SpringerLink
Log in

Comparative analysis of A, B, C and D genomes in the genus Oryza with C 0 t-1 DNA of C genome

  • Articles
  • Published:
Chinese Science Bulletin

Abstract

Fluorescence in situ hybridization (FISH) was applied to somatic chromosomes preparations of Oryza officinalis Wall. (CC), O. sativa L. (AA)×O. officinalis F1 hybrid (AC), backcross progenies BC1 (AAC and ACC), O. latifolia Desv. (CCDD), O. alta Swallen (CCDD) and O. punctata Kotschy (BBCC) with a labelled probe of C 0 t-1 DNA from O. officinalis. In O. officinalis, the homologous chromosomes showed similar signal bands probed by C 0 t-1 DNA and karyotype analysis was conducted based on the band patterns. Using no blocking DNA, the probe identified the chromosomes of C genome clearly, but detected few signals on chromosomes of A genome in the F1 hybrid and two backcross progenies of BC1. It is obvious that the highly and moderately repetitive DNA sequences were considerably different between C and A genomes. The chromosomes of C genome were also discriminated from the chromosomes of D-and B-genome in the tetraploid species O. latifolia, O. alta and O. punctata by C 0 t-1 DNA-FISH. Comparison of the fluorescence intensity on the chromosomes of B, C and D genomes in O. latifolia, O. alta, and O. punctata indicated that the differentiations between C and D genomes are less than that between C and B genomes. The relationship between C and D genomes in O. alta is closer than that of C and D genomes in O. latifolia. This would be one of the causes for the fact that both the genomes are of the same karyotype (CCDD) but belong to different species. The above results showed that the C 0 t-1 DNA had a high specificity of genome and species. In this paper, the origin of allotetraploid in genus Oryza is also discussed.

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

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price includes VAT (Germany)

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Lu B R. Taxonomy of the genus Oryza (Poaceae): A historical perspective and current status. Intern Rice Resour Notes, 1999, 24: 4–8

    Google Scholar 

  2. Aggarwal R K, Brar D S, Khush G S. Two new genomes in the Oryza complex identified on the basic of molecular divergence analysis using total genomic DNA hybridization. Mol Gen Genet, 1997, 254: 1–12

    Article  Google Scholar 

  3. Ge S, Sang T, Lu B R, et al. Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proc Natl Acad Sci USA, 1999, 96: 14400–14405

    Article  Google Scholar 

  4. Lu B R, Ge S, Sang T, et al. The current taxonomy and perplexity of the genus Oryza (Poaceae). Acta Phytotaxon Sin (in Chinese), 2001, 39: 373–388

    Google Scholar 

  5. Vaughan D A. The genus Oryza L. Current status of taxonomy. IRRI Res Paper Series, 1989, 138: 1–21

    Google Scholar 

  6. Vaughan D A, Morishima H, Kadowaki K. Diversity in the Oryza genus. Curr Opin Plant Biol, 2003, 6: 139–146

    Article  Google Scholar 

  7. Bao Y, Lu B R, Ge S. Identification of genomic constitutions of Oryza species with the B and C genomes by the PCR-RFLP method. Genet Resour Crop Ev, 2005, 52: 69–76

    Article  Google Scholar 

  8. Jena K K, Khush G S. Introgression of genes from Oryza officinalis Well ex Watt to cultivated rice, O.sativa L. Theor Appl Genet, 1990, 80: 737–745

    Article  Google Scholar 

  9. Kobayashi N, Ikeda R, Vaughan D A, et al. Resistance to Tungro in some wild relatives of rice. Rice Res Neusel, 1991, 16: 13

    Google Scholar 

  10. Multani D S, Khush G S, Reyes delos B G, et al. Alien genes introgression and development of monosomic alien addition lines from Oryza latifolia Desv. to rice, Oryza sativa L. Theor Appl Genet, 2003, 107: 395–405

    Article  Google Scholar 

  11. Liu L, Lafitte R, Guan D. Wild Oryza species as potential sources of drought-adaptive traits. Euphytica, 2004, 138: 149–161

    Article  Google Scholar 

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

    Article  Google Scholar 

  13. Shishido R, Apisitiwanich S, Ohmido N, et al. Detection of specific chromosome reduction in rice somatic hybrids with the A, B, and C genomes by multi-color genomic in situ hybridization. Theor Appl Genet, 1998, 97: 1013–1018

    Article  Google Scholar 

  14. Li C B, Zhang D M, Ge S, et al. Identification of genome constitution of Oryza malampuzhaensis, O. minuta, and O. punctataby multicolor genomic in situ hybridization. Theor Appl Genet, 2001, 103: 204–211

    Article  Google Scholar 

  15. Li C B, Zhang D M, Ge S, et al. Differentiation and inter-genomic relationships among C, E and D genomes in the Oryza officinalis complex (Poaceae) as revealed by multicolor genomic in situ hybridization. Theor Appl Genet, 2001, 103: 197–203

