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.
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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.
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.
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.
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.
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.
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.
Glaszmann, J.C. 1987. Isozymes and classification of Asian rice varieties. Theor. Appl. Genet. 74:21–30.
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.
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.
Murray, M.G., Thompson, W.F. 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 8:4321–4325.
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.
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.
Roy, J.K., Israel, P., Panwar, M.S. 1969. Breeding for insect resistance. Oryza 6:38–44.
Siddiq, E.A., Vemireddy, L.R., Nagaraju, J. 2012. Basmati rices: Genetics, breeding and trade. Agric. Res. 1:25–36.
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.
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.
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.
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.
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.
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.
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Vemireddy, L.R., Ranjithkumar, N., Vipparla, A. et al. Molecular Profiling of Major Indian Rice Cultivars Using a Set of Eight Hypervariable Microsatellite Markers. CEREAL RESEARCH COMMUNICATIONS 43, 189–203 (2015). https://doi.org/10.1556/CRC.2014.0035
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DOI: https://doi.org/10.1556/CRC.2014.0035