Skip to main content
SpringerLink
Log in
Book cover

Genetics and Genomics of Rice pp 71–79Cite as

Molecular Cytogenetics of Rice and Its Wild Relatives

  • Chapter
  • First Online:

  • 3239 Accesses

Part of the book series: Plant Genetics and Genomics: Crops and Models ((PGG,volume 5))

Abstract

Molecular cytogenetics has played an important role in the elucidation of chromosomal structure, behavior, and evolution in the genus Oryza. Extensive and elaborate analyses on rice chromosomes over the past few decades have uncovered cytological features such as gene locations, genome organization at centromeres and subtelomeres, repeat distributions, and epigenetic modifications. In fact, rice can be considered a model species for chromosome studies due to the available tools and information. Fluorescence in situ hybridization (FISH) on wild species and genomic in situ hybridization (GISH) on interspecific crosses revealed conservation and diversity of genomes within the genus Oryza, providing a better understanding of chromosomal evolution in the genus. Combined with genomics, we expect molecular cytogenetics to continue to be an essential tool to facilitate fundamental knowledge on chromosomes and their evolution and to contribute to breeding strategies.

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

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  1. Vaughan DA, Morishima H, Kadowaki K (2003) Diversity in the Oryza genus. Curr Opin Plant Biol 6(2):139–146

    Article  PubMed  CAS  Google Scholar 

  2. Kurata N, Fukui K (2003) Chromosome research in genus Oryza. In: Nanda JS, Sharma SD (eds) Monograph in genus Oryza. Science Publishers, New Hampshire, pp 213–261

    Google Scholar 

  3. Kamisugi Y, Furuya N, Iijima K, Fukui K (1993) Computer-aided automatic identification of rice chromosomes by image parameters. Chromosome Res 1(3):189–196

    Article  PubMed  CAS  Google Scholar 

  4. Fukui K (1996) Advances in rice chromosome research, 1990–95. In: Rice genetics, III: proceedings of the third international rice genetics. IRRI, Manila, Philippines, pp 117–130

    Google Scholar 

  5. Fukui K, Iijima K (1991) Somatic chromosome map of rice by imaging methods. Theor Appl Genet 81(5):589–596

    Article  Google Scholar 

  6. Cheng Z, Buell CR, Wing RA, Gu M, Jiang J (2001) Toward a cytological characterization of the rice genome. Genome Res 11(12):2133–2141

    Article  PubMed  CAS  Google Scholar 

  7. Ohmido N, Akiyama Y, Fukui K (1998) Physical mapping of unique nucleotide sequences on identified rice chromosomes. Plant Mol Biol 38(6):1043–1052

    Article  PubMed  CAS  Google Scholar 

  8. Wang CJR, Harper L, Cande WZ (2006) High-resolution single-copy gene fluorescence in situ hybridization and its use in the construction of a cytogenetic map of maize chromosome 9. Plant Cell 18(3):529–544

    Article  PubMed  CAS  Google Scholar 

  9. Danilova TV, Birchler JA (2008) Integrated cytogenetic map of mitotic metaphase chromosome 9 of maize: resolution, sensitivity, and banding paint development. Chromosoma 117(4):345–356

    Article  PubMed  Google Scholar 

  10. Jiang JM, Gill BS (2006) Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research. Genome 49(9):1057–1068

    Article  PubMed  CAS  Google Scholar 

  11. Jiang JM, Gill BS, Wang GL, Ronald PC, Ward DC (1995) Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes. Proc Natl Acad Sci U S A 92(10):4487–4491

    Article  PubMed  CAS  Google Scholar 

  12. Nakamura S, Asakawa S, Ohmido N, Fukui K, Shimizu N, Kawasaki S (1997) Construction of an 800-kb contig in the near-centromeric region of the rice blast resistance gene Pi-ta 2 using a highly representative rice BAC library. Mol Gen Genet 254(6):611–620

    Article  PubMed  CAS  Google Scholar 

  13. Cheng ZK, Presting GG, Buell CR, Wing RA, Jiang JM (2001) High-resolution pachytene chromosome mapping of bacterial artificial chromosomes anchored by genetic markers reveals the centromere location and the distribution of genetic recombination along chromosome 10 of rice. Genetics 157(4):1749–1757

    PubMed  CAS  Google Scholar 

  14. Kao FI, Cheng YY, Chow TY et al (2006) An integrated map of Oryza sativa L. Chromosome 5. Theor Appl Genet 112(5):891–902

    Article  PubMed  CAS  Google Scholar 

  15. Piegu B, Guyot R, Picault N et al (2006) Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res 16(10):1262–1269

    Article  PubMed  CAS  Google Scholar 

  16. Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33:479–532

    Article  PubMed  CAS  Google Scholar 

  17. Dong F, Miller JT, Jackson SA, Wang GL, Ronald PC, Jiang J (1998) Rice (Oryza sativa) centromeric regions consist of complex DNA. Proc Natl Acad Sci U S A 95(14):8135–8140

    Article  PubMed  CAS  Google Scholar 

  18. Miller JT, Dong F, Jackson SA, Song J, Jiang J (1998) Retrotransposon-related DNA sequences in the centromeres of grass chromosomes. Genetics 150(4):1615–1623

