Biologia Plantarum

, Volume 54, Issue 1, pp 135–140 | Cite as

Genetic diversity in important members of Cucurbitaceae using isozyme, RAPD and ISSR markers

  • B. Sikdar
  • M. Bhattacharya
  • A. Mukherjee
  • A. Banerjee
  • E. Ghosh
  • B. Ghosh
  • S. C. Roy
Brief Communication


Biochemical and molecular markers have been used on eleven species of Cucurbitaceae collected from lower Gangetic plains. Six enzyme systems were selected. Among 40 primers examined, 14 random amplified polymorphic DNA (RAPD) and 10 inter-simple sequence repeat (ISSR) primers were selected for the analysis. Generated RAPD (100) and ISSR (100) fragments showed high variations among the species. Jaccard similarity coefficients were used for the evaluation of pairwise genetic divergence; cluster analysis of the similarity matrices was performed to estimate interspecific diversity. Further, principal coordinate analysis was performed to evaluate the resolving power of the three marker systems to differenciate among the species.

Additional key words

cluster analysis Jaccard similarity coefficient molecular marker primer 



inter-simple sequence repeat


polymerase chain reaction


random amplified polymorphic DNA


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.



B. Sikdar is gratefully acknowledged to TWAS for financial support to the postdoctoral research.


  1. Ajibade, S.R., Weeden, N.F., Chite, S.M.: Inter simple sequence repeat analysis of genetic relationships in the genus Vigna. — Euphytica 111: 47–55, 2000.CrossRefGoogle Scholar
  2. Apavatjrut, P., Anuntalabhochai, S., Sirirugsa, P. Alisi, C.: Molecular markers in the identification of some early flowering Curcuma L. (Zingiberaceae) species. — Ann. Bot. 84: 529–534, 1999.CrossRefGoogle Scholar
  3. Aradhya, M.K., Kee, L.K., Zee, F.T., Manshardt, R.M.: Genetic variability in Macadamia. — Genet. Resour. Crop Evolut. 45: 19–32, 1998.CrossRefGoogle Scholar
  4. Arnau, G., Lallemand, J., Bourgoin, M.: Fast and reliable strawberry cultivar identification using inter simple sequence repeat (ISSR) amplification. — Euphytica 129: 69–79, 2002.CrossRefGoogle Scholar
  5. Blair, M.W., Panaud, O., McCouch, S.R.: Inter-simple sequence repeat (ISSR) amplification for analysis of microsatellite motif frequency and fingerprinting in rice (Oryza sativa L). — Theor. appl. Genet 98: 780–792, 1999.CrossRefGoogle Scholar
  6. Booy, G., Van Raamsdonk, L.W.D.: Variation in the enzyme esterase within and between Tulipa species; usefulness for the analysis of genetic relationships at different taxonomical levels. — Biochem. Syst. Ecol. 26: 199–224, 1998.CrossRefGoogle Scholar
  7. Brown-Guedira, G.L., Thompson, J.A., Nelson, R.L., Warburton, M.L.: Evaluation of genetic diversity of soybean introductions and North American ancestors using RAPD and SSR markers. — Crop Sci. 40: 815–823, 2000.CrossRefGoogle Scholar
  8. Das, M., Bhattacharya, S., Basak J., Pal A.: Phylogenetic relationships among the bamboo species as revealed by morphological characters and polymorphism analyses. — Biol. Plant. 51: 667–672, 2007.CrossRefGoogle Scholar
  9. Das, S., Mukherjee, K.K.: Morphological and biochemical investigations on Ipomoea seedlings and their species interrelationships. — Ann. Bot. 79: 565–571, 1997.CrossRefGoogle Scholar
