4.14.1 The microsatellite marker (2024)

This marker consists of a repeat in sequence of a few (2 or 3) bases. For example, the sequence of the bases T and A can result in a TATATATA, which is a four times repeat of TA. Microsatellite markers (micros) generally have 8 to 30 or even up to 40 repeats. They are also called tandem repeats. Each different number of repeats is considered to be an allele of the micro. Micros can have very many alleles and are, therefore, useful to describe genetic differences between animals (and homologous chromosomes). There are very large numbers (thousands) of micros available in many domestic animal species. In theory, these micros would be ideal for most of the purposes that genetic markers are used for.

However, it takes a lot of time and effort to genotype animals for many different micros. The reason is that the alleles of these markers differ in length and that is how they are genotyped: identify differences in length. Each micro has a distinct start and end code. Based on that, the marker part of the DNA is identified with specific primers that find those distinct bits of DNA on the genome. So for each different micro, different primers are required and a new analysis needs to be performed.

For large-scale genotyping single nucleotide polymorphism (SNP) markers are developed and much easier to automate.