, Volume 133, Issue 2, pp 243–252 | Cite as

Molecular Marker based Genetic Diversity Analysis in Rice (Oryza sativa L.) using RAPD and SSR markers

  • M. Ravi
  • S. Geethanjali
  • F. Sameeyafarheen
  • M. Maheswaran


The availability of an array of molecular marker systems allowed comparing the efficiency of two of these marker systems to estimate the relationships among various taxa. The objective of this study was to assess the genetic diversity among 40 cultivated varieties and five wild relatives of rice, Oryza sativa L. involving simple sequence repeat (SSR) randomly amplified polymorphic DNA (RAPD) markers. The accessions were evaluated for polymorphisms after amplification with 36 decamer primers and 38 SSR primer pairs. A total of 499 RAPD markers were produced among the 40 cultivated varieties and five wild relatives with a polymorphism percentage of 90.0. Out of 38 SSR primer pairs used, only one locus viz., RM115 was monomorphic. The average Polymorphism Information Content (PIC) value was 0.578 and it ranged from a low of zero (RM 115) to a high of 0.890 (RM 202). The Mantel matrix correspondence test was used to compare the similarity matrices and the correlation coefficient was 0. 582. The test indicated that clusters produced based on RAPD and SSR markers were not conserved since matrix correlation value was 0.582 as against the minimum required value of 0.800. The two marker systems contrasted most notably in pair-by-pair comparisons of relationships. SSR analysis resulted in a more definitive separation of clusters of genotypes indicating a higher level of efficiency of SSR markers for the accurate determination of relationships between accessions that are too close to be accurately differentiated by RAPD markers.

