Sesame (Sesamum indicum L.) is an important oilseed crop with high-quality seed oil and many antioxidant properties. Owing to its commercial and medicinal values, there is a renewed interest among agricultural scientists in this ancient crop. Efforts to strengthen the sesame-specific marker base have been initiated in the recent past; however, the available number of microsatellite markers is still not sufficient for the development of high-resolution genetic linkage maps for important agronomic traits and there is a need to increase the number of informative DNA markers in sesame. In the present study, we developed 25 microsatellite markers by employing the selective hybridization strategy and 95 mining expressed sequence tags of the NCBI database. This new set of microsatellite markers was characterized and screened for genetic diversity in an array of 16 sesame germplasms. Of the 120 SSRs, 92 were polymorphic, consisting of 18 SSRs from selective hybridization and 74 from the EST data set. The number of alleles per microsatellite locus ranged from 2 to 5, with an average of 3.11 alleles. The allele size ranged widely (100-510 bp) among the primer pairs. Polymorphic information content estimates ranged from 0.2982 to 0.912. Jaccard's similarity coefficient ranged from 0.21 to 0.82. The potential of the markers was assessed by diversity analysis using the sequential hierarchical agglomerative nonoverlapping clustering technique of the unweighted pair group method of arithmetic means on a set of 16 genotypes of sesame, including 2 wild species. Results supported the hypothesis that S. malabaricum could be the immediate progenitor of the cultivar species and that S. mulayanum is distinct from S. malabaricum and S. indicum, while suggesting hardly any diversity among the cultivars.

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