  10. Depeiges, A., Goubely, C., Lenoir, A., Cocherel, S., Picard, G., Raynal, M., Grellet, F., Delseny, M.: Identification of the most represented repeated motifs in Arabidopsis thaliana microsatellite loci. — Theor. appl. Genet. 91: 160–168, 1995.CrossRefGoogle Scholar
  11. Dikshit, H.K., Jhang, T., Singh, N.K., Koundal, K.R., Bansal, K. C., Chandra, N., Tickoo, J. L., Sharma, T.R.: Genetic differentiation of Vigna species by RAPD, URP and SSR markers. — Biol. Plant. 51: 451–457, 2007.CrossRefGoogle Scholar
  12. Doyle J.J., Doyle J.L.: A rapid DNA isolation procedure from small quantities of fresh leaf tissues. — Phytochem. Bull. 19: 11–15, 1987.Google Scholar
  13. Fernandez, M.E., Figueiras, A.M. Benito, C.: The use of ISSR and RAPD marker for detecting DNA polymorphism, genotype identification and genetic diversity among barley cultivars with known origin. — Theor. appl. Genet. 104: 845–851, 2002.CrossRefPubMedGoogle Scholar
  14. Hauser, L.A. Crovello, T.J.: Numerical analysis of genetic relationships in Thelypodieae (Brassicaceae). — Syst. Bot. 7: 249–268, 1982.CrossRefGoogle Scholar
  15. Helm, M.A., Hemleben, V.: Characterization of a new prominent satellite DNA of Cucumis metuliferus and differential distribution of satellite DNA in cultivated and wild species of Cucumis and in related genera of Cucurbitaceae. Euphytica 94: 219–226, 1997.CrossRefGoogle Scholar
  16. Hoey, B.K., Crowe, K.R., Jones, V.M.: A phylogenetic analysis of Pisum sativum based on morphological characters and allozyme and RAPD markers. — Theor. Appl. Genet. 92: 92–100, 1996.CrossRefGoogle Scholar
  17. Joshi, S.P., Gupta, V.S., Aggarwal, R.K., Ranjekar, P.K. Brar, D.S.: Genetic diversity and phylogenetic relationship as revealed by inter-simple sequence repeat (ISSR) polymorphism in the genus Oryza. — Theor. appl. Genet. 100: 1311–1320, 2000.CrossRefGoogle Scholar
  18. Kaga, A.N., Tomooka, N., Egawa, Y., Hosaka, K., Kamijima, O.: Species relationships in subgenus Ceratotropis (genus Vigna) as revealed by RAPD analysis. — Euphytica 88: 17–24, 1996.CrossRefGoogle Scholar
  19. Khasa, P.D., Dancik, B.P.: Rapid identification of white- Engelmann spruce species by RAPD markers. — Theor. appl. Genet. 92: 46–52, 1996.CrossRefGoogle Scholar
  20. Lakhanpaul, S., Velayudhan, K.C., Bhat, K.V.: Analysis of genetic diversity in Indian taro (Colocasia esculenta Schott) using random amplified polymorphic DNA (RAPD) markers. — Genet. Resour. Crop Evolut. 50: 603–609, 2003.CrossRefGoogle Scholar
  21. Lange, O., Schifino-Wittmann, M. T.: Isozyme variation in wild and cultivated species of the genus Trifolium L. (Leguminosae). — Ann. Bot. 86: 339–345, 2000.CrossRefGoogle Scholar
  22. Levi, A., Thomas, C.E., Simmons, A.M., Thies, J.A.: Analysis based on RAPD and ISSR markers reveals closer similarities among Citrullus and Cucumis species than with Praecitrullus fistulosus (Stocks) Pangalo. — Genet. Resour. Crop Evolut. 52: 465–472, 2005.CrossRefGoogle Scholar
  23. Loarce, Y., Gallego, R. Ferrer, E.: A comparative analysis of genetic relationships between rye cultivars using RFLP and RAPD markers. — Euphytica 88: 107–115, 1996.CrossRefGoogle Scholar
  24. Lowry, O.H., Rosebrough, N.J., Farr, A.L., Randall, R.J.: Protein measurement with the Folin-Phenol reagents. J. biol. Chem. 193: 265–275, 1951.PubMedGoogle Scholar
  25. Mantel, N.: The detection of disease clustering and generalized regression approach. — Cancer Res. 27: 209–220, 1967.PubMedGoogle Scholar
