Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Molecular Analysis of Small Grain Cereal Genomes: Current Status and Prospects

Abstract

Recent developments in cereal genome analysis include generation of RFLP maps, flow sorting of chromosomes, identification of landmarks for genes and a more advanced model for cereal genome organization. These developments are reviewed together with new prospects for the isolation of defined genes from large cereal genomes and for the production of a composite map of the ancestral grass genome to aid in the genetic analysis of all the Gramineae. The advances that can now come from comparative genome mapping are likely to promote further the new era of plant genetics.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Similar content being viewed by others

References

  1. Bennett, M.D. and Smith, J.B. 1991. Nuclear DNA amount in angiosperms. Phil. Trans. R. Soc. London (Biol) 334: 309–345.

    Article  CAS  Google Scholar 

  2. Smith, D.B. and Flavell, R.B. 1975. Characterization of the wheat genome by renaturation kinetics. Chromosoma 50: 223–242.

    Article  CAS  Google Scholar 

  3. Flavell, R.B., Rimpau, J. and Smith, D.B. 1977. Repeated sequence DNA relationships in four cereal genomes. Chromosoma 63: 205–222.

    Article  CAS  Google Scholar 

  4. Rimpau, J., Smith, D.B. and Flavell, R.B. 1978. Sequence organisation analysis of the wheat and rye genomes by interspecies DNA/DNA hybridization. J. Mol. Biol. 123: 327–359.

    Article  CAS  PubMed  Google Scholar 

  5. Deshpande, V.G. and Ranjekar, P.K. 1980. Repetitive DNA in three Gramineae species with low DNA content. Hoppe-Seylers's Z. Physiol. Chem. 361: 1223–1233.

    Article  CAS  Google Scholar 

  6. Saito, A., Yano, M., Kishimoto, N., et al. 1991. Linkage map of restriction fragment polymorphism loci in rice. Jpn. J. Breed. 41: 665–670.

    Article  CAS  Google Scholar 

  7. Moore, G., Abbo, S., Cheung, W., Foote, T., Gale, M., Koebner, R., Leitch, A., Leitch, I., Money, T., Stancombe, P., Yano, M. and Flavell, R. 1993. Key features of cereal genome organisation as revealed by the use of cytosine methylation-sensitive restriction endonucleases. Genomics, In press

  8. Gale, M.D., Chao, S. and Sharp, P. 1990. RFLP mapping in wheat. Progress and Problems, p. 353–363. In: Gene Manipulation in Plant Improvement, Vol. II. Gustafson, J. P. (Ed.). Plenum Press, New York.

    Chapter  Google Scholar 

  9. Chao, S., Sharp, P.J., Worland, A.J., Warham, E.J., Koebner, R.M.D. and Gale, M.D. 1989. RFLP-based genetic maps of wheat homoeologous group 7 chromosomes. Theor. Appl. Genet. 78: 495–504.

    Article  CAS  PubMed  Google Scholar 

  10. Heun, M., Kennedy, A.E., Anderson, J., Lapitan, N.L.V., Sorrells, M.E. and Tanksley, S.D. 1991. Construction of a restriction fragment length polymorphism map for barley (Hordeum vulgare). Genome 34: 437–447.

    Article  Google Scholar 

  11. Devos, K., Atkinson, M., Chinoy, C., Liu, C. and Gale, M.D. 1992. RFLP based genetic map of homoeologous group 3 chromosomes of wheat and rye. Theor. Appl. Genet. 83: 931–939.

    Article  CAS  PubMed  Google Scholar 

  12. Devos, K., Millan, T. and Gale, M.D. 1993. Comparative RFLP maps of homoeologous group 2 chromosomes of wheat, rye and barley. Theor. Appl. Genet. In press.

  13. Rice Genome Research Programme. 1992. Vol 1 nos 1–2, Minobe, Y. (Ed.). NIAR, Tsukuba, Ibaraki 305, Japan.

  14. Leitch, I.J. and Helsop-Harrison, J.S. 1993. Physical mapping of the 18s-5.8S-265 rRNA genes in barley by in situ hybridisation. Genome, In press

  15. Leitch, I.J. and Helsop-Harrison, J.S. 1993. Physical mapping of four sites of 5S ribosomal DNA sequences and one site of the a-amylase 2 gene in barley (Hordeum vulgare). Genome, In press.

