Development of genome-wide DNA polymorphism database for map-based cloning of rice genes

Plant Physiology

Volumn 135, Issue 3, 2004, Pages 1198-1205

  Shen, Ying Jia ^a   Jiang, Hua ^a   Jin, Jian Peng ^a   Zhang, Zai Bao ^a   Xi, Biao ^b   He, You Yu ^c   Wang, Guan ^a   Wang, Chen ^a   Qian, Lily ^d   Li, Xiang ^a   Yu, Qing Bo ^a   Liu, Hui Juan ^a   Chen, De Hui ^a   Gao, Jian Hua ^a   Huang, Hai ^e   Shi, Tie Liu ^c   Yang, Zhong Nan ^e  

^a SHANGHAI NORMAL UNIVERSITY   (China)

^b ZHEJIANG UNIVERSITY   (China)

^c Chinese Academy of Sciences   (China)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOMES; CLONING; CULTIVATION; DATABASE SYSTEMS; DNA;

MAP-BASED CLONING; POLYMORPHISM DATABASES;

GENES;

EMBRYOPHYTA; ILEX COOKII; INSERTION SEQUENCES; JAPONICA; ORYZA SATIVA;

EID: 3543034045     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.103.038463     Document Type: Article

References (37)

1. Albar L, Ndjiondjop MN, Esshak Z, Berger A, Pinel A, Jones M, Fargette D, Ghesquiere A (2003) Fine genetic mapping of a gene required for rice yellow mottle virus cell-to-cell movement. Theor Appl Genet 107: 371-378
2. Ashikari M, Wu J, Yano M, Sasaki T, Yoshimura A (1999) Rice gibberellin-insensitive dwarf mutant gene Dwarf 1 encodes the α-subunit of GTP-binding protein. Proc Natl Acad Sci USA 96: 10284-10289
3. Blair MW, Garris AJ, Iyer AS, Chapman B, Kresovich S, McCouch SR (2003) High resolution genetic mapping and candidate gene identification at the xa5 locus for bacterial blight resistance in rice (Oryza sativa L.). Theor Appl Genet 107: 62-73
4. Causse MA, Fulton TM, Cho YG, Ahn SN, Chunwongse J, Wu K, Xiao J, Yu Z, Ronald PC, Harrington SE, et al (1994) Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics 138: 1251-1274
5. Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR (1997) Development of a microsatellite framework map providing genome wide coverage in rice (Oryza sativa L.). Theor Appl Genet 95: 553-567
6. Delcher AL, Phillippy A, Carlton J, Salzberg SL (2002) Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res 30: 2478-2483
7. Feng Q, Zhang Y, Hao P, Wang S, Fu G, Huang Y, Li Y, Zhu J, Liu Y, Hu X, et al (2002) Sequence and analysis of rice chromosome 4. Nature 420: 316-320
8. Han B, Xue YB (2003) Genome-wide intraspecific DNA-sequence variations in rice. Curr Opin Plant Biol 6: 134-138
9. Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A, et al (1998) A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148: 479-494
10. Jander G, Norris SR, Rounsley SD, Bush DF, Levin IM, Last RL (2002) Arabidopsis map-based cloning in the post-genome era. Plant Physiol 129: 440-450
11. Joshi SP, Bhave SG, Chowdari KV, Apte GS, Dhonukshe BL, Lalitha K, Ranjekar PK, Gupta VS (2001) Use of DNA markers in prediction of hybrid performance and heterosis for a three-line hybrid system in rice. Biochem Genet 39: 179-200
12. Kojima S, Takahashi Y, Kobayashi Y, Monna L, Sasaki T, Araki T, Yano M (2002) Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions. Plant Cell Physiol 43: 1096-1105
13. Kurata N, Nagamura Y, Yamamoto K, Harushima Y, Sue N, Wu J, Antonio BA, Shomura A, Shimizu T, Lin SY, et al (1994) A 300 kilobase interval genetic map of rice including 883 expressed sequences. Nat Genet 8: 365-372
14. Li X, Qian Q, Fu Z, Wang Y, Xiong G, Zeng D, Wang X, Liu X, Teng S, Hiroshi F, et al (2003) Control of tillering in rice. Nature 422: 618-621
15. Lukowitz W, Gillmor CS, Scheible WR (2000) Positional cloning in Arabidopsis. Why it feels good to have a genome initiative working for you. Plant Physiol 123: 795-805
16. McCouch SR, Chen X, Panaud O, Temnykh S, Xu Y, Cho YG, Huang N, Ishii T, Blair M (1997) Microsatellite marker development, mapping and applications in rice genetics and breeding. Plant Mol Biol 35: 89-99
17. McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, et al (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 9: 199-207
18. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8: 4321-4325
19. Nagaraju J, Kathirvel M, Kumar RR, Siddiq EA, Hasnain SE (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 USA 99: 5836-5841
20. Nasu S, Suzuki J, Ohta R, Hasegawa K, Yui R, Kitazawa N, Monna L, Minobe Y (2002) Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufigogon) and establishment of SNP markers. DNA Res 9: 163-171
21. Ni JJ, Colowit MP, Mackill DJ (2002) Evaluation of genetic diversity in rice subspecies using microsatellite markers. Crop Sci 42: 601-607
22. The Rice Chromosome 10 Sequencing Consortium (2003) In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300: 1566-1569
23. Rice P, Longden I, Bleasby A (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16: 276-277
24. Sambrook J, Russell D (2001) Molecular Cloning: A Laboratory Manual, Ed 3. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
25. Saito A, Yano M, Kishimoto N, Nakagahra M, Yoshimura A, Saito K, Kuhara S, Ukai Y, Kawase M, Nagamine T, et al (1991) Linkage map of restriction fragment length polymorphism loci in rice. Jpn J Breed 41: 665-670
26. Sasaki T, Burr B (2000) International rice genome sequencing project: the effort to completely sequence the rice genome. Curr Opin Plant Biol 3: 138-141
27. Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, Katayose Y, Wu J, Niimura Y, Cheng Z, Nagamura Y, et al (2002) The genome sequence and structure of rice chromosome 1. Nature 420: 312-316
28. Takahashi Y, Shomura A, Sasaki T, Yano M (2001) Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the alpha subunit of protein kinase CK2. Proc Natl Acad Sci USA 98: 7922-7927
29. Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (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
30. Temnykh S, Park WD, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch SR (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100: 697-712
31. Wang YG, Xing QH, Deng QY, Liang FS, Yuan LP, Weng ML, Wang B (2003) Fine mapping of the rice thermo-sensitive genic male-sterile gene tms5. Theor Appl Genet 107: 917-921
32. Wu J, Maehara T, Shimokawa T, Yamamoto S, Harada C, Takazaki Y, Ono N, Mukai Y, Koike K, Yazaki J, et al (2002) A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell 14: 525-535
33. Yamanouchi U, Yano M, Lin H, Ashikari M, Yamada K (2002) A rice spotted leaf gene, Spl7, encodes a heat stress transcription factor protein. Proc Natl Acad Sci USA 99: 7530-7535
34. Yang H, Ren X, Weng Q, Zhu L, He G (2002) Molecular mapping and genetic analysis of a rice brown planthopper (Nilaparvata lugens Stal) resistance gene. Hereditas 136: 39-43
35. Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, et al (2000) Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12: 2473-2484
36. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. Indica). Science 296: 79-92
37. Zhao Q, Zhang Y, Cheng Z, Chen M, Wang S, Feng Q, Huang Y, Li Y, Tang Y, Zhou B, et al (2002) A fine physical map of the rice chromosome 4. Genome Res 12: 817-823