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Cereal Research Communications

, Volume 43, Issue 2, pp 189–203 | Cite as

Molecular Profiling of Major Indian Rice Cultivars Using a Set of Eight Hypervariable Microsatellite Markers

  • L. R. VemireddyEmail author
  • N. Ranjithkumar
  • A. Vipparla
  • M. Surapaneni
  • G. Choudhary
  • K. V. Sudhakarrao
  • E. A. Siddiq
Genetics

Abstract

India bred high yielding rice varieties have enriched to a great extent the global rice germplasm since the mid-sixties. Systematic research efforts for development of cultivar-specific DNA fingerprints of major Indian rice cultivars, however, have not received due attention. The present investigation was aimed at development of DNA fingerprints for 90 high yielding rice varieties using hypervariable microsatellite (hvRM) markers. A panel of eight markers, viz. RM11313, RM13584, RM15004, RM5844, RM22250, RM22565, RM24260 and RM8207 was chosen from 52 polymorphic markers based on their highly polymorphic nature, SSR repeat type and number and ability to distinguish genotypes, in order to develop DNA fingerprints of 90 varieties. The remaining high polymorphic hvRM markers could be of immense value in future to distinguish new cultivars, in case they could not be distinguished by the 8 marker panel. Four of the 8 markers, viz. RM22250, RM13584, RM24260 and RM5844 were located in expressed genes and could be of value in DUS (Distinctness, Uniformity and Stability) testing. Thus we suggested, that this set of 8 loci could be used as standard for DNA fingerprinting of Indian rice cultivars.

Keywords

molecular profiling hypervariable microsatellite markers genetic diversity rice 

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References

  1. Archak, S., Lakshminarayanareddy, V., Nagaraju, J. 2007. High-throughput multiplex microsatellite marker assay for detection and quantification of adulteration in basmati rice (Oryza sativa). Electrophoresis 28:2396–2405.CrossRefGoogle Scholar
  2. Bonow, S., VonPinho, E.V.R., Vieira, M.G.C., Vosman, B. 2009. Microsatellite markers in and around rice genes. Crop Sci. 49:880–886.CrossRefGoogle Scholar
  3. Choudhary, G., Ranjitkumar, N., Surapaneni, M., Deborah, D.A., Vipparla, A., Anuradha, G., Siddiq, E.A., Vemireddy, L.R. 2013. Molecular genetic diversity of major indian rice cultivars over decadal periods. PloS one 8:e66197.CrossRefGoogle Scholar
  4. Garris, A.J., Tai, T.H., Coburn, J., Kresovich, S., McCouch, S. 2005. Genetic structure and diversity in Oryza sativa L. Genetics 169:1631–1638.CrossRefGoogle Scholar
  5. Giancola, S., MarcucciPoltri, S., Lacaze, P., Hopp, H.E. 2002. Feasibility of integration of molecular markers and morphological descriptors in a real case study of a plant variety protection system for soybean. Euphytica 127:95–113.CrossRefGoogle Scholar
  6. Giarrocco, L.E., Marassi, M.A., Salerno, G.L. 2007. Assessment of the genetic diversity in Argentine rice cultivars with SSR. Crop Sci. 47:853–858.CrossRefGoogle Scholar
  7. Glaszmann, J.C. 1987. Isozymes and classification of Asian rice varieties. Theor. Appl. Genet. 74:21–30.CrossRefGoogle Scholar
  8. Gunjaca, J., Buhinicek, I., Jukic, M., Sarcevic, H., Vragolovic, A., Kozic, Z., Jambrovic, A., Pejic, I. 2008. Discriminating maize inbred lines using molecular and DUS data. Euphytica 161:165–172.CrossRefGoogle Scholar
  9. Marri, P., Sarla, N., Reddy, L., Siddiq, E.A. 2005. Identification and mapping of yield and yield related QTLs from an Indian accession of Oryza rufipogon. BMC Genetics 6:33.CrossRefGoogle Scholar
  10. Murray, M.G., Thompson, W.F. 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 8:4321–4325.CrossRefGoogle Scholar
  11. Narshimulu, G., Jamaloddin, M., Vemireddy, L.R., Anuradha, G., Siddiq, E.A. 2011. Potentiality of evenly distributed hypervariable microsatellite markers in marker-assisted breeding of rice. Plant Breeding 130:314–320.CrossRefGoogle Scholar
  12. Patra, N., Chawla, H.S. 2010. Biochemical and RAPD molecular markers for establishing distinctiveness of basmati rice (Oryza sativa L.) varieties as additional descriptors for plant variety protection. Indian J. Biotech. 9:371–377.Google Scholar
  13. Roy, J.K., Israel, P., Panwar, M.S. 1969. Breeding for insect resistance. Oryza 6:38–44.Google Scholar
  14. Siddiq, E.A., Vemireddy, L.R., Nagaraju, J. 2012. Basmati rices: Genetics, breeding and trade. Agric. Res. 1:25–36.CrossRefGoogle Scholar
  15. Srividhya, A., Vemireddy, L., Sridhar, S., Jayaprada, M., Ramanarao, P., Hariprasad, A., Reddy, H., Anuradha, G., Siddiq, E. 2011. Molecular mapping of QTLs for yield and its components under two water supply conditions in rice (Oryza sativa L.). J. Crop Sci. Biotechnol. 14:45–56.CrossRefGoogle Scholar
  16. Sundaram, R.M., Naveenkumar, B., Biradar, S.K., Balachandran, S.M., Mishra, B., IlyasAhmed, M., Viraktamath, B.C., Ramesha, M.S., Sarma, N.P. 2008. Identification of informative SSR markers capable of distinguishing hybrid rice parental lines and their utilization in seed purity assessment. Euphytica 163:215–224.CrossRefGoogle Scholar
  17. Vemireddy, L.R., Archak, S., Nagaraju, J. 2007. Capillary electrophoresis is essential for microsatellite marker based detection and quantification of adulteration of Basmati rice (Oryza sativa). J Agric Food Chem. 55:8112–8117.CrossRefGoogle Scholar
  18. Xu, K., Xu, X., Fukao, T., Canlas, P., Maghirang-Rodriguez, R., Heuer, S., Ismail, A.M., Bailey-Serres, J., Ronald, P.C., Mackill, D.J. 2006. Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442:705–708.CrossRefGoogle Scholar
  19. Yong-Sham, K., Je-Min, L., Gi-Bum, Y., Seung-In, Y., Kyung-Min, K., Eun-Hee, S., Kyung-Mi, B., Eun-Kyung, P., In-Ho, S., Byung-Dong, K. 2005. Use of SSR markers to complement tests of distinctiveness, uniformity, and stability (DUS) of pepper (Capsicum annuum L.) varieties. Mol. Cells 19:428–435.Google Scholar
  20. Zhang, Z., Deng, Y., Tan, J., Hu, S., Yu, J., Xue, Q., 2007. A genome-wide microsatellite polymorphism database for the indica and japonica rice. DNA Research 14:37–45.CrossRefGoogle Scholar

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© Akadémiai Kiadó, Budapest 2015

This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

Authors and Affiliations

  • L. R. Vemireddy
    • 1
    Email author
  • N. Ranjithkumar
    • 1
  • A. Vipparla
    • 1
  • M. Surapaneni
    • 1
  • G. Choudhary
    • 1
  • K. V. Sudhakarrao
    • 1
  • E. A. Siddiq
    • 1
  1. 1.Institute of BiotechnologyAcharya NG Ranga Agricultural UniversityRajendranagar, HyderabadIndia

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