Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.)

DNA Research

Volumn 9, Issue 6, 2002, Pages 199-207

  McCouch, Susan R ^a,i   Teytelman, Leonid ^b   Xu, Yunbi ^c   Lobos, Katarzyna B ^c   Clare, Karen ^c   Walton, Mark ^c   Fu, Binying ^d   Maghirang, Reycel ^d   Li, Zhikang ^d   Xing, Yongzhong ^e   Zhang, Qifa ^e   Kono, Izumi ^f   Yano, Masahiro ^g   Fjellstrom, Robert ^h   DeClerck, Genevieve ^a   Schneider, David ^a   Cartinhour, Samuel ^a   Ware, Doreen ^b   Stein, Lincoln ^b  

^a Department of Population Medicine and Diagnostic Sciences   (United States)

^b Watson School of Biological Sciences   (United States)

^c RiceTec Inc   (United States)

^d INTERNATIONAL RICE RESEARCH INSTITUTE   (Philippines)

^e HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^f Soc Tech Innov Agric Forest/F   (Japan)

^g NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^h AGRICULTURAL RESEARCH SERVICE   (United States)

ⁱ 240 Emerson Hall ^*  (United States)

Author keywords

Electronic PCR (e PCR); Rice (Oryza sativa L.); Simple sequence repeats (SSR)

Indexed keywords

GENOMIC DNA;

ARTICLE; DNA FLANKING REGION; GENE MAPPING; GENETIC POLYMORPHISM; GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT; POLYMERASE CHAIN REACTION; RICE; SIMPLE SEQUENCE REPEAT; UNINDEXED SEQUENCE;

CHROMOSOME MAPPING; CHROMOSOMES, PLANT; DNA PRIMERS; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; GENES, PLANT; GENETIC MARKERS; ORYZA SATIVA; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; REPETITIVE SEQUENCES, NUCLEIC ACID;

ORYZA SATIVA;

EID: 0036928793     PISSN: 13402838     EISSN: None     Source Type: Journal    
DOI: 10.1093/dnares/9.6.199     Document Type: Article

References (28)

1. Goff, S., Ricke, D., Lan, T-H. et al. 2002, A draft sequence of the rice genome (Oryza sativa L. spp. Japonica), Science, 296, 92-100.
2. Yu, J., Hu, S., Wang, J. et al. 2002, A draft sequence of the rice genome (Oryza sativa L. ssp. Indica), Science, 296, 79-92.
3. Causse, M., Fulton, T. M., Cho, Y. G. et al. 1994, Saturated molecular map of the rice genome based on an interspecific backcross population, Genetics, 138, 1251-1274.
4. Harushima, Y., Jano, M., Shomura, A. et al. 1998, A high-density rice genetic linkage map with 2275 markers using a single F2 population, Genetics, 148, 479-494.
5. Wu, J., Maehara, T., Shimokawa, T. et al. 2002, A Comprehensive Rice Transcript Map Containing 6591 Expressed Sequence Tag Sites, Plant Cell, 14, 525-535.
6. Akagi, H., Yokozeki, Y., Inagaki, A. et al. 1996, Microsatellite DNA markers for rice chromosomes, Theor. Appl. Genet., 94, 61-67.
7. Chen, X., Temnykh, S., Xu, Y. et al. 1997, Development of a microsatellite framework map providing genomewide coverage in rice (Oryza sativa L.), Theor. Appl. Genet., 95, 553-567.
8. Temnykh, S., Park, W. D., Ayres, N. et al. 2000, Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.), Theor. Appl. Genet., 100, 697-712.
9. Temnykh, S., DeClerck, G., Lukashova, A. et al. 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.
10. Coburn, J., Temnykh, S., Paul, E., and McCouch, S. R. 2002, Design and Application of Microsatellite Marker Panels for Semi-automated Genotyping of Rice (Oryza sativa L.), Crop Sci., 42, 2092-2099.
11. Cregan, P. B., Jarvik, T., Bush, A. L. et al. 1999, An integrated genetic linkage map of the soybean genome, Crop Sci., 39, 1464-1490.
12. McCouch, S. R., Chen, X., and Panaud, O. 1997, Microsatellite mapping and applications of SSLP's in rice genetics and breeding, Plant Mol. Biol., 35, 89-99.
13. Ponce, M. R., Robles, P., and Micol, J. L. 1999, High-throughput genetic mapping in Arabidopsis thaliana, Mol. Gen. Genet., 261, 408-415.
14. Sharopova, N., McMullen, M. D., Schultz, L. et al. 2002, Development and mapping of SSR markers for maize, Plant Mol. Biol., 48, 463-481.
15. Chen, X., Cho, Y., and McCouch, S. R. 2002, Sequence divergence of rice microsatellites in Oryza and other plant species, Mol. Gen. Genet., DOI.1007/s00438-002-0739-5.
16. Harrington, S. 2000, A survey of genetic diversity of eight AA genome species of Oryza using microsatellite markers, MS Thesis, Cornell University, Ithaca, New York.
17. Ni, J., Colowit, P. M., and Mackill, D. J. 2002, Evaluation of genetic diversity in rice subspecies using microsatellite markers, Crop Sci., 42, 601-607.
18. Panaud, O., Chen, X., and McCouch, S. R. 1996, Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.), Mol. Gen. Genet., 252, 597-607.
19. Yang, G. P., Saghai Maroof, M. A., Xu, C. G. et al. 1994, Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice, Mol. Gen. Genet., 245, 187-194.
20. Ware, D., Jaiswal, P., Ni, J. et al. 2002, Gramene: A Resource for Comparative Grass Genomics, Nucl. Acids. Res., 30, 103-105.
21. Schuler, G. D. 1997, Sequence Mapping by Electronic PCR, Genome Res., 7, 541-550.
22. Schuler, G. D. 1998, Electronic PCR: bridging the gap between genome mapping and genome sequencing [Focus], Trends in Biotechnology, 16, 456-459.
23. Cho, Y. G., Ishii, T., Temnykh, S. et al. 2000, Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.), Theor. Appl. Genet., 100, 713-722.
24. Morgante, M., Hanafey, M., and Powell, W. 2002, Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes, Nat. Genet., 30, 174-200.
25. Salse, J., Piegu, B., Cooke, R. et al. 2002, Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequencing project, Nucl. Acids Res., 30, 2318-2328.
26. Casa, A. M., Nrouwer, C., Nagel, A. et al. 2001, The MITE family heartbreaker (Hbr) molecular markers in maize, Proc. Natl. Acad. Sci. USA, 97, 10083-10089.
27. Van den Broeck, D., Maes, T., Sauer, M. et al. 1998, Transposon display identifies individual transposable elements in high copy number lines, Plant J., 13, 121-129.
28. Waugh, R., McLean, K., Flavell, A. J. et al. 1997, Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphism (S-SAP), Mol. Gen. Genet., 253, 687-694.