, Volume 107, Issue 1, pp 45–50 | Cite as

The effect of the number of RAPD markers on the evaluation of genotypic distances in Vitis vinifera

  • G. Fanizza
  • G. Colonna
  • P. Resta
  • G. Ferrara


The effect of the number of RAPD fragments on the estimation of genetic distances has been studied on 10 genotypes (Vitis vinifera) using 320 primers. A total number of 1683 scorable bands was obtained but only polymorphic bands (932) were considered in this work. The variation of the genetic distances, in relation to an increasing number of bands, was evaluated through a bootstrap sampling procedure. The mean coefficient of variation (CV) of the genetic distances decreased as the number of bands increased. A CV of 10% was obtained with about 100–150 bands while a CV of 5% with a large number of bands (400–500 and over). To reduce the cost and the time of the analyses, primers with different levels of polymorphism were compared. Genetic distance matrices, based on different numbers of bands and primer polymorphism, were highly correlated with the genetic distance matrix of the whole data set when they were determined with a large number of RAPD fragments, either from high or low polymorphic primers. The effect of the number of bands on the estimation of genetic distances was evaluated also through the variation of the pattern of aggregation among genotypes (cluster analysis). Stable clusterings were detected when a large number of polymorphic bands (400 and over) was used. Some rearrangements of the genotypes in the dendrograms was observed as the number of bands decreased; below 100–150 bands the clusterings were completely rearranged.

