Microsatellites, also known as simple sequence repeats (SSRs) or short tandem repeats (STRs) are repeat DNA sequence motifs consisting of 1-6 base pairs tandemly repeated several times at each locus. They are observed in almost all genomes with a significant percentage and suffer higher rates of mutation than the rest of the genome. A particular microsatellite locus can be identiﬁed by its ﬂanking sequences that are generally conserved across individuals of the same species and sometimes of different species. Oligonucleotide primers can be designed to bind to the ﬂanking region and ampliﬁcation of a microsatellite locus. Individual allele at a locus differ in the number of tandem repeats of unit sequence owing to gain or loss of one or more repeats and can be differentiated by high resolution gel electrophoresis according to their size.
Based on the number and kind of nucleotides in a repeating unit, microsatellites are classified into four kinds namely perfect, imperfect, compound, complex. Imperfect repeats (e.g. GCGCGCAGCGC) are more stable and are used in various genetic studies, including DNA fingerprinting and population genetics. Microsatellite can also be classified into mono-, di-, tri-, tetranucelotide repeat unit. Trinucleotide and tetranucleotide repeats are the most common choices for molecular genetic studies.
Microsatellites are widely distributed in both coding and non-coding regions of fish genome. As the allele variants at microsatellite loci are co-dominant and inherited in Mendelian fashion, traditional approaches such as Hardy-Weinberg equilibrium can be used in initial data analysis. The variations in non-coding microsatellites are independent of natural selection, hence such microsatellites are widely used to assess the effective population size of stocks, genetic diversity, stock identiﬁcation, levels of inbreeding, population structure and gene ﬂow, parentage and quantitative traits.