using randomly amplified polymorphic DNA (RAPD), universal rice primer (URP) and simple sequence repeat (SSR) markers. We identified RAPD marker, OPG13 which produced a species-specific fingerprint profile. This primer characterized all the Vigna species uniquely suggesting an insight for their co-evolution, domestication and interspecific relationship. The cluster analysis of combined data set of all the markers resulted in five major groups. Most of the genotypes belonging to cultivated species formed a specific group whereas all the wild species formed a separate cluster using unweighted paired group method with arithmetic averages and principle component analysis. The Mantel matrix correspondence test resulted in a high matrix correlation with best fit (r = 0.95) from combined marker data. Comparison of three-marker systems showed that SSR marker was more efficient in detecting genetic variability among all the Vigna species. The narrow genetic base of the V. radiata cultivars obtained in the present study emphasized that large germplasm collection should be used in Vigna improvement programme.

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Abbreviations

AFLP:

amplified fragment length polymorphism

CTAB:

cetyltrimethyl ammonium bromide

EMR:

effective multiplex ratio

Hav :

arithmetic mean heterozygosity

Hn:

expected heterozygosity

ISSR:

inter simple sequence repeats

MI:

marker index

PCA:

principal components analysis

PCR:

polymerase chain reaction

RAPD:

randomly amplified polymorphic DNA

Rp:

resolving power

SAHN:

sequential agglomerative hierarical nested

SAMPL:

selective amplification of microsatellite polymorphic loci

SSR:

simple sequence repeat

STMS:

sequence tagged microsatellite

UPGMA:

unweighted paired group method with arithmetic averages

URP:

universal rice primer

References

  • Ajibade, S.R., Weeden, N.F., Chite, S.M.: Inter simple sequence repeat analysis of genetic relationship in genus Vigna.-Euphytica 111: 47–55, 2000.

    Article  CAS  Google Scholar 

  • Banerjee, H., Pai, R.A., Sharma R.P.: Restriction fragment length polymorphism and random amplified polymorphic DNA analysis of chickpea accessions.-Biol. Plant. 42: 197–208, 1999.

    Article  CAS  Google Scholar 

  • Betal, S., Roy Chowdhury, P., Kundu, S., Sen Raychaudhuri, S.: Estimation of genetic variability of Vigna radiata cultivars by RAPD analysis.-Biol. Plant. 48: 205–209, 2004.

    Article  CAS  Google Scholar 

  • Kang, H.W., Park, D.S., Go, S.J., Eun, M.Y.: Fingerprinting of diverse genomes using PCR with universal rice primers generated from repetitive sequences of Korean weedy rice.-Mol. Cells 3: 281–287, 2002.

    Google Scholar 

  • Lakhanpaul, S., Chadha, S., Bhat, K.V.: Random amplified polymorphic DNA (RAPD) analysis in Indian mungbean (Vigna radiata L. Wilczek) cultivars.-Genetica 109: 227–234, 2000.

    Article  PubMed  CAS  Google Scholar 

  • Lambridges, C.L., Lawn, R.L.: Two genetic linkage maps of mungbean using RFLP and RAPD markers.-Aust. J. agr. Res. 51: 415–425, 2000.

    Article  Google Scholar 

  • Lawn, R.J., Williams, R.W., Imrie, B.C.: Potential of wild germplasm as a source of tolerance to environmental stresses in mungbean.-In: Shanmugasundaram, S., McLean, B.T. (ed.): Proceedings of the 2nd International Symposium on Mungbean. Pp. 136–180. AVRDC, Shanva 1987.

    Google Scholar 

  • Mantel, N.: The deduction of disease clustering and a generalized regression approach.-Cancer Res. 27: 209–220, 1967.

    PubMed  CAS  Google Scholar 

  • Murray, M.G., Thompson, W.F.: Rapid isolation of high molecular weight plant DNA.-Nucl. Acids Res. 8: 4321–4325, 1980.

    Article  PubMed  CAS  Google Scholar 

  • Nei, M.: Analysis of gene diversity in subdivided populations.-Proc. nat. Acad. Sci. USA 70: 3321–3323, 1973.

    Article  PubMed  CAS  Google Scholar 

  • Powell, W., Morgante, M., Andre, C., Hanafey, M., Vogel, J., Tingey, S., Rafalski, A.: The comparison of RFLP, AFLP and SSR (microsatellite) markers for germplasm analysis.-Mol. Breed. 2: 225–238, 1996.

