Microsatellite DNA markers, a fi sheries perspective Part 1: The nature of microsatellites

Many new classes of Polymerase Chain Reaction (PCR) -based genetic markers have been developed over the last decade. Of these, microsatellite markers are widely regarded as one of the most useful identifi ed so far1,2,3. The signifi cance of microsatellite markers derives from their abundance in the genome, single locus nature, simplicity of assay, high levels of allelic diversity, mendelian inheritance, co-dominance and selective neutrality. Microsatellites are defi ned as tandem arrays of short DNA sequence motifs of 1-6 base pairs in length. This structure has lead to a number of alternative names such as short or simple tandem repeats (STRs), simple sequence repeats (SSRs), simple sequence length polymorphisms (SSLPs) and variable number tandem repeats (VNTRs)4. These are represented as small arrays of repeats with lengths ranging from somewhere around a dozen up to a few hundred base pairs, with many being less than 100 base pairs in total length. Microsatellites are abundantly distributed across the genome, demonstrate high levels of allele polymorphism and can easily be amplifi ed with PCR. These features provide the underlying basis for their successful application in a wide range of fundamental and applied fi elds of biology and medicine. In the fi eld of fi sheries and aquaculture, microsatellites are useful for characterisation of genetic stocks, broodstock selection, constructing dense linkage maps, mapping economically important quantitative traits and identifying genes responsible for these traits and application in marker assisted breeding programmes5.