Skip to main content
Log in

Rice genome analysis to understand the rice plant as an assembly of genetic codes

  • Published:
Photosynthesis Research Aims and scope Submit manuscript

Abstract

Rice genome research is a recent topic in plant genomics. Because of its importance as the primary staple food for about half of the world's population, breeders, geneticists and molecular biologists in plant fields have strong interest in the resultant research. In this Minireview, results of rice genome research during the past 10 years and future prospects are presented.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  • Ahn S and Tanksley SD (1993) Comparative linkage maps of the rice and maize genome. Proc Natl Acad Sci 90 7980–7984

    Article  PubMed  CAS  Google Scholar 

  • Altschul SF, Gish W, Miller W, Meyers EW and Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403–410

    Article  PubMed  CAS  Google Scholar 

  • Altschul SF, Madden TL, Scaffer AA, Zhang J, Zhang Z, Miller W and Lipman DJ (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25: 3389–3402

    Article  PubMed  CAS  Google Scholar 

  • Botstein D, White RL, Skolnick M and Davis RW (1980) Construction of genetic linkage map using restriction fragment length polymorphisms. Am J Hum Genet 32: 314–331

    PubMed  CAS  Google Scholar 

  • Burge C and Karlin S (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol 268: 78–94 Causse MA, Fulton TM, Cho YG, Ahn SN, Chunwongse J, Wu K

    Article  PubMed  CAS  Google Scholar 

  • Xiao J, Yu Z, Ronald PC, Harrington SE, Second G, McCouch SR and Tanksley SD (1994) Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics 138: 1251–1274

    PubMed  Google Scholar 

  • Devos KM and Gale MD (1997) Comparative genetics in the grasses. Plant Mol Biol 35: 3–15

    Article  PubMed  CAS  Google Scholar 

  • Devos KM, Wang ZM, Beales J, Sasaki T and Gale MD (1998) Comparative genetic maps of foxtail millet (Setaria italica) and rice (Oryza sativa). Theor Appl Genet 96: 63–68

    Article  CAS  Google Scholar 

  • Drenkard E, Glazebrook J, Preuss D and Ausubel EM (1997) Use of cleaved amplified polymorphic sequences (CAPS) for genetic mapping and typing. In: Caetano-Anolles G and Gresshoff PM (eds) DNA Markers; Protocols, Applications and Overview, pp 187–197. Wiley-Liss, New York

    Google Scholar 

  • Gusella JF, Wexler NS, Conneally PM, Naylor SL, Anderson MA, Tanzi RE, Watkins PC, Ottina K, Wallace MR and Sakaguchi AV (1983) A polymorphic DNA marker genetically linked to Huntington's disease. Nature 306: 234–238

    Article  PubMed  CAS  Google Scholar 

  • Gordon D, Desmarais C and Green P (2001) Consed - a graphical tool for editing phrap assemblies. http://genome.Washington. edu/consed/consed.html

  • Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin S-Y, Antonio BA, Parco A, Kajiya H, Huang N, Yamamoto K, Nagamura Y, Kurata N, Khush GS and Sasaki T (1998) A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148: 479–494

    PubMed  CAS  Google Scholar 

  • Hiei Y, Ohta S, Komari T and Kumashiro T (1994) Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. Plant J 6: 271–282

    Article  PubMed  CAS  Google Scholar 

  • Hirochika H (1997) Retrotransposons of rice: Their regulation and use for genome analysis. Plant Mol Biol 35: 231–240

    Article  PubMed  CAS  Google Scholar 

  • Huang N, Angeles ER, Domingo J, Magpantay G, Singh S, Zhang G, Kumaravadivel N, Bennett J and Khush GS (1997) Pyramiding of bacterial blight resistance genes in rice: Markerassisted selection using RFLP and PCR. Theor Appl Genet 95: 313–320