    PubMed  CAS  Google Scholar 

  19. Cheng Z, Dong F, Langdon T et al (2002) Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14(8):1691–1704

    Article  PubMed  CAS  Google Scholar 

  20. Gao D, Gill N, Kim HR et al (2009) A lineage-specific centromere retrotransposon in Oryza brachyantha. Plant J 60(5):820–831

    Article  PubMed  CAS  Google Scholar 

  21. Lee HR, Zhang W, Langdon T et al (2005) Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species. Proc Natl Acad Sci U S A 102(33):11793–11798

    Article  PubMed  CAS  Google Scholar 

  22. Zhang WL, Yi CD, Bao WD et al (2005) The transcribed 165-bp CentO satellite is the major functional centromeric element in the wild rice species Oryza punctata. Plant Physiol 139(1):306–315

    Article  PubMed  CAS  Google Scholar 

  23. Bao W, Zhang W, Yang Q et al (2006) Diversity of centromeric repeats in two closely related wild rice species, Oryza officinalis and Oryza rhizomatis. Mol Genet Genomics 275(5):421–430

    Article  PubMed  CAS  Google Scholar 

  24. Nagaki K, Cheng Z, Ouyang S et al (2004) Sequencing of a rice centromere uncovers active genes. Nat Genet 36(2):138–145

    Article  PubMed  CAS  Google Scholar 

  25. Wu J, Yamagata H, Hayashi-Tsugane M et al (2004) Composition and structure of the centromeric region of rice chromosome 8. Plant Cell 16(4):967–976

    Article  PubMed  CAS  Google Scholar 

  26. Wu J, Fujisawa M, Tian Z et al (2009) Comparative analysis of complete orthologous centromeres from two subspecies of rice reveals rapid variation of centromere organization and structure. Plant J 60(5):805–819

    Article  PubMed  CAS  Google Scholar 

  27. Podlevsky JD, Bley CJ, Omana RV, Qi X, Chen J (2007) The telomerase database. Nucleic Acids Res 36:D339–D343

    Article  PubMed  Google Scholar 

  28. Mizuno H, Wu J, Kanamori H et al (2006) Sequencing and characterization of telomere and subtelomere regions on rice chromosomes 1S, 2S, 2L, 6L, 7S, 7L and 8S. Plant J 46(2):206–217

    Article  PubMed  CAS  Google Scholar 

  29. Ohmido N, Kijima K, Akiyama Y, de Jong JH, Fukui K (2000) Quantification of total genomic DNA and selected repetitive sequences reveals concurrent changes in different DNA families in indica and japonica rice. Mol Gen Genet 263(3):388–394

    Article  PubMed  CAS  Google Scholar 

  30. Mizuno H, Wu J, Katayose Y, Kanamori H, Sasaki T, Matsumoto T (2008) Characterization of chromosome ends on the basis of the structure of TrsA subtelomeric repeats in rice (Oryza sativa L.). Mol Genet Genomics 280(1):19–24

    Article  PubMed  CAS  Google Scholar 

  31. Fransz PF, Alonso-Blanco C, Liharska TB, Peeters AJ, Zabel P, de Jong JH (1996) High-resolution physical mapping in Arabidopsis thaliana and tomato by fluorescence in situ hybridization to extended DNA fibres. Plant J 9(3):421–430

    Article  PubMed  CAS  Google Scholar 

  32. Jackson SA, Wang ML, Goodman HM, Jiang J (1998) Application of fiber-FISH in physical mapping of Arabidopsis thaliana. Genome 41(4):566–572

    PubMed  CAS  Google Scholar 

  33. Cheng Z, Buell CR, Wing RA, Jiang J (2002) Resolution of fluorescence in-situ hybridization mapping on rice mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibers. Chromosome Res 10(5):379–387

    Article  PubMed  CAS  Google Scholar 

  34. Fukui K, Ohmido N, Kijima K, Akiyama Y, de Jong JH (2000) Quantification of total genomic DNA and selected repetitive sequences reveals concurrent changes in different DNA families in indica and japonica rice. Mol Gen Genet 263(3):388–394

    Article  PubMed  Google Scholar 

  35. Ohmido N, Kijima K, Ashikawa I, de Jong JH, Fukui K (2001) Visualization of the terminal structure of rice chromosomes 6 and 12 with multicolor FISH to chromosomes and extended DNA fibers. Plant Mol Biol 47(3):413–421

    Article  PubMed  CAS  Google Scholar 

  36. Feng Q, Zhang YJ, Hao P et al (2002) Sequence and analysis of rice chromosome 4. Nature 420(6913):316–320

    Article  PubMed  CAS  Google Scholar 

  37. Sasaki T, Matsumoto T, Yamamoto K et al (2002) The genome sequence and structure of rice chromosome 1. Nature 420(6913):312–316

    Article  PubMed  CAS  Google Scholar 

  38. Rice Chromosome 10 Sequencing Consortium (2003) In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300(5625):1566–1569

