Skip to main content

2D random walk representation of Begonia × tuberhybrida multiallelic loci used for germplasm identification

Abstract

In this study, we wanted to inspect whether the evolutionary driven differences in primary sequences could correlate, and thus predict the genetic diversity of related marker loci, which is an important criterion to assess the quality of any DNA marker. We adopted new approach of quantitative symbolic DNA sequence analysis called DNA random walk representation to study multiallelic marker loci from Begonia × tuberhybrida Voss. We described significant correlation of random walk-derived digital invariants to genetic diversity of the marker loci. Specifically, on the 3D-contour plot of multivariate principal component analysis (PCA), we revealed statistical correlation between the first two PCA factors and the number of alleles per marker locus. Based on that correlation, we suggest that DNA walk representation may predict allele-rich loci solely from their primary sequences, which improves current design of new DNA germplasm identificators.

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

Abbreviations

PCA:

pricipal component analysis

References

  • Bai, F-L., Liu, Y-Z., Wang, T-M.: A representation of DNA primary sequences by random walk. — Math. Biosci. 209: 282–291, 2007.

    Article  CAS  PubMed  Google Scholar 

  • Berger, J.A., Mitra, S.K., Carli, M., Neri, A.: Visualization and analysis of DNA sequences using DNA walks. — J. Franklin. Inst. Eng. Appl. Math. 341: 37–53, 2004.

    Article  Google Scholar 

  • Cordeiro, A.I., Sanchez-Sevilla, J.F., Alvarez-Tinaut, M.C., Gomez-Jimenez, M.C.: Genetic diversity assessment in Portugal accessions of Olea europaea by RAPD markers. — Biol. Plant 52: 642–647, 2008.

    Article  CAS  Google Scholar 

  • Dodin, G., Pierre, V., Levoiretal, P.: Fourier and wavelet transform analysis: a tool for visualizing regular patterns in DNA sequences. — J. theor. Biol. 206: 323–326, 2000.

    Article  CAS  PubMed  Google Scholar 

  • Griga, M., Horáček, J., Klenotičová, H.: Protein patterns associated with Pisum sativum somatic embryogenesis. — Biol. Plant. 51: 201–211, 2007.

    Article  CAS  Google Scholar 

  • Li, H., Zhang, S.G., Gao, J.M., Wang, C.G., Zhang, Y., Qi, L.W., Chen, L., Song, W. Q.: Development of a sequence characterized amplified region (SCAR) marker associated with high rooting ability in Larix. — Biol. Plant. 52: 525–528, 2008.

    Article  CAS  Google Scholar 

  • Nandy, A., Harle, M., Basak, S.C.: Mathematical descriptors of DNA sequences: development and applications. — Arkivoc 9: 211–238, 2006.

    Google Scholar 

  • Nandy, A., Basak, S.C., Gute, B.D.: Graphical representation and numerical characterization of H5N1 avian flu neuraminidase gene sequence. — J. Chem. Inform. Model. 47: 945–951, 2007.

    Article  CAS  Google Scholar 

  • Peng, C.-K., Buldyrev, S.V., Goldberger, A.L., Havlin, S., Sciortino, F., Simons, M., Stanley, H.E.: Long-range correlations in nucleotide sequences. — Nature 356: 168–170, 1992.

    Article  CAS  PubMed  Google Scholar 

  • Stajich, J.E., Block, D., Boulez, K., Brenner, S.E., Chervitz, S.A., Dagdigian, C., Fuellen, G., Gilbert, J.G., Korf, I., Lapp, H., Lehväslaiho, H., Matsalla, C., Mungall, C.J., Osborne. B.I., Pocock, M.R., Schattner, P., Senger, M., Stein, L.D., Stupka, E., Wilkinson, M.D., Birney, E.: The Bioperl toolkit: Perl modules for the life sciences. — Genome Res. 12: 1611–1618, 2002.

    Article  CAS  PubMed  Google Scholar 

  • Tsonis, A.A., Kumar, P., Elsner, J.B., Tsonis, P.A.: Wavelet analysis of DNA sequences. — Phys. Rev. E 53: 1828–1834, 1996.

    Article  CAS  Google Scholar 

  • Wiesner, I., Wiesnerova, D.: Sequence characterized markers from Begonia × tuberhybrida Voss. — Eur. J. hort. Sci. 73: 244–247, 2008.

    CAS  Google Scholar 

Download references

Acknowledgements

This study was supported by the program of Targeted Research DP3-PP2 of the National Research Program, project No. 1QS500510566 of the Academy of Sciences of the Czech Republic, and by the project AV CR No. VZ-AVOZ 50510513. We thank Jan Wiesner for technical assistance.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to I. Wiesner.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Wiesner, I., Wiesnerová, D. 2D random walk representation of Begonia × tuberhybrida multiallelic loci used for germplasm identification. Biol Plant 54, 353–356 (2010). https://doi.org/10.1007/s10535-010-0062-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10535-010-0062-7

Additional key words

  • bioinformatics
  • information entropy
  • Markov chain
  • primary sequence analysis
  • principal component analysis