STR marker

Dinucleotide repeat: --------CACACACACACACACACACACA---------- (11 CA units)

Trinucleotide repeat: ------GATGATGATGATGATGATGATGATGAT------ (9 GAT units)

Tetranucleotide repeat: --------GATAGATAGATAGATAGATAGATAGATAGATA----- (8 GATA units)

If there are more than two variants at a particular locus within a population, the locus is called multiallelic. This is typical of STR markers.

The number of repeats is variable, so a certain number of repeats results in a defined length of the marker. The length is measurable and defines the corresponding allele of the marker. In the laboratory, the marker is amplified by PCR and the fragment length is determined by capillary electrophoresis.

The different variants found in a population are the result of mutations that are passed on through the generations and occur with certain frequencies (allele frequencies) in a population over time. In STR markers, such mutations arise comparatively often: during DNA replication, the strands occasionally slip (replication slippage), so that a repeat unit is gained or lost. Depending on the marker, the mutation rate is around 1 in 1,000 to 1 in 10,000 per generation (Ellegren 2004).

An individual is either homozygous (2 identical alleles) or heterozygous (2 different alleles) at a marker.

Since the 1990s, STR markers have been the method of choice for individual identification and parentage verification (see Genetic Proof of Origin and Likelihood Ratio (LR)). Because of the high mutation rate, a single mismatch between offspring and parent does not reliably exclude parentage; an exclusion is based on several mismatches.

STR markers are now increasingly being supplemented or replaced by SNP panels. SNPs can be genotyped in large numbers on arrays in an automated way, and results are easier to compare between laboratories. In cattle, SNP panels for parentage control are already widely used (Schütz & Brenig 2015).

SNP identity at Generatio: Generatio uses SNP marker sets for DNA identity and parentage verification. For dogs, this is the ISAG2020 set. For horses, we use a SNP set based on the ISAG comparison tests (ring trials); in these interlaboratory comparisons, Generatio ranked first. For camelids, i.e. alpacas, Bactrian camels and dromedaries, Generatio has developed its own SNP ID sets. We also make this method available for DNA programmes.

At the population level, STR markers can be used to reconstruct the migration and evolutionary history of species and to assess biodiversity at different levels of biological organisation.

Other applications, which have now largely been replaced by array analysis, are:

• the construction of genetic maps (mapping)
• the localisation of genes
• genetic linkage analyses

The ISAG (International Society for Animal Genetics) recommends marker sets for individual typing of dogs, horses, cats, alpacas and other animal species, so that results are comparable between laboratories.

Lexicon:

• Genetic Proof of Origin
• Likelihood Ratio (LR) calculations in Parentage Assessments

Literature:

• Ellegren, H.: Microsatellites: simple sequences with complex evolution.Nat Rev Genet 5:435-445, 2004. DOI: 10.1038/nrg1348
• Schütz, E., Brenig, B.: Analytical and statistical consideration on the use of the ISAG-ICAR-SNP bovine panel for parentage control, using the Illumina BeadChip technology: example on the German Holstein population.Genet Sel Evol 47:3, 2015. DOI: 10.1186/s12711-014-0085-1