    Article  Google Scholar 

  16. Rokka V M, Clark M S, Knudson D L, et al. Cytological and molecular characterization of repetitive DNA sequences of Solanum brevidens and Solanum tuberosum. Genome, 1998, 41: 487–494

    Article  Google Scholar 

  17. Ohmido N, Kijima K, Akiyama Y, et al. Quantification of total genomic DNA and selected repetitive sequences reveals concurrent changes in different DNA families in indica and japonica rice. Mol Gen Genet, 2000, 263: 388–394

    Article  Google Scholar 

  18. Flavell R B, Bennett M D, Smith J B, et al. Genome size and proportion of repeated sequence DNA in plant. Biochem Genet, 1974, 12: 257–269

    Article  Google Scholar 

  19. Bennetzen J L, Jianxin M A, Devos K M. Mechanisms of recent genome size variation in flowering plants. Ann Bot-London, 2005, 95: 127–132

    Article  Google Scholar 

  20. McCouch S R, Tanskley S D. The world rice economy: Challenges ahead. In: Khush G S, Toenniessen G H, eds. Rice Biotechnology: Biotechnology in Agriculture Series, No. 6. Wallingford: Commonwealth Agricultural Bureaux International Press, 1991

    Google Scholar 

  21. Galasso I, Schmidt T, Pignone D, et al. The molecular cytogenetics of Vigna unguiculata (L) Walp: The physical organization and characterization of 18s-58s-25s rRNA genes, 5s rRNA genes, telomere-like sequences, and a family of centromeric repetitive DNA sequences. Theor Appl Genet, 1995, 91: 928–935

    Article  Google Scholar 

  22. Wang Z X, Kurata N, Saji S, et al. A chromosome 5-specific repetitive DNA sequence in rice (Oryza sativa L). Theor Appl Genet, 1995, 90: 907–913

    Article  Google Scholar 

  23. Matyasek R, Gazdova B, Fajkus J, et al. NTRS, a new family of highly repetitive DNAs specific for the T1 chromosome of tobacco. Chromosoma, 1997, 106: 369–379

    Article  Google Scholar 

  24. Hall A E, Keith K C, Hall S E, et al. The rapidly evolving field of plant centromeres. Curr Opin Plant Biol, 2004, 7: 108–114

    Article  Google Scholar 

  25. Linares C, Ferrer E, Fominaya A. Discrimination of the closely related A and D genomes of the hexaploid oat Avena sativa L. Proc Natl Acad Sci USA, 1998, 95: 12450–12455

    Article  Google Scholar 

  26. Cheng Z K, Stupar R M, Gu M H, et al. A tandemly repeated DNA sequence is associated with both knob-like heterochromatin and a highly decondensed structure in the meiotic pachytene chromosomes of rice. Chromosoma, 2001, 110: 24–31

    Google Scholar 

  27. Cheng Z K, Buell C R, Wing R A, et al. Toward a cytological characterization of the rice genome. Genome Res, 2001, 11: 2133–2141

    Article  Google Scholar 

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

    Article  Google Scholar 

  29. Yan H H, Liu G Q, Cheng Z K, et al. A genome-specific repetitive DNA sequence from Oryza eichingeri: Characterization, localization, and introgression to O. sativa. Theor Appl Genet, 2002, 104: 177–183

    Article  Google Scholar 

  30. Mishima M, Ohmido N, Fukui K, et al. Trends in site-number change of rDNA loci during polyploid evolution in Sanguisorba (Rosaceae). Chromosoma, 2002, 110: 550–558

    Google Scholar 

  31. ** W W, Melo J R, Nagaki K, et al. Maize centromeres: Organization and functional adaptation in the genetic background of oat. Plant Cell, 2004, 16: 571–581

    Article  Google Scholar 

  32. ** W W, Lamb J C, Vega J M, et al. Molecular and functional dissection of the maize B chromosome centromere. Plant Cell, 2005, 17: 1412–1423

    Article  Google Scholar 

  33. Zwick M S, Hanson R E, Mcknight T D, et al. A rapid procedure for the isolation of C 0t-1 DNA from plants. Genome, 1997, 40: 138–142

    Article  Google Scholar 

  34. Ren N, Song Y C, Bi X Z, et al. The physical location of genes cdc2 and prh1 in Maize (Zea mays L.). Hereditas, 1997, 126: 211–217

    Article  Google Scholar 

  35. Doyle J J, Doyle J L. Isolation of plant DNA from fresh tissue. Focus, 1990, 12: 13–15

    Google Scholar 

  36. Jiang J M, Gill B S, Wang G L, et al. Metaphase and interphase fluorescence in situ hybridization map** of the rice genome with bacterial artificial chromosome. Proc Natl Acad Sci USA, 1995, 92: 4487–4491

