Development of Genic SSR (Simple Sequence Repeat) Markers Based on an Oregano (Origanum vulgare L.) Transcriptome Assembly

Developments in next generation sequencing technologies and bioinformatic analyses enable the identification of sequence specific DNA markers at the whole genome/transcriptome level. During the last decade, diversification of the next generation sequencing platforms as well as the associated sequence analysis algorithms have made generic marker systems such as RAPD (random amplified polymorphic DNA) and ISSR (inter simple sequence repeat) almost obsolete and sequence specific markers constitute useful genomic tools for applications in plant molecular genetics. The aim of the present work was to develop genic SSR (simple sequence repeat) markers specific for the well-known medicinal and aromatic herb, oregano (Origanum vulgare L.). Although the Origanum genus hosts widely-recognized medicinal and aromatic species, only 33 genome-specific markers have been developed to date for the genus. In the course of the present work, the transcriptome sequence of O. vulgare L. ssp. vulgare, one of the most widely known members of the Origanum genus, was assembled via a de novo transcriptome assembly approach. The assembly was scanned for the identification of trinucleotide SSRs. GC rich loci were found to be the most abundant simple sequence repeats, which is indeed characteristic for coding sequences. While genic SSRs are more conserved compared to genomic SSRs, markers that represent transcribed loci are more likely to be useful for trait association studies. In the course of the present work, the loci identified in the transcriptome sequences were used in the high-throughput marker development process, yielding a total of 1731 sequence-specific genic SSR markers. Since SSR polymorphisms located in open reading frames and 5’/3’ UTR (untranslated region) carry the potential to affect the amino acid sequence or protein folding and the level of gene expression, the markers introduced in the present work constitute a genome-specific set of candidate functional markers.