In silicocomparative analysis of SSR markers in plants

Abstract

BackgroundThe 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.ResultsIn 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.ConclusionsThe 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.

Mining of microsatellites using next generation sequencing of seabuckthorn (Hippophae rhamnoides L.) transcriptome

“…4). In our data, there is a higher preference for GC3 and similar preference has been reported in case of other plants (Victoria et al 2011). …”

“…Among trinucleotide motifs, (AAG)n repeat class was the most predominant as also observed in earlier studies in other plant species (Tang et al 2009;Roorkiwal and Sharma 2011;Victoria et al 2011). Grover and Sharma (2004) suggested tendency of making alternative DNA structures by repeat motif as the reason underlying such abundance.…”

“…Similar abundance of GA dinucletide repeats, has been observed in many other plant species in the recent past (Tang et al 2009;Roorkiwal and Sharma 2011;Victoria et al 2011). This repeat class is known to play an active role in gene regulation in both animal and plant species (Trivedi 2004).…”

Biodiversity Measures in Agriculture Using DNA

“…The primers to reveal SSR loci are designed to be complementary to these non repetitive flanking sequences -so the disadvantage of SSR markers is the necessity of knowing the sequences before the primers design. SSR markers are more frequently in no coding regions of the genome, those which will not be transcribed or translated into DNA or proteins (Victoria et al, 2011). SSR are used multialellic, what means that for a single locus more than two forms of the marker, composed by various number of repetitions, may be found (Figure 4).…”

Microsatellites mining in date palm (Phoenix dactylifera L.) and their cross transferability across Arecaceae family

“…Several reports on the mining of SSRs across plant genomes are reported over the years. There is a non-random distribution of microsatellite repeats in coding and noncoding regions in chloroplast genome of Brassicaceae family (Sumit et al 2010 (Victoria et al 2011). In human genome, 3% encompasses SSR motifs (Subramanian et al 2003).…”