Molecular Marker based Genetic Diversity Analysis in Rice (Oryza sativa L.) using RAPD and SSR markers
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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.
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- Duwick, D.N., 1984. Genetic diversity in major farm crops on the farm and reserve. Econ Bot 32: 161–178.Google Scholar
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Weir, B.S., 1990. Genetic Data Analysis: Methods for Discrete Population Genetic Data. Sinauer Associates, Inc. Publishers. Sunderland, Massachusetts, 377 pp.Google Scholar
- 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