Microsatellites, also known as Simple Sequence Repeats (SSRs), or sometimes Short Tandem Repeats (STRs), are short stretches of DNA which consist of an array of simple tandemly repeated mono, di-, tri-, tetra-, penta or hexanucleotide repeats such as (A)n, (CA)n, (GA)n, (GTA)n, (ATT)n, (GATA)n, (ATTTT)n, (ACGTCG)n.Based on the length of the repeated stretch, they are classified as:

1) Satellites: Highly repeated segments of 100 nt or greater forming more or less uniform tracts 103 - 107 nt long.

2) Minisatellites: Moderately repeated segments of 10 - 100 nt forming more or less uniform tracts 102 - 105 long.

3) Microsatellites: Short segments of 1-6 bp repeated in more or less uniform tracts upto ~102 bp long. They are classified as Mono-, Di-, Tri-, Tetra-, Penta-, and Hexanucleotide repeats.

Microsatellites as markers in common carp

Microsatellites have become premier genetic markers because:

1) They are unaffected by environment, detectable in all stages of development and ubiquitous in number covering the entire genome;

2) differences in the number of repeats of microsatellite result in multiple alleles at a locus;

3) microsatellites are inherited in a Mendelian fashion.

4) Development of molecular markers is important in common carp for construction of linkage map, fingerprinting of strains for breeding, and marker-assisted selection.

As a result, microsatellites are used extensively as markers in studies involving forensics and establishment of kinship. Microsatellites have found widespread use as markers for genetic analysis at or below the species level. Their general high mutation rate ensures high level of polymorphism and hence become useful for examining relationships among individuals and breeding groups within populations; conservation genetics; population genetic structure analysis; linkage mapping; marker assisted breeding etc. Though, development of microsatellite markers is quite labour intensive, it turns out to be effective and cost-effective in the long run.

Detection of Microsatellite

The most common way to detect microsatellites is to design PCR primers that are unique to one locus in the genome and that base pair on either side of the repeated portion (Figure. 1). Therefore, a single pair of PCR primers will work for every individual in the species and produce different sized products for each of the different length microsatellites. What¡¯s more important, cost effectiveness of the assay can be achieved by combining two or more loci for simultaneous analysis through multiplex PCR. By using the fluorescent-labelled primers and automated sequencers, the entire process of microsatellite analysis can be automated (Figure. 2).

Figure.1 Stylized examples of microsatellite data. Data were produced by gel electrophoresis.

Figure.2 These data were produced in our lab by analysis on an automated capillary electrophoresis-based DNA sequencer (ABI 3130xl). The data are line graphs with the location of each peak on the X-axis representing a different sized PCR product and the color of each peak indicates the alleles of microsatellite.

Chinese Academy Of Fishery Science