Potentiality of evenly distributed hypervariable microsatellite markers in marker-assisted breeding of rice

Plant Breeding

Volumn 130, Issue 3, 2011, Pages 314-320

  Narshimulu, Gonela ^a   Jamaloddin, Mohammed ^a   Vemireddy, Lakshminarayana R ^a   Anuradha, Ghnata ^a   Siddiq, Eea ^a  

^a ACHARYA N G RANGA AGRICULTURAL UNIVERSITY   (India)

Author keywords

Diversity; Hypervariable microsatellite markers; Marker assisted breeding; Rice

Indexed keywords

EID: 79957885094     PISSN: 01799541     EISSN: 14390523     Source Type: Journal    
DOI: 10.1111/j.1439-0523.2010.01834.x     Document Type: Article

References (32)

1. Akagi, H., Y. Yokozeki, A. Inagaki, K. Mori, and T. Fujimura, 2001: Micron, a microsatellite-targeting transposable element in the rice genome. Mol. Genet. Genomics. 266, 471-480.
2. Archak, S., V. Lakshminarayanareddy, and J. Nagaraju, 2007: High-throughput multiplex microsatellite marker assay for detection and quantification of adulteration in Basmati rice (Oryza sativa). Electrophoresis. 28, 2396-2405.
3. Botstein, D., R. L. White, M. Skolnick, and R. W. Davis, 1980: Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32, 314-331.
4. Chen, J. Q., X. P. Meng, Y. Zhang, M. Xia, and X. P. Wang, 2008: Over-expression of OsDREB genes lead to enhanced drought tolerance in rice. Biotechnol. Lett. 30, 2191-2198.
5. Cho, Y. G., T. Ishii, S. Temnykh, X. Chen, L. Lipovich, W. D. Ark, N. Ayres, S. Cartinhour, and S. R. McCouch, 2000: Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor. Appl. Genet. 100, 713-722.
6. Dai, L. Y., X. L. Liu, Y. H. Xiao, and G. L. Wang, 2007: Recent advances in cloning and characterization of disease resistance genes in rice. J. Integr. Plant Biol. 49, 112-119.
7. Garris, A. J., T. H. Tai, J. Coburn, S. Kresovich, and S. R. McCouch, 2005: Genetic structure and diversity in Oryza sativa L. Genetics 169, 1631-1638.
8. Glaszman, J.C., 1987: Isozymes and classification of Asian rice varieties. Theor. Appl. Genet. 74, 21-30.
9. Grover, A., V. Aishwarya, and P. C. Sharma, 2007: Biased distribution of microsatellite motifs in the rice genome. Mol Genet Genomics 277, 469-480.
10. Harrington, S., 2000: A Survey of Genetic Diversity of Eight AA Genome Species of Oryza using Microsatellite Markers. MS thesis. Cornell University, Ithaca, NY.
11. Hospital, F., C. Chevalet, and P. Mulsant, 1992: Using markers in gene introgression breeding programs. Genetics 132, 1199-1210.
12. IRGSP, 2005: The map-based sequence of the rice genome. Nature 436, 793-800.
13. Jena, K. K., and D. J. Mackill, 2008: Molecular markers and their use in marker-assisted selection in rice. Crop Sci. 48, 1266-1276.
14. Kurata, N. Y., Nagamura, K. Yamamoto, Y. Harushima, N. Sue, J. Wu, B. A. Antonio, A. Shomura, T. Shimizu, S-Y. Lin, T. Inoue, A. Fukuda, T. Shimano, Y. Kuboki, T. Toyama, Y. Miyamoto, T. Kirihara, K. Hayasaka, A. Miyao, L. Monna, H. S. Zhong, Y. Tamura, Z-X Wang, T. Momma, Y. Umehara, M. Yano, T. Sasaki and Y. Minobe, 1994: A 300 kilobase interval genetic map of rice including 883 expressed sequences. Nat. Genet. 8, 365-372.
15. Lorieux, M., M. N. Ndjiondjop, and A. Ghesquière, 2000: A first interspecific Oryza sativa x O. glaberrima microsatellite-based genetic linkage map. Theor. Appl. Genet. 100, 593-601.