  26. Moreno, S., Martin, J.P., Ortiz, J.M.: Inter-simple sequence repeats PCR for characterization of closely related grapevine germplasm. — Euphytica 101: 117–125, 1998.CrossRefGoogle Scholar
  27. Nebauer, S.G., del Castillo-Agudo, L., Segura, J.: RAPD variation within and among natural populations of outcrossing willow-leaved foxglove (Digitalis obscura L.). — Theor. appl. Genet. 98: 985–994, 1999.CrossRefGoogle Scholar
  28. Nei, M.: Estimation of average heterozygosity and genetic distance from a small number of individual. — Genetics 89:583–590, 1978.PubMedGoogle Scholar
  29. Paterson, A.H., Tanksley, S.D., Sorrells, M.E.: DNA markers in plant improvement. — Adv. Agron. 46: 39–90, 1991.CrossRefGoogle Scholar
  30. Ray, T., Roy, S.C.: Phylogenetic relationships between members of Amaranthaceae and Chenopodiaceae of lower gangetic plains using RAPD and ISSR markers. — Bangladesh J. Bot. 36: 21–28, 2007.Google Scholar
  31. Rohlf, F.J.: NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System. — Exeter Software, Setauket — New York 2000.Google Scholar
  32. Sanjur, O.I., Piperno, D.R., Andres, T.C., Wessel-Beaver L.: Phylogenetic relationships among domesticated and wild species of Cucurbita (Cucurbitaceae) inferred from a mitochondrial gene: Implications for crop plant evolution and areas of origin. — Proc. nat. Acad. Sci. USA 99: 535–540, 2002.CrossRefPubMedGoogle Scholar
  33. Santalla, M., Power, J.B., Davey, M.R.: Genetic diversity in mungbean germplasm revealed by RAPD markers. — Plant Breed. 117: 473–478, 1998.CrossRefGoogle Scholar
  34. Skroch, P.W., Dos Santos, J.B., Nienhuis, J.: Genetic relationships among Phaseolus vulgaris genotypes based on RAPD marker data. — Annu. Rep. Bean Improv. Coop. 35:23–24, 1992.Google Scholar
  35. Soller, M., Beckmann, J.S.: Genetic polymorphism in varietal identification and genetic improvement. — Theor. appl. Genet. 67: 25–33, 1983.CrossRefGoogle Scholar
  36. Souframanien, J., Gopalakrishna, T.: A comparative analysis of genetic diversity in blackgram genotypes using RAPD and ISSR markers. — Theor. appl. Genet. 109: 1687–1693, 2004.CrossRefPubMedGoogle Scholar
  37. Williams, J.G.K., Kubelik, A.R., Livak, K.J., Rafalaski, J.A., Tingey, S.V.: DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. — Nucleic Acids Res. 18: 6531–6535, 1990.CrossRefPubMedGoogle Scholar
  38. Yang, R.W., Zhou, C.B., Ding, Y.H., Zheng, Y.L., Zhang, L.: Relationships among Leymus species assessed by RAPD markers. — Biol. Plant. 52(2) 237–241, 2008.CrossRefGoogle Scholar
  39. Yao, H., Zhao, Y., Chen, D.F., Chen, J.K., Zhou, T.S.: ISSR primer screening and preliminary evaluation of genetic diversity in wild populations of Glycyrrhiza uralensis. — Biol. Plant. 52: 117–120, 2008.CrossRefGoogle Scholar
  40. Zietkiewicz, E., Rafalski, A., Labuda, D.: Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. — Genomics 20:176–183, 1994.CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • B. Sikdar
    • 1
  • M. Bhattacharya
    • 2
  • A. Mukherjee
    • 3
  • A. Banerjee
    • 2
  • E. Ghosh
    • 2
  • B. Ghosh
    • 2
  • S. C. Roy
    • 2
  1. 1.Department of Genetic Engineering and BiotechnologyUniversity of RajsahiRajsahiBangladesh
  2. 2.Department of BotanyUniversity of CalcuttaKolkataIndia
  3. 3.Department of BotanyDinabandhu MahavidyalayaBongaonIndia

Personalised recommendations