bootstrap cluster analysis grapevines RAPD marker 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Botta, R., N.S. Scott, I. Eynard & M.R. Thomas, 1995. Evaluation of microsatellite sequence-tagged site markers for characterizing Vitis vinifera cultivars. Vitis 34(2): 99–102.Google Scholar
  2. Bourquin, J.C., A. Sonko, L. Otten & B. Walter, 1993. Restriction fragment length polymorphism and molecular taxonomy in Vitis vinifera L. Theor Appl Genet 87: 431–438.CrossRefGoogle Scholar
  3. Bowers, J.E., E.B. Bandman & C.P. Meredith, 1993. DNA fingerprint characterization of some wine grape cultivars. Amer J Enol Viticult 44: 266–274.Google Scholar
  4. Bowers, J.E., G.S. Dangl, R. Vignani & C.P. Meredith, 1996. Isolation and characterization of new polymorphic simple sequence repeat loci in grape (Vitis vinifera). Genome 39: 628–633.Google Scholar
  5. Buscher, N., E. Zyprian, O. Bachmann, & R. Blaich, 1994. On the origin of the grapevine variety Muller-Thurgau as investigated by the inheritance of random amplified polymorphic DNA (RAPD). Vitis 33: 15–17.Google Scholar
  6. Cipriani, G., G. Frazza, E. Peterlunger & R. Testolin, 1994. Grapevine fingerprinting using microsatellite repeats. Vitis 33: 211–215.Google Scholar
  7. Efron, B. & R. Tibshirani, 1991. Statistical analysis with computer age. Science 253: 390–395.Google Scholar
  8. Gogorcena, Y., S. Arulsekar, A.M. Dandekar & D.E. Parfitt, 1993. Molecular markers for grape characterization. Vitis 32: 183–185.Google Scholar
  9. Grando, S.M., L. De Micheli, L. Biasetto & A. Scienza, 1995. RAPD markers in wild and cultivated Vitis vinifera. Vitis 34: 37–39.Google Scholar
  10. Guerra, B. & C.P. Meredith, 1995. Comparison of Vitis berlandieri × Vitis riparia rootstock cultivars by restriction fragment length polymorphism analysis. Vitis 34: 109–112.Google Scholar
  11. Jean-Jaques, I., A. Defontaine & J.N. Hallet, 1993. Characterization of Vitis vinifera cultivars by Random Amplified Polymorphic DNA markers. Vitis 32: 189–190.Google Scholar
  12. Mauro, M.C., M. Strefeler, N.F. Weeden & B.I. Reisch, 1992. Genetic analysis of restriction fragment length polymorphisms in Vitis. J Hered 83: 18–21.Google Scholar
  13. Moreno, S., Y. Gogorcena & J.M. Ortiz, 1995. The use of RAPD markers for identification of cultivated grapevine (Vitis vinifera L.). Sci Hort 62: 237–243.CrossRefGoogle Scholar
  14. Mulcahy, D.L., M. Cresti, H.P. Liskens, L. Intrieri, O. Silvestroni, R. Vignani & M. Pancaldi, 1995. DNA fingerprinting of italian grape varieties: a test of reliability in RAPDs. Adv Hort Sci 9: 185–187.Google Scholar
  15. Nienhuis, J., J. Tivang, P. Skroch & J.B. dos Santos, 1995. Genetic relationship among cultivars and landraces of lima bean (Phaseolus lunatus L) as measured by RAPD markers. J Amer Soc Hort Sci 120(2): 300–306.Google Scholar
  16. Resta, P, G. Fanizza & B. Zhuang, 1995. Polymorphisms among grape cultivars (V. vinifera L.) revealed by replicated RAPD profiles. In: Shejbal J. (Ed), Atti del Convegno Biotecnologie avanzate e agricoltura, pp. 320–329.Google Scholar
  17. Rohlf, F.J., 1992. NTSYS-pc-Numerical Taxonomy and Multivariate Analysis System. Exeter Software, Setauket, New York.Google Scholar
  18. Skroch, P.W. & J. Nienhuis, 1995. Impact of scoring error and reproducibility of RAPD data on RAPD based estimates of genetic distance. Theor Appl Genet 91: 1086–1091.Google Scholar
  19. Smith, J.J., J.S. Scott-Craig, J.R. Leadbetter, G.L. Busch, D.L. Roberts & D.W. Fulbright, 1994. Characterization of random amplified polymorphic DNA (RAPD) products from Xanthonomas campestris and some comments on the use of RAPD products in phylogenetic analysis. Mol Phylo Evol 3: 135–145.CrossRefGoogle Scholar
  20. Sneath, P.H.A. & R.R. Sokal, 1973. Numerical taxonomy. WH Freeman and Company. San Francisco.Google Scholar
  21. Striem, M.J., P. Spiegel-Roy, E. Ben-Hayyim, J. Beckmann & D. Gidoni, 1990. Genomic DNA fingerprinting of Vitis vinifera by the use of multiloci probes. Vitis 29: 223–227.Google Scholar
  22. Thomas, M.S. & N.S. Scott, 1993. Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence tagged sites (STSs). Theor Appl Genet 86: 985–990.Google Scholar
  23. Thomas, M.S., P. Cain & N.S. Scott, 1994. DNA typing of grapevines: a universal methodology and database for describing cultivars and evaluating genetic relatedness. Plant Mol Biol 25: 937–949.CrossRefGoogle Scholar
  24. Thormann, C.E., M.E. Ferriera, L.E.A. Camargo, J.G. Tivang & T.C. Osborne, 1994. Comparison of RFLP and RAPD genetic relationships within and among cruciferous species. Theor Appl Genet 88: 973–980.CrossRefGoogle Scholar
  25. Tivang, J.G., J. Nienhuis & O.S. Smith, 1994. Estimation of sampling variance of molecular marker data sites using the bootstrap procedure. Theor Appl Genet 89: 259–264.CrossRefGoogle Scholar
  26. Weeden, N.F., G.M. Timmerman, M. Hemmat, B.E. Kneen & M.A. Lodhi, 1992. Inheritance and reliability of RAPD markers pp. 12–17. In: Applications of RAPD technology to plant breeding. Crop Sci Soc Amer, Madison Wis.Google Scholar
  27. Xianping, Q., J. Lu & O Lamikanra, 1996. Genetic diversity in Muscadine and American bunch grapes based on random amplified polymorphic DNA (RAPD) analysis. J Amer Soc Hort Sci 121: 1020–1023.Google Scholar
  28. Xu, H. & A.T. Bakalinsky, 1996. Identification of grape (Vitis) rootstocks using sequence characterized amplified region DNA markers. HortScience 3(2): 267–268.Google Scholar
  29. Yamamoto, N., G. Ono, K. Takashima & A. Totsuka, 1991. Restriction fragment length polymorphism of grapewine DNA with the phenylalamine ammonia-lyase cDNA. Japan J Breed 41: 365–368.Google Scholar

Copyright information

© Kluwer Academic Publishers 1999

Authors and Affiliations

  • G. Fanizza
    • 1
  • G. Colonna
    • 2
  • P. Resta
    • 1
  • G. Ferrara
    • 1
  1. 1.Istituto di Miglioramento Genetico delle Piante Agrarie, Università di BariBariItaly
  2. 2.Dipartimento Farmaco-ChimicoUniversità di BariBariItaly

Personalised recommendations