16. 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. Dclerck, D. Schneider, S. Cartinhour, D. Ware, and L. Stein, 2002: Development and MAPPING of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res. 9, 199-207.
17. Murray, M. G., and W. F. Thompson, 1980: Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 8, 4321-4325.
18. Nagaraju, J., M. Kathirvel, R. R. Kumar, E. A. Siddiq, and S. E. Hasnain, 2002: Genetic analysis of traditional and evolved Basmati and non-Basmati rice varieties by using fluorescence based ISSR-PCR and SSR markers. Proc. Natl. Acad. Sci. U.S.A. 99, 5836-5841.
19. Orjuela, J., A. Garavito, M. Bouniol, J. D. Arbelaez, L. Moreno, J. Kimball, G. Wilson, J. F. Rami, J. Tohme, S. R. McCouch, and M. Lorieux, 2010: A universal core genetic map for rice. Theor. Appl. Genet. 120, 563-572.
20. Perrier, X., A. Flori, and F. Bonnot, 2003: Data analysis methods. In: P. Hamon, M. Seguin, X. Perrier, and J. C. Glaszmann (eds), Genetic Diversity of Cultivated Tropical Plants, 43-76. Science Publishers, Montpellier.
21. Pradeep, M., N. Sarla, V. R. Laxminarayana, and E. A. Siddiq, 2005: Identification and mapping of yield and yield related QTLs from an Indian accession of Oryza rufipogon. BMC Genet. 6, 33.
22. Prigge, V., A. E. Melchinger, B. S. Dhillon, and M. Frisch, 2009: Efficiency gain of marker-assisted backcrossing by sequentially increasing marker densities over generations. Theor. Appl. Genet. 119, 23-32.
23. Rajendrakumar, P., A. K. Biswal, K. Sakthivel, M. S. Madhav, C. N. Neeraja, S. M. Balachandran, K. Srinivasarao, P. Natarajkumar, Y. Hari, K. Sujatha, and R. M. Sundaram, 2009: Development and validation of class I SSR markers targeting (GATA)n repeat motifs in rice. Euphytica. 169, 263-271.
24. Servin, B., and F. Hospital, 2002: Optimal positioning of markers to control genetic background in marker-assisted backcrossing. J. Hered. 93, 214-217.
25. Singh, H., K. Rupesh, D. A. Singh, A. K. Singh, K. Gaikwad, T. R. Sharma, T. Mohapatra, and N. K. Singh, 2009: Highly variable SSR markers suitable for rice genotyping using agarose gels. Mol. Breeding 2, 359-364.
26. Sundaram, R. M., M. R. Vishnupriya, S. K. Biradar, G. S. Laha, G. A. Reddy, N. S. Rani, N. P. Sarma, and R. V. Sonti, 2008: Marker assisted introgression of bacterial blight resistance in Samba Mahsuri, an elite indica rice variety. Euphytica 160, 411-422.
27. Temnykh, S., W. D. Park, N. Ayres, S. Cartinhour, N. Hauck, L. Lipovich, Y. G. Cho, T. Ishii, and S. R. McCouch, 2000: Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor. Appl. Genet. 100, 697-712.
28. Temnykh, S., G. DeClerck, A. Lukashova, L. Lipovich, S. Cartinhour, and S. R. McCouch, 2001: Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 11, 1441-1452.
29. Vemireddy, L. R., S. Archak, and J. Nagaraju, 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.
30. Visscher, P., C. Haley, and R. Thompson, 1996: Marker-assisted introgression in backcross breeding programs. Genetics 144, 1923-1932.
31. Yashitola, J., T. Thirumurugan, R. M. Sundaram, M. K. Naseerullah, M. S. Ramesha, N. P. Sarma, and R. V. Sonti, 2002: Assessment of purity of hybrids using microsatellite and STS markers. Crop Sci. 42, 1369-1373.
32. Zhang, Z. H., Y. J. Deng, J. Tan, S. N. Hu, J. Yu, and Q. Z. Xue, 2007: A genome-wide microsatellite polymorphism database for the indica and japonica rice. DNA Res. 14, 37-45.