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Genomics of Rice: Markers as a Tool for Breeding

  • Y. Kishima
  • K. Onishi
  • Y. Sano
Part of the Biotechnology in Agriculture and Forestry book series (AGRICULTURE, volume 55)

Keywords

Amplify Fragment Length Polymorphism Bacterial Artificial Chromosome Rice Genome Amplify Fragment Length Polymorphism Marker Amplify Fragment Length Polymorphism Analysis 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. Aggarwal RK, Brar DS, Nandi S, Huang N, Khush GS (1999) Phylogenetic relationships among Oryza species revealed by AFLP markers. Theor Appl Genet 98:1320–1328CrossRefGoogle Scholar
  2. Akagi H, Yokozeki Y, Inagaki A, Fujimura T (1996) Microsatellite DNA markers for rice chromosomes. Theor Appl Genet 93:1071–1077CrossRefGoogle Scholar
  3. Bostein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphism. Am J Hum Genet 32:314–331PubMedGoogle Scholar
  4. Bureau TE, Wessler SR (1994a) Stowaway: a new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants. Plant Cell 6:907–916CrossRefPubMedGoogle Scholar
  5. Bureau TE, Wessler SR (1994b) Mobile inverted-repeat elements of the Tourist family are associated with the genes of many cereal grasses. Proc Natl Acad Sci USA 91:1411–1145PubMedGoogle Scholar
  6. Bureau TE, Ronald PC, Wessler SR (1996) A computer-based systematic survey reveals the predominance of small inverted-repeat elements in wild-type rice genes. Proc Natl Acad Sci USA 93:8524–8529PubMedGoogle Scholar
  7. Casa AM, Brouwer C, Nagel A, Wang L, Zhang Q, Kresovich S, Wessler SR (2000) The MITE family heartbreaker (Hbr): molecular markers in maize. Proc Natl Acad Sci USA 97:10083–10089CrossRefPubMedGoogle Scholar
  8. Causse MA, Fulton TM, Cho YG, Ahn SN, Chunwongse J, Wu KS, Xiao JH, Yu ZH, Ronald PC, Harrinton SE, Second G, McCouch SR, Tanksley SD (1994) Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics 138:1251–1274PubMedGoogle Scholar
  9. 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 95:553–567CrossRefGoogle Scholar
  10. Feschotte C, Jiang N, Wessler SR (2002) Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3:329–341PubMedGoogle Scholar
  11. Goff SA, Ricke D, Lan TH et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100CrossRefPubMedGoogle Scholar
  12. Harushima Y, Yano M, Shomura P, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A, Kajiya H, Huang N, Yamamoto K, Nagamura Y, Kurata N, Khush GS, Sasaki T (1998) A high-density rice genetic linkage map with 2275 markers using a single F-2 population. Genetics 148:479–494PubMedGoogle Scholar
  13. Hirochika H (2001) Contribution of the Tos17 retrotransposon to rice functional genomics. Curr Opin Plant Biol 4:118–122CrossRefPubMedGoogle Scholar
  14. Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H, Kanda M (1996) Retrotransposons of rice involved in mutations induced by tissue culture. Proc Natl Acad USA 93:7783–7788CrossRefGoogle Scholar
  15. Ishikawa R, Harada T, Niizeki M, Saito K (1992) Reconstruction of linkage map with isozyme, morphological and physiological markers in rice chromosome-12. Jpn J Breeding 42:235–244Google Scholar
  16. Ito T, Motohashi R, Kuromori T, Mizukado S, Sakurai T, Kanahara H, Seki M, Shinozaki K (2002) A new resource of locally transposed dissociation elements for screening geneknockout lines in silico on the Arabidopsis genome(1)[(w)]. Plant Physiol 129:1695–1699PubMedGoogle Scholar
  17. Jiang N, Bao Z, Zhang X, Hirochika H, Eddy SR, McCouch S, Wessler SR (2003) An active DNA transposon family in rice. Nature 421:163–167CrossRefPubMedGoogle Scholar