genetic diversity molecular markers Oryza sativa RAPD SSR 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Akagi, H., Y. Yokozeki. A. Inagaki & T. Fujimura, 1997. Highly polymorphic microsatellites of rice consist of AT repeats, and a classification of closely related cultivars with these microsatellite loci. Theor Appl Genet 94: 61–67.CrossRefPubMedGoogle Scholar
  2. Bligh, H.F.J., 2000. Detection of adulteration of Basmati rice with non-premium long grain rice. Int J Food Sci & Technol 35: 257–265.CrossRefGoogle Scholar
  3. Chen, X., S. Temnykh. Y. Xu. Y.G. Cho & S.R. McCouch. 1997. Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor Appl Genet 95: 553–567.CrossRefGoogle Scholar
  4. Duwick, D.N., 1984. Genetic diversity in major farm crops on the farm and reserve. Econ Bot 32: 161–178.Google Scholar
  5. Fukuoka, S., K. Hosaka & O. Kamijima, 1992. Use of random amplified polymorphic DNA (RAPD) for identification of rice accessions. Japan J Genet 67: 247–252.CrossRefGoogle Scholar
  6. Garland, S.H., L. Lewinm M. Abedinia, R. Henry & A. Blakeney, 1999. The use of microsatellite polymorphisms for the identification of Australian breeding lines of rice (Oryza sativa L.). Euphytica 108: 53–63.CrossRefGoogle Scholar
  7. Ge Song, G., C.X. Oliveria, B.A. Schaal, G.L. Zhi & H.D. Yuan, 1999. RAPD variation within and between natural populations of the wild rice Oryza rufipogon from China and Brazil. Heredity 82: 638–644.CrossRefGoogle Scholar
  8. Liu, X.C & J.L. Wu, 1998. SSR heterogenic patterns of parents for making and predicting heterosis in rice breeding. Mol Breed 4: 263–268.CrossRefGoogle Scholar
  9. Mackill, D.J., Z. Zhang, E.D. Redona & P.M. Colowit, 1996. Level of polymorphism and genetic mapping of AFLP markers in rice. Genome 39: 969–977.PubMedGoogle Scholar
  10. Mantel, N., 1967. The detection of disease clustering and a generalized repression approach. Cancer Res 27: 209–220.PubMedGoogle Scholar
  11. McCouch, S.R., G. Kochert, Z.H. Yu, Z.Y. Wang, G.S. Khush, W.R. Coffman & S.D. Tanksley, 1988. Molecular mapping of rice chromosomes. Theor Appl Genet 76: 815–829.CrossRefGoogle Scholar
  12. McCouch, S.R., X. Chen, O. Panaud, S. Temnykh, Y. Xu, Y.G. Cho, N. Huang, T. Ishii & M. Blair, 1997. Microsatellite marker development, mapping and applications in rice genetics and breeding. Plant Mol Biol 35: 89–99.PubMedCrossRefGoogle Scholar
  13. McCouch, S.R., L. Teytelman, Y. Xu, K.B. Lobos, K. Clare, M. Walton, B. Fu, R. Maghirang, Z. Li, Y. Xing, Q. Zhang, I. Kono, M. Yano, R. Fjellstrom, G. DeClerck, D. Schneider, S. Cartinhour, D. Ware & L. Stein, 2002. Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 9: 257–279.PubMedCrossRefGoogle Scholar
  14. Melchinger, A.E., M. Messmer, M. Lee, W.L. Woodman & K.R. Lamkey, 1991. Diversity and relationships among U.S. maize inbreds revealed by restriction fragment length polymorphisms. Crop Sci 31: 669–678.CrossRefGoogle Scholar
  15. Nei, M., 1973. Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70: 3321–3323.PubMedCrossRefGoogle Scholar
  16. Ohtsubo, K., T. Fujii, Y. Hashino, H. Toyoshima, H. Okadome, S. Nakamura, T. Fuse & S. Kawasaki, 1999a. Identification of domestic rice cultivars by RAPD method using milled rice grains as samples. J Jap Soc Food Sci Tech 46: 117–122.Google Scholar
  17. Ohtsubo, K., S. Nakamura, H. Morooka, T. Fujii, T. Fuse & S. Kawasaki, 1999b. Identification of domestic rice cultivars by RAPD method using a single grain of cooked rice as a sample. J Jap Soc Food Sci Tech 46: 262–267.Google Scholar
  18. Olufowote, J.O., Y. Xu, X. Chen, W.O. Park, H.M. Beachell, R.H. Dilday, M. Goto & S.R. McCouch, 1997. Comparative evaluation of within-cultivar variation or rice (Oryza sativa L.) using microsatellite and RFLP markers. Genome 40: 370–378.PubMedGoogle Scholar
  19. Panaud, O., X.L. Chen & S.R. McCouch, 1996. Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet 252: 597–607.PubMedGoogle Scholar
  20. Provan, J., G. Corbett, J.W. McNiol & W. Powell, 1997. Chloroplast DNA variability in wild and cultivated rice (Oryza spp.) revealed by polymorphic chloroplast simple sequence repeats. Genome 40: 104–110.PubMedGoogle Scholar
  21. Ravi, M., 2000. Molecular marker based varietal profiling and monitoring in rice (Oryza sativa L.). Thesis submitted to the Tamil Nadu Agricultural University, Coimbatore, India, 85 p.Google Scholar
  22. Qiang,W., L.L. Jie, Y.D. Chang, H.G. Cun & S.L. Hui, 1998. RAPD analysis of wild rice genomes. J Trop Subtrop Bot 6: 260–266.Google Scholar
  23. Rohlf, F.J., 1994. NTSYS-PC: Numerical Taxonomy and Multivariate Analysis System Version 2.2. State University of New York, Stony Brook N.Y.Google Scholar
  24. Temnykh, S., W.D. Park, N. Ayres, S. Cartinhour, N. Hauck, L. Lipovich, Y.G. Cho, T. Ishii & S.R. McCouch, 2000. Mapping and genome organization of microsatellite sequences in rice. Theor Appl Genet 100: 697–712.CrossRefGoogle Scholar
  25. Virk, P.S., J. Zhu, H.J. Newbury, G.J. Bryan, M.T. Jackson & B.V. Ford-Lloyd, 2000. Effectiveness of different classes of molecular marker for classifying and revealing variation in rice (Oryza sativa) germplasm. Euphytica 112: 275–284.CrossRefGoogle Scholar
  26. Weeden, N.F., G.M. Timmerman, M. Hemmat, B.E. Kneen & M.A. Lofhi, 1992. Inheritance and reliability of RAPD markers. In: Applications of RAPD markers to plant breeding. Crop Sci Soc Am, pp. 12–17.Google Scholar
  27. Weir, B.S., 1990. Genetic Data Analysis: Methods for Discrete Population Genetic Data. Sinauer Associates, Inc. Publishers. Sunderland, Massachusetts, 377 pp.Google Scholar
  28. Welsh, J. & M. McClelland, 1990. Fingerprinting genomes: using PCR with arbitrary primers. Nucl Acids Res 18: 7213–7218.PubMedGoogle Scholar
  29. Williams, J.G.K., A.R. Kubelik, K.J. Livak, J.A. Rafalski & S.V. Tingey, 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl Acids Res 18: 6531–6535.PubMedGoogle Scholar
  30. Wu, K.S & S.D. Tanksley, 1993. Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet 241: 225–235.PubMedCrossRefGoogle Scholar
  31. Xiao, J., J. Li, L. Yuan, S.R. McCouch & S.D. Tanksley, 1996. Genetic diversity and its relationship to hybrid performance and heterosis in rice as revealed by PCR-based markers. Theor Appl Genet 92: 637–643.CrossRefGoogle Scholar
  32. Zhao, M.F., X.H. Li, J.B. Yang, C.G. Xu, R.Y. Hu, D.J. Liu & Q. Zhang, 1999. Relationship between molecular marker heterozygosity and hybrid performance in intra and inter subspecific crosses of rice. Plant Breed 118: 139–144.CrossRefGoogle Scholar
  33. Zheng, K.L., B. Shen & H.R. Qian, 1991. DNA polymorphisms generated by arbitrary primed PCR in rice. Rice Genet Newsl 8: 134–136.Google Scholar

Copyright information

© Kluwer Academic Publishers 2003

Authors and Affiliations

  • M. Ravi
    • 1
  • S. Geethanjali
    • 1
  • F. Sameeyafarheen
    • 1
  • M. Maheswaran
    • 2
  1. 1.Centre for Plant Breeding and GeneticsIndia
  2. 2.Centre for Plant Molecular BiologyTamil Nadu Agricultural UniversityCoimbatoreIndia

Personalised recommendations