<i>In Silico</i> Exploration of <i>Cannabis sativa</i> L. Genome for Simple Sequence Repeats (SSRs)

Abstract

Simple sequence repeat (SSR) or microsatellite markers, are a valuable tool for several purposes such as evaluation of genetic diversity, fingerprinting, marker assisted selection, and breeding. Recent developments in sequencing technologies and bioinformatics analyses provide new opportunity to produce a high number of less costly SSRs. Here, we used for the first time a wholegenome shotgun sequencing of the nuclear genome and transcriptome of hemp to develop microsatellite markers for C. sativa L. (hemp). Hemp is an ancient crop that is widely cultivated as a source of fiber, seeds and medicine. The analysis using the MISA program revealed a total of 407,491 SSRs (from mono-nucleotide to deca-nucleotide) in the hemp genome and 15,655 SSRs in the transcriptome. Analysis of the frequency and distribution of SSRs showed that the mono-nucleotide repeats were the most abundant (55.4%) in the genome whereas the tri-nucleotide motifs (30.4%) resulted highly predominant in the transcriptome. Poly A/T was predominant over poly G/C in both genome and transcriptome sequences. Among the tri-nucleotide repeats AAG/CTT (34.5%) resulted the most abundant in the transcriptome. Repeats larger than tri-nucleotide were also observed in the hemp genome and transcriptome. Dinucleotide and tri-nucleotide repeat expansion of 8605 and 1401 times iteration were observed however, other SSR expansion more than 387 times repetition was not found. Primers were designed for amplification of few long microsatellite sequences which could be used to identify polymorphism and to study genetic diversity among hemp cultivars.