In silico comparative analysis of SSR markers in plants

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.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.In agriculture, productivity is affected by environmental conditions such as drought, salinity, high radiation and extreme temperatures faced by plants during their life cycle, that impose severe limitations to the growth and propagation, restricting their genetic potential and, ultimately, reflecting yield losses of agricultural crops. Although, advances have been achieved through classical breeding, further progress is needed to increase abiotic stress tolerance in cultivated plants. New gene targets need to be identified in order to reach these goals, requiring extensive studies concerning the biological processes related to abiotic stresses. Comparative analysis between primitive and related groups of cultivated species may shed some light on the understanding of these processes.Microsatellites or SSRs (Simple Sequence Repeats) are sequences in which one or few bases are tandemly repeated, ranging from 1-6 base pair (bp) long units. They are ubiquitous in prokaryotes and eukaryotes, present even in the smallest bacterial genomes [1-3]. Variations in SSR regions originate mostly from errors during the replication process, frequently DNA Polymerase slippage. These errors generate base pair i