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Genetic diversity of SIRE-1 retroelements in annual and perennial glycine species revealed using SSAP

Cellular & Molecular Biology Letters volume 12, pages 103–110 (2007)Cite this article

Abstract

Sequence Specific Amplification Polymorphisms (SSAP) were used to measure the distribution and structure of SIRE-1 retroelement populations in annual and perennial Glycine species. For SSAP analysis, primers corresponding to a region immediately upstream of the 3’LTR of the soybean retroelement SIRE-1 were chosen. Analysis reveals that SIRE-1 is present throughout the Glycine genus and shows that the annual species have similar SIRE-1 populations whilst the perennial species have much more distinct and diverse populations. The high number of species-specific subgroups suggest that SIRE-1 has been active and evolving independently in each species during the course of Glycine evolution.

References

  1. Doyle, J.J., Doyle, J.L., Rauscher, J.T. and Brown, A.H.D. Diploid and polyploid reticulate evolution throughout the history of the perennial soybeans (Glycine subgenus Glycine) New Phytol. 161 (2003) 121–132.

    Article  CAS  Google Scholar 

  2. Ahrent, D.K. and Caviness, C.E. Natural cross-pollination of twelve soybean cultures in Arkansas. Crop Sci. 34 (1994) 376–378.

    Article  Google Scholar 

  3. Hymowitz, T., Singh, R.J. and Kollipara, K.P. The genomes of Glycine. Plant Breed. Rev. 16 (1998) 289–317.

    CAS  Google Scholar 

  4. Laten, H.M. Phylogenetic evidence for Ty1-copia-like endogenous retroviruses in plant genomes. Genetica 107 (1999) 87–93.

    Article  PubMed  CAS  Google Scholar 

  5. Laten, H.M., Havecker, E.R. and Voytas, D.F. SIRE-1, an endogenous retrovirus family from Glycine max, is highly homogeneous and evolutionarily young. Mol. Biol. Evol. 20 (2003) 1222–1230.

    Article  PubMed  CAS  Google Scholar 

  6. Gribbon, B.M., Pearce, S.R., Kalendar, R., Schulman, A., Paulin, L., Jack, P., Kumar, A. and Flavell, A.J. Phylogeny and transpositional activity of Ty1-copia group retrotransposons in cereal genomes. Mol. Gen. Genet. 261 (1999) 883–891.

    Article  PubMed  CAS  Google Scholar 

  7. Pearce, S.R., Knox, M., Ellis, T.H.N., Flavell, A.J. and Kumar, A. Pea Ty1-copia group retrotransposons: Transpositional activity and use as molecular markers to study genetic diversity in Pisum. Mol. Gen. Genet. 263 (2000) 898–907.

    Article  PubMed  CAS  Google Scholar 

  8. Tam, S.M., Mhiri, C., Vogelaar, A., Kerkveld, M., Pearce, S.R. and Grandbastien, M-A. Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR. Theor. Appl. Genet. 110 (2005) 819–831.

    Article  PubMed  CAS  Google Scholar 

  9. Waugh, R., McLean, K., Flavell, A.J., Pearce, S.R., Kumar, A., Thomas, B.B.T. and Powell, W. Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence specific amplification polymorphisms (SSAP). Mol. Gen. Genet. 253 (1997) 687–694.

    Article  PubMed  CAS  Google Scholar 

  10. Pearce, S.R., Stuart-Rogers, C., Kumar, A. and Flavell, A.J. Rapid isolation of plant Ty1-copia group retrotransposons LTR sequences for molecular marker studies. Plant J. 19 (1999) 1–7.

    Article  Google Scholar 

  11. Nei, M. and Takezaki, N. Estimation of genetic distances and phylogenetic trees from DNA analysis. Proc. 5 th World Cong. Genet. Appl. Livestock Prod. 21 (1983) 405–412.

    Google Scholar 

  12. Liu, K. and Muse, S.V. PowerMarker: Integrated analysis environment for genetic marker data. Bioinformatics 21 (2005) 2128–2129.

    Article  PubMed  CAS  Google Scholar 

  13. Felsenstein, J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (1985) 783–791.

    Article  Google Scholar 

  14. Peterson-Burch, B.D., Wright, D.A., Laten, H.M. and Voytas, D.F. Retroviruses in plants? Trends Genet. 16 (2000) 151–152.

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK

    Catherine Chesnay & Amar Kumar

  2. School of Life-Sciences, University of Sussex, Brighton, BN1 9QG, UK

    Stephen R. Pearce

Authors
  1. Catherine Chesnay
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  2. Amar Kumar
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  3. Stephen R. Pearce
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Correspondence to Stephen R. Pearce.

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Chesnay, C., Kumar, A. & Pearce, S.R. Genetic diversity of SIRE-1 retroelements in annual and perennial glycine species revealed using SSAP. Cell Mol Biol Lett 12, 103–110 (2007). https://doi.org/10.2478/s11658-006-0054-y

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  • DOI: https://doi.org/10.2478/s11658-006-0054-y

Key words

  • Glycine
  • Retroelement
  • SSAP
  • phylogeny
  • SIRE-1
  • copia

Cellular & Molecular Biology Letters

ISSN: 1689-1392

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