    Article  CAS  Google Scholar 

  • Prevost, A., Wilkinson, M.J.: A new system of comparing PCR primers applied to ISSR finger printing of potato cultivars.-Theor. appl. Genet. 102: 440–449, 1999.

    Google Scholar 

  • Rohlf, F.J.: NTSYS-PC: Numerical Taxonomy and Multivariate Analysis System. Version 2.11T.-Exeter Software, Setauket 2000.

  • Samec, P., Pošvec, Z., Stejskal, J., Našinec, V., Griga, M.: Cultivar identification and relationships in Pisum sativum L. based on RAPD and isoenzymes.-Biol. Plant. 41: 39–48, 1998.

    Article  CAS  Google Scholar 

  • Santalla, M., Power, J.B., Davery, M.R.: Genetic diversity in mungbean germplasm revealed by RAPD markers.-Plant Breed. 5: 473–478, 1998.

    Article  Google Scholar 

  • Singh, K.P., Sareen, M., Ashwini, P.K., Kumar, A.: Interspecific hybridization studies in V. radiata (L.) Wilczek and Vigna umbellata.-Nat. J. Plant Improv. 3: 16–18, 2003

    Google Scholar 

  • Souframanien, J., Gopalakrishna, T.: A comparative analysis of genetic diversity in blackgram genotypes using RAPD and ISSR markers.-Theor. appl. Genet. 109: 1687–93, 2004.

    Article  PubMed  CAS  Google Scholar 

  • Srinivas, P., Haulpalai, N., Saengehot, S., Ngampongsai, N.: The use of wild relatives and gamma radiation in mungbean and blackgram.-In: Vaughan, D. (ed.): Wild Legumes. The VII MAAF International workshop on Genetic Resources. Pp. 205–218. NIAB, Tsukuba 1999.

    Google Scholar 

  • Tosti, N., Negri, V.: Efficiency of three PCR based markers in assessing genetic variation among cowpea (Vigna unguiculata) landraces.-Genome 45: 268–275, 2002.

    Article  PubMed  CAS  Google Scholar 

  • Wang, X.W., Kaga, A., Tomooka, N., Vaughan, D.A.: The development of SSR markers by a new method in plants and their application to gene flow studies in adzuki bean [Vigna angularis (Willd.) Ohwi & Ohashi].-Theor. appl. Genet. 109: 352–360, 2004.

    PubMed  CAS  Google Scholar 

  • Willams, J.G.K., Kubelik, A.R., Lavak, K.J., Rafalski, J.A., Tingey, S.V.: DNA polymorphism amplified by arbitrary primers are useful as genetic markers.-Nucl. Acids Res. 18: 6531–6535, 1990.

    Article  Google Scholar 

  • Yu, K., Park, S.J., Poysa, V., Gepts, P.: Integration of simple sequence repeat (SSR) markers into a molecular linkage map of common bean (Phaseolus vulgaris L.)-J. Heredity 91: 429–434, 2000.

    Article  CAS  Google Scholar 

  • Zong, X.X., Kaga, A., Tomooka, N., Wang, X.W., Han, O.K., Vaughan, D.: The genetic diversity of the Vigna angularis complex in Asia.-Genome 46: 647–58, 2003.

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Indian Agricultural Research Institute, Division of Genetics, New Delhi, 110012, India

    H. K. Dikshit, N. Chandra & J. L. Tickoo

  2. Indian Agricultural Research Institute, National Research Center on Plant Biotechnology, New Delhi, 110012, India

    T. Jhang, N. K. Singh, K. R. Koundal, K. C. Bansal & T. R. Sharma

Authors
  1. H. K. Dikshit
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  2. T. Jhang
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  3. N. K. Singh
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  4. K. R. Koundal
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  5. K. C. Bansal
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  6. N. Chandra
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  7. J. L. Tickoo
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  8. T. R. Sharma
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Correspondence to T. R. Sharma.

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Dikshit, H.K., Jhang, T., Singh, N.K. et al. Genetic differentiation of Vigna species by RAPD, URP and SSR markers. Biol Plant 51, 451–457 (2007). https://doi.org/10.1007/s10535-007-0095-8

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  • DOI: https://doi.org/10.1007/s10535-007-0095-8

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