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Molecular Genetic Diversity of Landraces, Cultivars and Wild Relatives of Rice of Goa


Affiliations
1 Department of Botany, Goa University, Goa 403 206, India
 

We studied 51 rice varieties to understand their genetic diversity. Out of 19 ISSR primers, 15 primers produced reproducible bands. Out of 110 ISSR bands, 104 were polymorphic bands with an average of 6.93 bands per primer. The amount of polymorphism varied from 50% to 100%, with an average of 92%. Genetic identity value ranged from 0.5091 to 0.9727, with an average of 0.740. Dendrogram revealed the formation of four major clusters. Wild rice Oryza rufipogon formed a separate clade, indicating its uniqueness. Our study opens up avenues for use of traditional rice varieties for rice breeding, genome-wide association mapping and conservation of rice germplasm.

Keywords

Genetic Diversity, ISSR Markers, Landraces, Oryza sativa, Oryza rufipogon.
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  • Yu, S. B., Xu, W. J., Vijayakumar, C. H. M., Ali, J., Fu, B. Y. and Xu, J. L., Molecular diversity and multilocus organization of the parental lines used in the International Rice Molecular Breeding Program. Theor. Appl. Genet, 2003, 108, 131–140.

  • Garris, A. J., Tai, T. H., Coburn, J., Kresovich, S. and McCouch, S., Genetic structure and diversity in Oryza sativa L. Genetics, 2005, 169, 1631–1638.

  • Caicedo, A. L., Williamson, S. H., Hernandez, R. D., Boyko, A., Fledel-Alon, A. and York, T. L., Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genetics, 2007, 163(3), 1754–1756.

  • Jain, S., Jain, R. and McCouch, S., Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently labelled microsatellite markers. Theor. Appl. Genet, 2004, 109(5), 965–977.

  • Gao, L. Z., ChiHong, Z., LiPing, C., JiZeng, J., ZongEn, Q. and YuShen, D., Microsatellite diversity within Oryza sativa with emphasis on indica-japonica divergence. Genet. Res., 2005, 85, 1–14.

  • Pessoa-Filho, M., Belo, A., Alcochete, A., Rangel, P. and Ferreira, M., A set of multiplex panels of microsatellite markers for rapid molecular characterization of rice accessions. BMC Plant Biol., 2007, 7–23.

  • Thomson, M., Septiningsih, E., Suwardjo, F., Santoso, T., Silitonga, T. and McCouch, S., Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers. Theor. Appl. Genet., 2007, 114, 559–568.

  • Thomson, M. J., Polato, N. R., Prasetiyono, J., Trijatmiko, K. R., Silitonga, T. S. and McCouch, S. R., Genetic diversity of isolated populations of Indonesian landraces of rice (Oryza sativa L.) collected in East Kalimantan on the island of Borneo. Rice, 2009, 2, 80–92.

  • Datta, S. K., Lina, B., Jumin, T., Norman, T., Olive, P. and Datta, K., Production and Molecular Evaluation of Transgenic Rice Plants, International Rice Research Institute (IRRI), Philippines, 1997, pp. 35–36.

  • Parab, G. V. and Krishnan, S., Assessment of genetic variation among populations of Rhynchostylis retusa, an epiphytic orchid from Goa, India using ISSR and RAPD markers. Indian J. Biotechnol., 2008, 7, 313–319.

  • Rohlf, F. J., NTSYS-PC: Numerical Taxonomy and Multivariate Analysis System Version 2.0. State University of New York, Stony Brook, New York, USA, 1992.

  • Tesfaye, K., Genetic diversity of wild Cofea arabica populations in Ethiopia as a contribution to conservation and use planning. ecology and development series (Ph D thesis), University of Bonn, Germany, 2006.

  • Hou, X. L. et al., Regulation of the expression of OsIPS1 and OsIPS2 in rice via systemic and local Pi signalling and hormones. Plant Cell Environ., 2005, 28(3), 353–365.

  • Parab, G. V., Krishnan, S., Janarthanam, M. K., Sivaprakash, K. R. and Parida, A., ISSR and RAPD markers assessed genetic variation of Aerides maculosum – an epiphytic orchid from Goa, India. J. Plant Biochem. Biot., 2008, 17(1), 107–109.

  • Ge, S., Oliveira, G. C. X., Schaal, B. A., Gao, L. Z. and Hong, D. Y., RAPD variation within and between natural populations of the wild rice Oryza rufipogon from China and Brazil. Heredity, 1999, 82, 638–644.

  • Qian, W., Ge, S. and Hong, D. Y., Genetic variation within and among populations of a wild rice Oryza granulata from China detected by RAPD and ISSR markers. Theor. Appl. Genet, 2001, 102, 440–449.

  • Joshi, S. P., Gupta, V. S., Aggarwal, R. K., Ranjekar, P. K. and Brar, D. S., Genetic diversity and phylogenetic relationship as revealed by inter-simple sequence repeat (ISSR) polymorphism in the genus Oryza. Theor. Appl. Genet., 2000, 100, 1311–1320.

  • Reddy, M. P., Sarla, N., Neeraja, C. N. and Siddiq, E. A., Assessing genetic variation among Asian A-genome Oryza species using inter simple sequence repeat (ISSR) polymorphism. In Fourth International Rice Genetics Symposium, IRRI, Philippines, 22–27 October 2000.

  • Vanniarajan, C., Vinod, K. K. and Pereira, A., Molecular evaluation of genetic diversity and association studies in rice (Oryza sativa L.). J. Genet., 2012, 91(1), 9–19.

  • Tateoka, T., Taxonomic studies of Oryza. III, Key to the species and their enumeration. Botanical Magazine Tokyo, 1963, 76, 165–173.

  • Sharma, S. D. and Shastry, S. V. S., Taxonomic studies in genus Oryza L. III. O. rufipogon Griff. sensu stricto and O. nivara Sharma et Shastry nom. nov. Indian J. Genet. Pl. Br., 1965, 25, 157–167.


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  • Molecular Genetic Diversity of Landraces, Cultivars and Wild Relatives of Rice of Goa

Abstract Views: 331  |  PDF Views: 123

Authors

Shilpa J. Bhonsle
Department of Botany, Goa University, Goa 403 206, India
S. Krishnan
Department of Botany, Goa University, Goa 403 206, India

Abstract


We studied 51 rice varieties to understand their genetic diversity. Out of 19 ISSR primers, 15 primers produced reproducible bands. Out of 110 ISSR bands, 104 were polymorphic bands with an average of 6.93 bands per primer. The amount of polymorphism varied from 50% to 100%, with an average of 92%. Genetic identity value ranged from 0.5091 to 0.9727, with an average of 0.740. Dendrogram revealed the formation of four major clusters. Wild rice Oryza rufipogon formed a separate clade, indicating its uniqueness. Our study opens up avenues for use of traditional rice varieties for rice breeding, genome-wide association mapping and conservation of rice germplasm.

Keywords


Genetic Diversity, ISSR Markers, Landraces, Oryza sativa, Oryza rufipogon.

References





DOI: https://doi.org/10.18520/cs%2Fv111%2Fi10%2F1675-1679