    Article  CAS  Google Scholar 

  • Izawa T, Ohnishi T, Nakano T, Ishida N, Enoki H., Hashimoto H, Itoh K, Terada R, Wu C, Miyazaki C, Endo T, Iida S and Shimamoto K (1997) Transposon tagging in rice. Plant Mol Biol 35: 219–229

    Article  PubMed  CAS  Google Scholar 

  • Kilian A, Kudrna N, Kleinhofs A, Yano M, Kurata N, Stefenson B and Sasaki T (1995) Rice-barley synteny and its application to saturation mapping of the barley Rpg1 region. Nucleic Acids Res 23: 2729–2733

    PubMed  CAS  Google Scholar 

  • Kono I, Takeuchi Y, Shimano T, Sasaki T and Yano M (2000) Comparison of efficiency of detection of polymorphism among japonica varieties in rice using RFLP, RAPD, AFLP and SSR markers. Breeding Res 2: 197–203 [in Japanese]

    Google Scholar 

  • Kurata N, Moore G, Nagamura Y, Foote T, Yano M, Minobe Y and Gale MD (1994) Conservation of genomic structure between rice and wheat. Bio/Technology 12: 276–278

    Article  CAS  Google Scholar 

  • Kurata N, Nagamura Y, Yamamoto K, Harushima Y, Sue N, Wu J, Antonio BA, Shomura A, Shimizu T, Lin S-Y, Inoue T, Fukuda A, Shimano T, Kuboki Y, Toyama T, Miyamoto Y, Kirihara T, Hayasaka K, Miyao A, Monna L, Zhong HS, Tamura Y, Wang Z-X, Momma T, Umehara Y, Yano M, Sasaki T and Minobe Y (1994) Molecular analysis of small grain cereal genomes - current status and prospects. Nature Genet 8: 365–372

    Article  PubMed  CAS  Google Scholar 

  • Leister D, Kurth J, Laurie DA, Yano M, Sasaki T, Devos km, Graner A and Schulze-Lefert P (1998) Rapid reorganization of resistance gene homologues in cereal genomes. Prot Natl Acad Sci USA 95: 370–375

    Article  CAS  Google Scholar 

  • Liu Y-G and Whittier RF (1995) Thermal asymmetric interlaced PCR: Automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking. Genomics 25: 674–681

    Article  PubMed  CAS  Google Scholar 

  • Lukashin AV and Borodovsky M (1998) GeneMark.hmm:new solutions for gene finding. Nucleic Acids Res 26: 1107–1115

    Article  PubMed  CAS  Google Scholar 

  • McCouch SR, Kochert G, Yu ZH, Wang ZY, Khush GS, Coffman WR and Tanksley SD (1988) Molecular mapping of rice chromosomes. Theor Appl Genet 76: 815–829

    Article  CAS  Google Scholar 

  • Miyao A, Yamazaki M and Hirochika H (1998) Systematic screening of mutants of rice by sequencing retrotransposon-insertion sites. Plant Biotechnol 15: 253–256

    CAS  Google Scholar 

  • Moore G, Foote T, Helentjaris T, Devos K, Kurata N and Gale MD (1995) Was there a single ancestral cereal chromosome? Trends Genet 11: 81–82

    Article  PubMed  CAS  Google Scholar 

  • Moore G, Aragon- Alcaide L, Roberts M, Reader S, Miller T and Foote T (1997) Are rice chromosomes components of a holocentric chromosome ancestor? Plant Mol Biol 35: 17–23

    Article  PubMed  CAS  Google Scholar 

  • Nagamura Y, Tanaka T, Nozawa H, Kaidai H, Kasuga S and Sasaki T (1998) Syntenic regions between rice and sorghum genomes. In: Nakagawa H and Kobayashi M (eds) Proceedings of the International Workshop; Utilization of Transgenic Plant and Genome Analysis in Forage Crops, pp 97–103. National Grassland Research Institute, Japan

