Genome-wide in silico analysis of microsatellites in Sorghum bicolor

Abstract

Simple sequence repeats (SSRs) are highly variable DNA sequences that were widely used for genetic and breeding studies in several plant species. In this study, 94698 genome-SSRs of Sorghum was in silico predicted by searching its genomic sequence. After mining, the frequency and density of the SSRs have been analyzed in detailed. Results showed that the density of SSRs was 154.98 counts/Mbp in sorghum genomes, and trinucleotide repeats(27.35%) motifs appeared to be the most abundant type in sorghum, the dinucleotide, tetranucleotide, hexanucleotide, pentanucleotide and mononucleotide repeats are 20.69%, 17.04%, 15.21%, 14.99% and 4.76%, respectively. Moreover, Tri- and di- motif were the most common motif followed by tri-, tetr-, and pen-nucleotide motif. The A-rich repeats are predominant in the most frequency SSRs. The SSR sizes was not evenly distributed, hexa-motif giving the longest SSRs. Following with the length increasing, the number of SSRs was decreased. The further analysis suggest that 2621 SSRs contained more than one microsatellites which recognized as compound SSRs, of which (AT-AC)279 giving the highest frequency. Furthermore, the results showed that Sorghum genome was enrich for SSR developing and microsatellite markers can be expected to enhance the power and resolution of genome analysis in sorghum.