TITLE:
In Silico Exploration of Cannabis sativa L. Genome for Simple Sequence Repeats (SSRs)
AUTHORS:
Incoronata Galasso, Elena Ponzoni
KEYWORDS:
Microsatellite, Relative Density, Relative Abundance, PCR Amplification
JOURNAL NAME:
American Journal of Plant Sciences,
Vol.6 No.19,
December
18,
2015
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.