Microsatellites (simple sequence repeats, SSRs) that consist of repetitive sequences of one to six bases are ubiquitous in most eukaryotic genomes. The use of molecular markers for this region is efficacious in molecular-assisted breeding, molecular phylogenetics, and population genetics. Recently, the detection of a number of SSRs using a high-throughput DNA sequencing assay has become possible. Particularly, microsatellite capture sequencing using our developed protocol can detect SSRs more effectively by enriching the DNA library using an SSR probe. Our protocol used in this study demonstrates the possibility of using low-input DNA (≥1 ng), and while the use of restriction enzymes was more suitable for identifying the heterozygous genotype than sonication was, sonication facilitated the detection of various SSR flanking regions with both species-specific and common characteristics more than restriction enzyme digestion did. Moreover, a simulation analysis using various scale reads estimated that a few thousand SSRs could be detected from 50 K reads per sample. Furthermore, we described an in silico polymorphic detection and phylogenetic analysis method based on microsatellite capture sequencing data.
Part of the book: Genotyping