    Article  Google Scholar 

  37. Uozu S, Ikehashin H, Ohmido N, et al. Repetitive sequences: cause for variation in genome size and chromosome morphology in the genus Oryza. Plant Mol Biol, 1997, 35: 791–799

    Article  Google Scholar 

  38. Bennett M D, Leitch I J. Plant genome size research: A field in focus. Ann Bot-London, 2005, 95: 1–6

    Article  Google Scholar 

  39. Cheng Z K, Yan H H, Yu H X, et al. Development and applications of a complete set of rice telotrisomics. Genetics, 2001, 157: 161–168

    Google Scholar 

  40. Feng Q, Zhang Y, Hao P, et al. Sequence and analysis of rice chromosome 4. Nature, 2002, 420: 316–320

    Article  Google Scholar 

  41. Ren F G, Lu B R, Li S Q, et al. A comparative study of genetic relationships among the AA-genome Oryza species using RAPD and SSR markers. Theor Appl Genet, 2003, 108: 113–120

    Article  Google Scholar 

  42. Zhang Y, Huang Y C, Zhang L, et al. Structural features of the rice chromosome 4 centromere. Nucleic Acids Res, 2004, 32: 2023–2030

    Article  Google Scholar 

  43. Qin R, Wei W H, ** W W, et al. Physical location of rice Gm-6, Pi-5(t) genes in O. officinalis with BAC-FISH. Chin Sci Bull, 2001, 46: 2427–2430

    Article  Google Scholar 

  44. Yan H H, Cheng Z K, Liu G Q, et al. Identification of Oryza×Oryza officinalis F1 and backcross progenies using genomic in situ hybridization. Acta Genet Sin (in Chinese), 1999, 26: 157–162

    Google Scholar 

  45. Feuillet C, Keller B. High gene density is conserved at syntenic loci of small and large grass genomes. Proc Natl Acad Sci USA, 1999, 96: 8265–8270

    Article  Google Scholar 

  46. Choi H K, Mun J H, Kim D J, et al. Estimating genome conservation between crop and model legume species. Proc Natl Acad Sci USA, 2004, 101: 15289–15294

    Article  Google Scholar 

  47. Schwarzacher T, Leitch A R, Bennett M D, et al. In situ hybridization of parental genomes in a wide hybrid. Ann Bot, 1989, 64: 315–324

    Google Scholar 

  48. Ku H M, Vision T, Liu J P, et al. Comparing sequenced segments of the tomato and Arabidopsis genomes: Large-scale duplication followed by selective gene loss creates a network of synteny. Proc Natl Acad Sci USA, 2000, 97: 9121–9126

    Article  Google Scholar 

  49. Multani D S, Khush G S, Reyes B G, et al. Alien genes introgression and development of monosomic alien addition lines from Oryza latifolia Desv. to rice, Oryza sativa L. Theor Appl Genet, 2003, 107: 395–405

    Article  Google Scholar 

  50. Yin P, Hartemink A J. Theoretical and practical advances in genome halving. Bioinformatics, 2005, 21: 869–879

    Article  Google Scholar 

  51. Yogeeswaran K, Frary A, York T L, et al. Comparative genome analyses of Arabidopsis spp.: Inferring chromosomal rearrangement events in the evolutionary history of A.thaliana. Genome Res, 2005, 15: 505–515

    Article  Google Scholar 

  52. Jena K K, Kochert G. Restriction fragment length polymorphism analysis of CCDD genome species of the genus Oryza L. Plant Mol Bio, 1991, 16: 831–839

    Article  Google Scholar 

  53. Wang Z Y, Second G, Tanksley S D. Polymorphism and phylogenetic relationships among species in the genus Oryza as determined by analysis of nuclear RFLPs. Theor Appl Genet, 1992, 83: 565–581

    Article  Google Scholar 

  54. Lim K Y, Leitch I J, Leitch A R. Genomic characterization and the detection of raspberry chromatin in polyploid Rubus. Theor Appl Genet, 1998, 97: 1027–1033

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074, China

    Lan Weizhen & Qin Rui

  2. Key Laboratory of Ministry of Education for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, China

    Qin Rui, Li Gang & He Guangcun

Authors
  1. Lan Weizhen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Qin Rui
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Li Gang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. He Guangcun
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to He Guangcun.

Additional information

These authors contributed equally to this work.

About this article

Cite this article

Lan, W., Qin, R., Li, G. et al. Comparative analysis of A, B, C and D genomes in the genus Oryza with C 0 t-1 DNA of C genome. CHINESE SCI BULL 51, 1710–1720 (2006). https://doi.org/10.1007/s11434-006-2049-5

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11434-006-2049-5

Keywords

Search

Navigation