Microsatellites

Microsatellites, also called simple sequence repeats (SSRs) or short tandem repeats (STRs), are short blocks of DNA in which a motif of 1–6 base pairs is repeated in tandem. They are highly abundant and widely distributed in eukaryotic genomes, occurring in both noncoding and coding regions. Common motifs include dinucleotide repeats such as (CA)n or (GT)n, and tri- or tetranucleotide repeats such as (CAG)n or (GATA)n. The number of repeats varies among individuals, making microsatellites among the most polymorphic genetic markers known.

Mutation and polymorphism: Microsatellites have relatively high mutation rates, primarily due to DNA polymerase slippage during replication. This generates new allele lengths by changing the number of repeats, producing many alleles per locus. Mutation rates are typically in the range of 10^-3 to 10^-5 per generation, depending on motif length, repeat number, and genomic context. Because of their codominant inheritance, both alleles at a locus can be observed in heterozygotes.

Applications: Microsatellites are widely used as genetic markers in linkage mapping, population genetics, forensic science, paternity testing, and conservation genetics. In laboratories, they are amplified by polymerase chain reaction using locus-specific primers, and allele sizes are determined by capillary electrophoresis or similar sizing methods. They can be multiplexed to assay many loci in a single reaction. Microsatellites are typically considered neutral markers, though some may be linked to functional regions or genes of interest.

Limitations and notes: Scoring can be affected by stutter bands and null alleles (non-amplifying alleles due to primer binding-site mutations). Cross-species transferability of primers is variable. With the rise of SNP genotyping and sequencing-based approaches, the use of microsatellites remains prominent in many studies due to their high informativeness per locus, but data comparability across platforms requires standardization.