    Google Scholar 

  • Peng J, Richards DE, Hartley NM, Murphy GP, Devos KM, Flintham JE, Beales J, Fish LJ, Worland JE, Pelica F, Sudhakar D, Christou P, Snape JW, Gale MD and Harberd NP (1999) ‘Green revolution’ genes encode mutant gibberellin response modulators. Nature 400: 256–261

    Article  PubMed  CAS  Google Scholar 

  • Richmond T and Somerville S (2000) Chasing the dream: Plant EST microarray. Curr Opin Plant Biol 3: 108–116

    Article  PubMed  CAS  Google Scholar 

  • Sakata K, Antonio BA, Mukai Y, Nagasaki H, Sakai Y, Makino K and Sasaki T (2000) INE: A rice genome database with an integrated map view. Nucleic Acids Res 28: 97–102

    Article  PubMed  CAS  Google Scholar 

  • Sato Y, Sentoku N, Miura Y, Hirochika H, Kitano H and Matsuoka M (1999) Loss-of-function mutations in the rice homeobox gene OSH15 affect the architecture of internodes resulting dwarf plants. EMBO J 18: 992–1002

    Article  PubMed  CAS  Google Scholar 

  • Salamov A and Solovyev V (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res 10: 516–522

    Article  PubMed  CAS  Google Scholar 

  • Sasaki T and Burr B (2000) International rice genome sequencing project: the effort to completely sequence the rice genome. Curr Opin Plant Biol 3: 138–141

    Article  PubMed  CAS  Google Scholar 

  • Siebert PD, Chenchik A, Kellogg DE, Lukyanov KA and Lukyanov SA (1995) An improved PCR method for walking in uncloned genomic DNA. Nucleic Acids Res 23: 1087–1088

    PubMed  CAS  Google Scholar 

  • Tanksley SD, Young ND, Paterson AH and Bonierbale MW (1989) RFLP mapping in plant breeding: New tools for old sciences. Biotechnology 7: 257–264

    Article  CAS  Google Scholar 

  • Temnykh S, Park WD, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T and McCouch SR (2000) Mapping and genopme organization of microsatellite sequences in rice (Oryza sativa L.) Theor Appl Genet 100: 697–712

    Article  CAS  Google Scholar 

  • Yamamoto T, Kuboki Y, Lin S-Y, Sasaki T and Yano M (1998) Fine mapping of quantitative trait loci Hd-1, Hd-2 and Hd-3, controlling heading date of rice, as single Mendelian factors. Theor Appl Genet 97: 37–44

    Article  CAS  Google Scholar 

  • Yano M (2000) The latest high-density rice genetic map, including 3267 markers. http://rgp.dna.affrc.go.jp/publicdata/geneticmap 2000/index.html

  • Yano M and Sasaki T (1997) Genetic and molecular dissection of quantitative traits in rice. Plant Mol Biol 35: 145–153

    Article  PubMed  CAS  Google Scholar 

  • Yano M, Harushima Y, Nagamura, Y, Kurata N, Minobe Y and Sasaki T (1997) Identification of quantitative trait loci controlling heading date in rice using a high-density linkage map. Theor Appl Genet 95: 1025–1032

    Article  CAS  Google Scholar 

  • Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y and Sasaki T (2001) 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

    Article  Google Scholar 

  • Uberbacher EC and Mural RJ (1991) Locating protein-coding regions in human DNA sequences by a nultiple sensor-neural network approach. Proc Natl Acad Sci USA 88: 11261–11265

    Article  PubMed  CAS  Google Scholar 

  • Ye X, Al-Babili S, Kloti A, Zhang J, Lucca P, Beyer P and Potrykus I (2000) Engineering the provitamin A (β-carotene) biosynthetic pathway into (carotenoid-free) rice endosprm. Science 287: 303–305

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

About this article

Cite this article

Sasaki, T. Rice genome analysis to understand the rice plant as an assembly of genetic codes. Photosynthesis Research 70, 119–127 (2001). https://doi.org/10.1023/A:1013844110497

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1013844110497

Navigation