Tracing and introducing SSR markers in Cannabis sativa by exploring in transcriptome

Cannabis sativa L. is an important economic plant for the production of medical, food, fiber and oils. Nevertheless, lack of sufficient simple sequence repeat (SSR) markers has limited the development of cannabis genetic research. In this study, transcriptome sequences were used for identification and introduction of SSR markers in order to assess genetic diversity and separation of fiber and drug types. Based on the cannabis RNA-Seq data, 3383 SSR were identified from 1402 reads in fiber type whiles this number was 10381 for 4743 reads in drug type. Among these markers, trinucleotide repeat motifs were the most abundant, followed by mononucleotide and dinucleotide. Primers were successfully designed for amplification of 234 SSR markers from 152 individual sequences in fiber and 1543 SSR markers from 1372 individual sequences in drug using Primer3 with default parameters. This study outlines the first large-scale development of SSR markers for cannabis. The effectiveness of these molecular markers should be tested using different Iranian Marijuana populations and could be particularly useful for cannabis populations breeding.