  18. Kikuchi K, Terauchi K, Wada M, Hirano H-Y (2003) The plant MITE mPing is mobilized in anther culture. Nature 421:167–170PubMedGoogle Scholar
  19. Kumar LS (1999) DNA markers in plant improvement: An overview. Biotechnology Advances 17:143–182PubMedGoogle Scholar
  20. Kurata N, Nagamura Y, Yamamoto K et al. (1994) A 300 kilobase interval genetic-map of rice including 883 expressed sequences. Nat Genet 8:365–372CrossRefPubMedGoogle Scholar
  21. Lisch DR, Freeling M, Langham RJ, Choy MY (2001) Mutator transposase is widespread in the grasses. Plant Physiol 125:1293–1303CrossRefPubMedGoogle Scholar
  22. Mackill DJ, Ni J (2001) Molecular mapping and marker-assisted selection for major-gene traits in rice. In: Khush GS, Brar DS, Hardy B (eds) Rice genetics IV. International Rice Research Institute, Science Publ, Philippines, pp 137–151Google Scholar
  23. Maheswaran M, Subudhi PK, Nandi S, Xu JC, Parco A, Yang DC, Huang N (1997) Polymorphism, distribution, and segregation of AFLP markers in a doubled haploid rice population. Theor Appl Genet 94:39–45CrossRefGoogle Scholar
  24. Mao L, Wood TC, Yu YS, Budiman MA, Tomkins J, Woo SS, Sasinowski M, Presting G, Frisch D, Goff S, Dean RA, Wing RA (2000) Rice transposable elements: a survey of 73,000 sequence-tagged-connectors. Genome Res 10:982–990PubMedGoogle Scholar
  25. McCouch SR, Kochert G, Yu ZH, Wang ZY, Khush GS, Coffman WR, Tanksley SD (1988) Molecular mapping of rice chromosome. Theor Appl Genet 76:815–829CrossRefGoogle Scholar
  26. McCouch SR, Chen XL, Panaud O, Temnykh S, Xu YB, Cho YG, Huang N, Ishii T, Blair M (1997) Microsatellite marker development, mapping and applications in rice genetics and breeding. Plant Mol Biol 35:89–99CrossRefPubMedGoogle Scholar
  27. McCouch SR, Temnykh S, Lukashova A, Coburn J, DeClerck G, Cartinhour S, Harrington S, Thomson M, Septiningsih E, Semon M, Moncada P (2001) Microsatellite markers in rice: abundance, diversity, and applications. In: Khush GS, Brar DS, Hardy B (eds) Rice genetics IV. International Rice Research Institute, Science Publ, Philippines, pp 117–135Google Scholar
  28. Nagano H, Kunii M, Azuma T, Kishima Y, Sano Y (2002) Characterization of the repetitive sequences in a 200-kb region around the rice waxy locus: diversity of transposable elements and presence of veiled repetitive sequences. Genes Genet Syst 77:69–79CrossRefPubMedGoogle Scholar
  29. Nagao S, Takahashi M-E (1963) Trial construction of twelve linkage groups in Japanese rice. J Fac Agric Hokkaido Univ 53:72–130Google Scholar
  30. Nakazaki T, Okumoto Y, Horibata A, Yamahira S, Teraishi M, Nishida H, Inoue H, Tanisaka T (2003) Mobilization of a transposon in the rice genome. Nature 421:170–172CrossRefPubMedGoogle Scholar
  31. Panaud O, Chen X, McCouch SR (1995) Frequency of microsatellite sequences in rice (Oryza sativa L.). Genome 38:1170–1176PubMedGoogle Scholar
  32. Panaud O, Chen X, McCouch SR (1996) Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet 252:597–607PubMedGoogle Scholar
  33. Parinov S, Sevugan M, Ye D, Yang WC, Kumaran M, Sundaresan V (1999) Analysis of flanking sequences from Dissociation insertion lines: a database for reverse genetics in Arabidopsis. Plant Cell 11:2263–2270CrossRefPubMedGoogle Scholar
  34. Paterson AH (1995) Molecular dissection of quantitative traits-progress and prospects. Genome Res 5:321–333PubMedGoogle Scholar
  35. Putterill J, Robson F, Lee K, Simon R, Coupland G (1995) The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factors. Cell 80:847–857CrossRefPubMedGoogle Scholar
