| Summary: | This study reports the development of a set of 20 highly polymorphic genomic SSR markers which can be used for both cultivar identification and genetic diversity studies in several <i>Origanum</i> species, including some of the most popular ones like Greek oregano (<i>Origanum vulgare</i> L. ssp. <i>hirtum</i>), common oregano (<i>O. vulgare</i> L. ssp. <i>vulgare</i>), and sweet marjoram (<i>O. majorana</i> L.). Analysis of the polymorphic information content (PIC) showed an average PIC value of 0.75 with a minimum of 0.41 and a maximum of 0.89, where 17 of the markers showed PIC values above 0.73. Comparative analysis of the genetic diversity of eight natural populations of Greek oregano in Bulgaria showed that six of the genomic SSR markers revealed significantly higher portions of genetic diversity in the populations, compared to 12 EST SSR markers used in our previous study. We also compared the performance of the same six genomic SSR markers with the results for eight SRAP primer combinations, which showed that SRAP markers captured more precisely the genetic structure in natural populations. The developed highly polymorphic genomic SSR markers can be successfully applied to evaluation of the genetic diversity in the genus <i>Origanum,</i> based on the expected and observed heterozygosity in the populations as well as for easy identification of breeding lines and cultivars based on unique SSR fingerprints.
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