Simple sequence repeats (SSRs), also known as microsatellites, have been shown to be one of the most powerful genetic markers in biology. They are common, readily identified DNA features consisting of short (1–6 bp), tandemly repeated sequences, widely distributed throughout eukaryotic genomes and have been found in all prokaryotic and eukaryotic genomes.

SSRs are highly polymorphic, owing to the mutation affecting the number of repeat units which makes them informative and excellent markers for a wide range of applications including high-density genetic mapping, molecular tagging of genes, genotype identification, analysis of genetic diversity, paternity exclusion, phenotype mapping and marker assisted selection of crop plants.

SSRs were initially considered to be evolutionally neutral. SSRs are a source of abundant, non-deleterious mutations that provide recognized role in the process of evolutionary adaptatio.SSR stability may be correlated with overall levels of genomic stability as mutations which affect SSR stability, such as those involved in DNA mismatch repair, can also influence genomic stability.

The nature of SSRs gives them a number of advantages over other molecular markers; (i) multiple SSR alleles may be detected at a single locus using a simple PCR based screen (ii) SSRs are evenly distributed all over the genome, (iii) they are co-dominant, (iv) very small quantities of DNA are required for screening, and (v) analysis may be semi-automated. Furthermore, SSRs demonstrate a high degree of transferability between species, as PCR primers designed to an SSR within one species frequently amplifies a corresponding locus in related species, making them excellent markers for comparative genetic and genomic analysis.

The potential biological function and evolutionary relevance of SSRs is currently under scrutiny and leading to a greater understanding of genomes and genomics.Initial suggestions that the majority of DNA was either ‘junk’ or had no biological function are being challenged by the discovery of new functions for these sequences. Various functional roles have now been attributed to SSRs. For example, SSRs are believed to be involved in gene expression, regulation and function and there are numerous lines of evidence suggesting that SSRs in noncoding regions may also be of functional significance.

Furthermore, SSRs provide hotspots of recombination, a variety of SSRs have been found to bind nuclear proteins and there is direct evidence that SSRs can function as transcriptional activating elements