  16. Lawrence, G.J. and Appels, R. 1986. Mapping the nucleolus organizer, seed protein loci and isozyme loci on chromosome 1R in rye. Theor. Appl. Genet. 71: 742–749.

    Article  CAS  PubMed  Google Scholar 

  17. Linde-Laursen, I. 1982. Linkage map of the long arm of barley chromosome 3 using C-bands and marker genes. Heredity 49: 27–35.

    Article  Google Scholar 

  18. Dvorak, J. and Chen, K.-C. 1984. Distribution of nonstructural variation between wheat cultivars along chromosome arm 6Bp:evidence from the linkage map and physical map of the arm. Genetics 106: 325–333.

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Snape, J.W., Flavell, R.B., O'Dell, M., Hughes, W.G. and Payne, P.I. 1985. Intrachromosomal mapping of the nucleolar organiser region relative to three marker loci on chromosome 1B of wheat (Triticum aestivum). Theor. Appl. Genet. 69: 263–270.

    Article  CAS  PubMed  Google Scholar 

  20. Wang, M.L., Atkinson, M.D., Chinoy, C.N., Devos, K.M., Liu, C., Rogers, W.J. and Gale, M. 1991. RFLP-based map of rye (S. cereale) chromosome 1R. Theor. Appl. Genet. 82: 174–178.

    Article  CAS  PubMed  Google Scholar 

  21. Bird, A.P. 1987. CpG islands as markers in the vertebrate nucleus. Trends Genet. 3: 342–347.

    Article  CAS  Google Scholar 

  22. Brown, W.R.A. 1988. A physical map of the human pseudoautosomal region. EMBO. J. 7: 2377–2385.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Gardiner-Garden, M. and Frommer, M. 1987. CpG islands in vertebrate genomes. J. Mol. Biol. 196: 261–282.

    Article  CAS  PubMed  Google Scholar 

  24. Poustka, A. and Lehrach, H. 1986. Jumping and linking libraries. Trends Genet 2: 174–179.

    Article  CAS  Google Scholar 

  25. Salinas, J., Matassi, G., Montero, L.M. and Bernardi, G. 1988. Compositional compartmentilization and compositional patterns in nuclear genomes of plants. Nucl. Acids Res. 16: 4269–4285.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Matassi, G., Montero, L.M., Salinas, J. and Bernardi, G. 1989. The isochore organisation and compositional distribution of homologous coding sequences in nuclear genomes of plants. Nucl. Acids Res. 17: 5273–5290.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Swartz, M.N., Trautner, T.A. and Kornberg, A. 1962. Enzymatic synthesis of deoxyribonucleic acid. J. Biol. Chem. 237: 1961–1967.

    CAS  PubMed  Google Scholar 

  28. Russell, G.J., Follett, E.A.C., Subak-Sharpe, J.H. and Harrison, B.D. 1971. The double stranded DNA of cauliflower mosaic virus. J. Gen. Virol. 11: 129–138.

    Article  CAS  PubMed  Google Scholar 

  29. Gruenbaum, Y., Naveh-Many, T., Cedar, H. and Razin, A. 1981. Sequence specificity of methylation in higher plant DNA. Nature 292: 860–862.

    Article  CAS  PubMed  Google Scholar 

  30. Cheung, W.Y., Chao, S. and Gale, M.D. 1991. Long-range mapping of the α-amylase (α-Amy-1) loci on homoeologous group 6 chromosomes of wheat. Mol. & Gen. Genet. 229: 373–379.

    Article  CAS  Google Scholar 

  31. Cheung, W.Y., Moore, G., Money, T. and Gale, M.D. 1992. HpaII library indicates methylation-free islands in wheat and barley. Theor. Appl. Genet. 84: 739–749.

    Article  CAS  PubMed  Google Scholar 

  32. Anamthawat-Jonsson, K. and Heslop-Harrison, J.S. 1990. Centromeres, telomeres, and chromatin in the interphase nucleus of cereals. Caryologia 43: 205–213.

