Conversion of AFLP markers to sequence-specific markers for closely related lines in rice by use of the rice genome sequence

Molecular Breeding

Volumn 14, Issue 3, 2004, Pages 283-292

  Shirasawa, Kenta ^a   Kishitani, Sachie ^a   Nishio, Takeshi ^a  

^a TOHOKU UNIVERSITY   (Japan)

Author keywords

CAPS; DNA marker; Japonica cultivar; Oryza sativa; PCR RF SSCP; SNP

Indexed keywords

DNA; DNA SEQUENCES; NUCLEOTIDES; POLYMERASE CHAIN REACTION; POLYMORPHISM;

AFLP MARKERS; CAPS; DNA FRAGMENT; DNA MARKERS; JAPONICUM CULTIVAR; KOSHIHIKARI; ORYZA SATIVA; PCR-RF-SSCP; RICE GENOMES; SNP;

GENES;

JAPONICA; ORYZA SATIVA;

EID: 20844462637     PISSN: 13803743     EISSN: None     Source Type: Journal    
DOI: 10.1023/B:MOLB.0000047791.94870.40     Document Type: Article

References (26)

1. Arabidopsis Genome Initiative 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
2. Bensch S., Akesson S. and Irwin D.E. 2002. The use of AFLP to find an informative SNP: genetic differences across a migratory divide in willow warblers. Mol. Ecol. 11: 2359-2366.
3. Brugmans B., van der Hulst R.G.M., Visser R.G.F., Lindhout P. and van Eck H.J. 2003. A new and versatile method for the successful conversion of AFLP™ markers into simple single locus marker. Nucleic Acid Res. 31: e55.
4. Evans K.M. and James C.M. 2003. Identification of SCAR markers linked to Pl-w mildew resistance in apple. Theor. Appl. Genet. 106: 1178-1183.
5. Goff S., Ricke D., Land T.- H., Presting G., Wang R. et al. 2002. A draft sequence of three rice genome Oryza sativa L. ssp. japonica. Science 296: 92-100.
6. 2 population. Genetics 148: 479- 494.
7. Kikuchi K., Terauchi K., Wada M. and Hirano H. 2003. The plant MITE mPing is mobilized in anther culture. Nature 42: 167-169.
8. Konieczny A. and Ausubel F.M. 1993. A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J. 4: 403-410.
9. Kono I., Takeuchi Y., Shimano T., Sasaki T. and Yano M. 2000. Comparison of efficiency of detecting polymorphism among japonica varieties in rice using RFLP, RAPD, AFLP, and SSR markers. Breeding Research 2: 197-203.
10. McCouch S.R., Teytelman L., Xu Y., Lobos K.B., Clare K., Walton M., Fu B., Maghirang R., Li Z., Xing Y., Zhang Q., Kono I., Yano M., Fjellstrom R., DeClerck G., Schneider D., Cartinhour S., Ware D. and Stein L. 2002. Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res. 9: 199-207.
11. Murry M.G. and Thompson W.F. 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acid Res. 8: 4321-4325.
12. Neff M.M., Neff J.D., Chory J. and Pepper A.E. 1998. dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics. Plant J. 14: 387-392.
13. Parker G.D. and Langridge P. 2000. Development of a STS marker linked to a major locus controlling flour colour in wheat (Triticum aestivum L.). Mol. Breed. 6: 169-174.
14. Rozen S. and Skaletsky H. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 132: 365-386.
15. Sardesai N., Kumar A., Rajyashri R., Nair S. and Mohan M. 2002. Identification and mapping of an AFLP marker linked to Gm7, a gall midge resistance gene and its conversion to a SCAR marker for its utility in marker aided selection in rice. Theor. Appl. Genet. 105: 691-698.
16. Sato Y. and Nishio T. 2002. Efficient detection of DNA polymorphism in cabbage and rice cultivars by PCR-RF-SSCP PRS. Plant Cell Rep. 21: 276-281.
17. Shan X., Blake T.K. and Talbert L.E. 1999. Conversion of AFLP markers to sequence-specific PCR markers in barley and wheat. Theor. Appl. Genet. 98: 1072-1078.
18. Song W.- Y., Wang G.- L., Chen L.- L., Kim H.- S., Pi L.- Y., Holsten T., Gardner J., Wang B., Zhai W.- X., Zhu L.- H., Fauquet C. and Ronald P. 1995. A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 270: 1804-1806.
19. Stracke S., Schilling A.G., Forster J., Weiss C., Glass C., Miedaner T. and Geiger H.H. 2003. Development of PCR-based markers linked to dominant genes for male-fertility restoration in Pampa CMS of rye (Secale cereale L.). Theor. Appl. Genet. 106: 1184-1190.
20. Takeuchi Y., Hayasaka H., Chiba B., Tanaka I., Shimano T., Yamagishi M., Nagano K., Sasaki T. and Yano M. 2001. Mapping quantitative trait loci controlling cool-temperature tolerance at booting stage in temperate japonica rice. Breed. Sci. 51: 191-197.
21. von Stackelberg M., Lindemann S., Menke M., Riesselmann S. and Jacobsen H.J. 2003. Identification of AFLP and STS markers closely linked to the def locus in pea. Theor. Appl. Genet. 106: 1293-1299.
22. Vos P., Hoger R., Bleeker M., Reijans M., van de Lee T., Hornes M., Frijters A., Pot J., Peleman J., Kuiper M. and Zabeau M. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23: 4407-4414.
23. Wang Z.- X., Yano M., Yamanouchi Y., Iwamoto M., Monna L., Hayasaka H., Katayose Y. and Sasaki T. 1999. The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat class of plant disease resistance genes. Plant J. 19: 55-64.
24. Yano M., Katayose Y., Ashikari M., Yamanouchi U., Monna L., Fuse T., Baba T., Yamamoto K., Umehara Y., Nagamura Y. and Sasaki T. 2000. Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12: 2473-2483.
25. Yu J., Hu S., Wang J., Wong G.K.- S., Li S. et al. 2002. A draft sequence of thee rice genome Oryza sativa L. ssp. indica. Science 296: 79-91.
26. Zenbayashi K., Ashizawa T., Tani T. and Koizumi S. 2002. Mapping of the QTL quantitative trait locus conferring partial resistance to leaf blast in rice cultivar Chubu 32. Theor. Appl. Genet. 104: 547-552.