  36. Saito A, Yano M, Kishimoto N et al. (1991) Linkage map of restriction-fragment-lengthpolymorphism loci in rice. Jpn J Breed 41:665–670Google Scholar
  37. Smith D, Yanai Y, Liu YG, Ishiguro S, Okada K, Shibata D, Whittier RF, Fedoroff NV (1996) Characterization and mapping of Ds-GUS-T-DNA lines for targeted insertional mutagenesis. Plant J 10:721–732CrossRefPubMedGoogle Scholar
  38. Takagi K, Nagano H, Kishima Y, Sano Y (2003) MITE-transposon display efficiently detects polymorphisms among the Oryza AA-genome species. Breed Sci 53:125–132CrossRefGoogle Scholar
  39. Tanksley SD (1993) Mapping polygenes. Annu Rev Genet 27:205–233CrossRefPubMedGoogle Scholar
  40. 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 100:697–712CrossRefGoogle Scholar
  41. Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis ofmicrosatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452CrossRefPubMedGoogle Scholar
  42. The Arabidopsis Genome Initiative (2000) Analysis of genome sequence of flowering plant Arabidopsis thaliana. Nature 408:796–815Google Scholar
  43. Tissier AF, Marillonnet S, Klimyuk V, Patel K, Torres MA, Murphy G, Jones JDG (1999) Multiple independent defective Suppressor-mutator transposon insertions in Arabidopsis: a tool for functional genomics. Plant Cell 11:1841–1852CrossRefPubMedGoogle Scholar
  44. Turcotte K, Srinivasan S, Bureau T (2001) Survey of transposable elements from rice genomic sequences. Plant J 25:169–179CrossRefPubMedGoogle Scholar
  45. Vos P, Hogers R, Bleeker M et al. (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414PubMedGoogle Scholar
  46. Weber JL, May PE (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain-reaction. Am J Hum Genet 44:388–396PubMedGoogle Scholar
  47. Wessler SR, Bureau TE, White SE (1995) LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. Curr Opin Genet Dev 5:814–821CrossRefPubMedGoogle Scholar
  48. Williams JG, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535PubMedGoogle Scholar
  49. Wu KS, Tanksley SD (1993) Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet 241:225–235CrossRefPubMedGoogle Scholar
  50. Yamazaki M, Tsugawa H, Miyao A, Yano M, Wu J, Yamamoto S, Matsumoto T, Sasaki T, Hirochika H (2001) The rice retrotransposon Tos17 prefers low-copy-number sequences as integration targets. Mol Genet Genom 265:336–344CrossRefGoogle Scholar
  51. Yano M (2001) Genetic and molecular dissection of naturally occurring variation. Curr Opin Plant Biol 4:130–135PubMedGoogle Scholar
  52. Yano M, Sasaki T (1997) Genetic and molecular dissection of quantitative traits in rice. Plant Mol Biol 35:145–153CrossRefPubMedGoogle Scholar
  53. Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, 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 12:2473–2483CrossRefPubMedGoogle Scholar
  54. Yu J, Hu SN, Wang J et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92CrossRefPubMedGoogle Scholar
  55. Zhang QF, Maroof MAS, Lu TY, Shen BZ (1992) Genetic diversity and differentiation of Indica and Japonica rice detected by RFLP. Theor Appl Genet 83:495–499Google Scholar
  56. Zhu J, Gale MD, Quarrie S, Jackson MT, Bryan GJ (1998) AFLP markers for the study of rice biodiversity. Theor Appl Genet 96:602–611CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Y. Kishima
  • K. Onishi
  • Y. Sano
    • 1
  1. 1.Laboratory of Plant Breeding, Graduate School of AgricultureHokkaido UniversitySapporoJapan

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