    Article  Google Scholar 

  33. Dennis, E., Gerlach, W.L. and Peacock, W. 1980. Identical polypyrimidine-polypurine satellite DNAs in wheat and barley. Heredity 44: 349–366

    Article  CAS  Google Scholar 

  34. Hutchinson, J. and Lonsdale, D.M. 1982. The chromosomal distribution of cloned highly repetitive sequences from Hexaploid wheat. Heredity 48: 371–376.

    Article  CAS  Google Scholar 

  35. Gerlach, W.L. and Bedbrook, J.R. 1979. Cloning and characterization of ribosomal RNA genes from wheat and barley. Nucl. Acids Res. 7: 1869–1885.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Flavell, R.B., Bennett, M.D. and Hutchinson-Brace, J. 1987. Chromosome structure and organisation, p. 211–268. In:Wheat. Lupton, F. (Ed.). Chapman and Hall. London.

    Google Scholar 

  37. Bedbrook, J.R., Jones, J., O'Dell, M., Thompson, R.D. and Flavell, R.B. 1980. A molecular description of telomeric heterochromatin in Secale species. Cell 19: 545–560.

    Article  CAS  PubMed  Google Scholar 

  38. Dallas, J.F. 1988. Detection of DNA fingerprints of cultivated rice by hybn-diation with a human minisatellite probe. Proc. Natl. Acad. Sci. USA 85: 6831–6835.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Balcells, L., Swinburne, J. and Coupland, G. 1991. Transposons as tools for the isolation of plant genes. Tibtech. 9: 31–36.

    Article  Google Scholar 

  40. Moore, G., Lucas, H., Batty, N. and Flavell, R.B. 1991. A family of retrotransposons and associated genomic variation in wheat. Genomics 10: 461–468.

    Article  CAS  PubMed  Google Scholar 

  41. Flavell, R.B. 1986. Repetitive DNA and chromosome evolution in plants. Phil. Trans. R. Soc. London (Biol) 312: 227–242.

    Article  CAS  Google Scholar 

  42. Lucas, H., Moore, G., Murphy, G. and Flavell, R.B. 1992. Inverted repeats in the long-terminal repeats of the wheat retrotransposon WIS-2-1A. Mol. Biol. Evol. 9: 716–728.

    CAS  PubMed  Google Scholar 

  43. Murphy, G.J.P., Lucas, H., Moore, G. and Flavell, R.B. 1992. Sequence analysis of WIS-2-1A, a retrotransposon-like element from wheat. Plant Mol. Biol. 20: 991–995.

    Article  CAS  PubMed  Google Scholar 

  44. Moore, G., Cheung, W., Schwarzacher, T. and Flavell, R. 1991. BIS-1, a major component of cereal genome and a tool for studying genomic organisation. Genomics 10: 469–476.

    Article  CAS  PubMed  Google Scholar 

  45. Martienssen, R.A. and Baulcombe, D.C. 1989. An unusual wheat insertion sequence (WIS-1) lies upstream of an α-amylase gene in hexaploid wheat, and carries a minisatellite array. Mol. & Gen. Genet. 217: 401–410.

    Article  CAS  Google Scholar 

  46. Linskens, M.H.K. and Huberman, J.A. 1990. The two faces of higher eukaryotic DNA replication origins. Cell 62: 845–847.

    Article  CAS  PubMed  Google Scholar 

  47. Gasser, S.M. and Laemmli, U.K. 1987. A glimpse at chromosomal order. Trends Genet. 3: 16–22.

    Article  CAS  Google Scholar 

  48. Jenkins, G. 1985. Synaptonemal complex formation in hybrids of Lolium temulentum x Lolium perenne (L). Chromosoma 92: 81–88.

    Article  Google Scholar 

  49. Dover, G.A. 1986. Molecular drive in multigene families:how biological novelties arise, spread and are assimilated. Trends Genet. 2: 159–165.

    Article  CAS  Google Scholar 

  50. O'Brien, S.J. (Ed.). 1993. Plants, Genetic Maps, Locus Maps of Complex Genomes. Sixth Ed. Cold Spring Harbor Laboratory Press, NY.