    Article  Google Scholar 

  39. Fukui K, Shishido R, Kinoshita T (1997) Identification of the rice D-genome chromosomes by genomic in situ hybridisation. Theor Appl Genet 95(8):1239–1245

    Article  CAS  Google Scholar 

  40. Shishido R, Ohmido N, Fukui K (2001) Chromosome painting as a tool for rice genetics and breeding. Methods Cell Sci 23(1–3):125–132

    Article  PubMed  CAS  Google Scholar 

  41. Yan H, Liu G, Cheng Z, Min S, Zhu L (2001) Characterization of euploid backcross progenies derived from interspecific hybrids between Oryza sativa and O. eichingeri by restriction fragment length polymorphism (RFLP) analysis and genomic in situ hybridization (GISH). Genome 44(1):86–95

    Article  PubMed  CAS  Google Scholar 

  42. Tan G, Jin H, Li G, He R, Zhu L, He G (2005) Production and characterization of a complete set of individual chromosome additions from Oryza officinalis to Oryza sativa using RFLP and GISH analyses. Theor Appl Genet 111(8):1585–1595

    Article  PubMed  CAS  Google Scholar 

  43. Jin H, Tan G, Brar DS et al (2006) Molecular and cytogenetic characterization of an Oryza officinalis-O. sativa chromosome 4 addition line and its progenies. Plant Mol Biol 62(4–5):769–777

    Article  PubMed  CAS  Google Scholar 

  44. Xiong ZY, He GC, Tan GX, He GY, Song YC (2006) Cytogenetic comparisons between A and G genomes in Oryza using genomic in situ hybridization. Cell Res 16(3):260–266

    Article  PubMed  CAS  Google Scholar 

  45. Jackson JP, Johnson L, Jasencakova Z et al (2004) Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma 112(6):308–315

    Article  PubMed  CAS  Google Scholar 

  46. Jasencakova Z, Soppe WJJ, Meister A, Gernand D, Turner BM, Schubert I (2003) Histone modifications in Arabidopsis: high methylation of H3 lysine 9 is dispensable for constitutive heterochromatin. Plant J 33(3):471–480

    Article  PubMed  CAS  Google Scholar 

  47. Yan HH, Kikuchi S, Neumann P et al (2010) Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice. Plant J 63(3):353–365

    Article  CAS  Google Scholar 

  48. Iwata A (2008) Cytological research of rice chromosomes. Kobe University Graduation thesis, pp 1–51

    Google Scholar 

  49. Wing RA, Ammiraju JS, Luo M et al (2005) The Oryza Map Alignment Project: the golden path to unlocking the genetic potential of wild rice species. Plant Mol Biol 59(1):53–62

    Article  PubMed  CAS  Google Scholar 

  50. International Rice Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436(7052):793–800

    Article  Google Scholar 

  51. Ammiraju JS, Luo M, Goicoechea JL et al (2006) The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza. Genome Res 16(1):140–147

    Article  PubMed  Google Scholar 

  52. Iyengar GAS, Sen SK (1978) Nuclear-DNA content of several wild and cultivated Oryza species. Environ Exp Bot 18(4):219–224

    Article  CAS  Google Scholar 

  53. Uozu S, Ikehashi H, Ohmido N, Ohtsubo H, Ohtsubo E, Fukui K (1997) Repetitive sequences: cause for variation in genome size and chromosome morphology in the genus Oryza. Plant Mol Biol 35(6):791–799

    Article  PubMed  CAS  Google Scholar 

  54. Martínez CP, Arumuganathan K, Kikuchi H, Earle ED (1994) Nuclear DNA content of ten rice species as determined by flow cytometry. Jpn J Genet 69:513–523

    Article  Google Scholar 

Download references

Acknowledgements

We would like to acknowledge and thank the USA National Science Foundation for funding to support this work (NSF DBI 105048).

Author information

Authors and Affiliations

  1. Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA

    Aiko Iwata Ph.D., Dongying Gao Ph.D. & Scott A. Jackson Ph.D.

  2. Graduate School of Human Development and Environment, Kobe University, Kobe, Hyogo, Japan

    Nobuko Ohmido Ph.D.

Authors
  1. Aiko Iwata Ph.D.
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Dongying Gao Ph.D.
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Nobuko Ohmido Ph.D.
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Scott A. Jackson Ph.D.
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Scott A. Jackson Ph.D. .

Editor information

Editors and Affiliations

  1. of Crop Genetic Improvement, Huazhong Agricultural University National Key Laboratory, Wuhan, China, People's Republic

    Qifa Zhang

  2. The School of Plant Sciences, University of Arizona Arizona Genomics Institute, Tucson, Arizona, USA

    Rod A. Wing

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media New York

About this chapter

Cite this chapter

Iwata, A., Gao, D., Ohmido, N., Jackson, S.A. (2013). Molecular Cytogenetics of Rice and Its Wild Relatives. In: Zhang, Q., Wing, R. (eds) Genetics and Genomics of Rice. Plant Genetics and Genomics: Crops and Models, vol 5. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-7903-1_6

Download citation

Publish with us

Policies and ethics

Search

Navigation