Identification, characterization and validation of SSR markers from the gerbera EST database.

Genic microsatellites, are currently among the best DNA markers because they often represent transcribed genes with putative function, and their cost is relatively low. In this study, 7,529 non-redundant (nr) ESTs from gerbera, obtained from public databases, were identified and characterized to validate their use as genic microsatellite markers. Of the assembled nr ESTs, 1,244 contained SSRs, and trinucleotides (GAA) were found to be the most abundant repeats at 42.3%, followed by dinucleotides (GA) at 25.3% and tetranucleotides (TTTG) at 6.2%. Gene ontology (GO) characterization was used to perform functional annotation of unigenes containing SSRs, of which 36.87% revealed significant sequence similarities with other species, indicating the top species with the highest similarity. A total of 647 primer pairs may be designed from the nr SSR-positive ESTs (excluding those with only mononucleotide repeats) for amplification of potential genic markers. A sample of 50 primer pairs was tested, and 17 were validated. The identified markers were highly polymorphic and able to differentiate 34 genotypes, representing the genetic variation within commercial and wild varieties. This study provides insight as to the frequency and distribution of SSRs in the gerbera transcriptome and demonstrates the successful development of genic SSRs. We expect that the potential markers described here can greatly expand the repertoire of DNA markers available for both breeding and genetic studies in 'Gerbera spp'.