    Google Scholar 

  51. Gale, M.D. and Youssefian, S. 1985. Dwarfing genes in wheat, p. 1–35. In: Progress in Plant Breeding. Russell, G. E. (Ed.). Butterworths and Co., London.

    Google Scholar 

  52. Hoppe, H.E., Favret, G.C. and Favret, E.A. 1982. The physiogenetic regulation of dwarfness in barley, p. 81–83. In: Semidwarf Cereal Mutants and Their Use in Cross-breeding. IAEA-TECDOC-268, Vienna.

    Google Scholar 

  53. Plaschke, J., Borner, A., Xie, D.X., Koebner, R.M.D., Schlegel, R. and Gale, M.D. 1992. RFLP mapping of genes affecting plant height and growth habit in rye. Theor. Appl. Genet. (Submitted).

  54. Gallagher, L.W., Soliman, K.M. and Vivar, H. 1991. Interactions among loci conferring photoperiod insensitivity for heading time in Spring barley. Crop Sci. 31: 256–261.

    Article  Google Scholar 

  55. Law, C., Dean, C. and Coupland, G. 1993. Genes controlling flowering and Strategies for their isolation and characterisation. In: Molecular Biology of Flowering. Jordan, B. (Ed). CAB International. Location?

    Google Scholar 

  56. Takahashi, R. and Yasuda, S. 1971. Genetics of earliness and growth habit in barley, p. 388–408. In: Barley Genetics II. Nilan, R.A. (Ed.). Washington State University Press, Seattle.

    Google Scholar 

  57. Murray, E.E., Lotzer, J. and Eberle, M. 1989. Codon usage in plant genes. Nucl. Acids Res. 17: 477–498.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Devos, K.M. and Gale, M.D. 1992. The use of randem amplified polymorphic markers in wheat. Theor. Appl. Genet. 84: 567–572.

    Article  CAS  PubMed  Google Scholar 

  59. Wang, M.L., Leitch, A.R., Schwarzacher, T., Heslop-Harrison, J.S. and Moore, G. 1992. Construction of a chromosome-enriched Hpall library from flow sorted wheat chromosomes. Nucl. Acids Res 20: 1897–1901.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Houben, A. and Schlegel, R. 1991. The isolation of individual chromosomes of diploid barley by micromampulation, p. 279. In: Barley Genetics VI, Munch, L. (Ed.). Helsingborg, Sweden.

    Google Scholar 

  61. Clarke, B., Stancombe, P., Money, T., Foote, T. and Moore, G. 1992. Targeting deletion (homoeologous chromosome pairing locus) or addition line single copy sequences from cereal genomes. Nucl. Acids Res. 20: 1289–1292.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Wolfe, K.H., Gouy, M., Yang, Y.-W., Sharp, P.M. and Li, W.-H. 1989. Date of the monocot-dicot divergence estimated from the chloroplast DNA sequence data. Proc. Natl. Acad. Sci. USA 86: 6201–6205.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Martin, W., Gierl, A. and Saedler, H. 1989. Molecular evidence for pre-Cretaceous angiosperm origins. Nature 39: 46–48.

    Article  CAS  Google Scholar 

  64. Whitkus, R., Doebley, J. and Lee, M. 1992. Comparative genome mapping of sorghum and maize. Genetics 132: 1119–1130.

    CAS  PubMed  PubMed Central  Google Scholar 

  65. Devos, K.M., Atkinson, M.D., Chinoy, C.N., Francis, H.A., Harcourt, R.L., Koebner, R.M.D., Liu, C.J., Masojc, P., Xie, D.X. and Gale, M.D. 1993. Chromosomal rearrangments in rye genome relative to that of wheat. Theor. Appl. Genet. In press.

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

About this article

Cite this article

Moore, G., Gale, M., Kurata, N. et al. Molecular Analysis of Small Grain Cereal Genomes: Current Status and Prospects. Nat Biotechnol 11, 584–589 (1993). https://doi.org/10.1038/nbt0593-584

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt0593-584

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing