In silico comparative analysis of SSR markers in plants

BMC Plant Biol. 2011 Jan 19;11:15. doi: 10.1186/1471-2229-11-15.


Background: The adverse environmental conditions impose extreme limitation to growth and plant development, restricting the genetic potential and reflecting on plant yield losses. The progress obtained by classic plant breeding methods aiming at increasing abiotic stress tolerances have not been enough to cope with increasing food demands. New target genes need to be identified to reach this goal, which requires extensive studies of the related biological mechanisms. Comparative analyses in ancestral plant groups can help to elucidate yet unclear biological processes.

Results: In this study, we surveyed the occurrence patterns of expressed sequence tag-derived microsatellite markers for model plants. A total of 13,133 SSR markers were discovered using the SSRLocator software in non-redundant EST databases made for all eleven species chosen for this study. The dimer motifs are more frequent in lower plant species, such as green algae and mosses, and the trimer motifs are more frequent for the majority of higher plant groups, such as monocots and dicots. With this in silico study we confirm several microsatellite plant survey results made with available bioinformatics tools.

Conclusions: The comparative studies of EST-SSR markers among all plant lineages is well suited for plant evolution studies as well as for future studies of transferability of molecular markers.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics
  • Base Composition / genetics
  • Bryopsida / genetics
  • Chlamydomonas reinhardtii / genetics
  • Codon / genetics
  • Computational Biology / methods*
  • Databases, Nucleic Acid
  • Dimerization
  • Expressed Sequence Tags
  • Genetic Loci / genetics
  • Genetic Markers
  • Genome, Plant / genetics
  • Minisatellite Repeats / genetics*
  • Molecular Sequence Annotation
  • Nucleotides / genetics
  • Open Reading Frames / genetics
  • Oryza / genetics
  • Plants / genetics*
  • Regulatory Sequences, Nucleic Acid / genetics
  • Selection, Genetic
  • Species Specificity


  • Codon
  • Genetic Markers
  • Nucleotides