biologia plantarum

Biologia plantarum 54:353-356, 2010 | DOI: 10.1007/s10535-010-0062-7

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

I. Wiesner^1,*, D. Wiesnerová¹

¹ Institute of Plant Molecular Biology, Group of Molecular Biodiversity, Biology Centre AS CR, České Budějovice, Czech Republic

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.

Keywords: bioinformatics; information entropy; Markov chain; primary sequence analysis; principal component analysis

Subjects: Begonia × tuberhybrida; DNA random walk; multiallelic loci; principal component analysis

Received: July 15, 2008; Accepted: April 9, 2009; Published: June 1, 2010  Show citation