Genotyping: Microsatellites vs SNPs

Genotyping is the laboratory testing and analysis of deoxyribonucleic acid (DNA) to investigate the genetic makeup (profile) of an individual. Genotyping is often referred to as a genetic ‘map’ or ‘fingerprint’ of an individual which is inherited from both of their parents. DNA can be extracted from biological samples such as hair, blood, semen or tissue sampling units (TSUs). Once the DNA is extracted from the biological sample, it can then be genotyped.

Genotyping is often used interchangeably with the term ‘genomics’. While genotyping is the actual testing and analysis of the genetic profile of an individual, genomics is generally used to refer to the study of the entire genome of an individual, usually at the molecular level, and associated technologies to do so. For example, one of the fundamental technologies in genomics is the use of genetic markers to genotype individuals.

Genetic markers are locations (loci) in the genome where the DNA sequence is known. Microsatellites and single nucleotide polymorphisms (SNPs) are examples of genetic markers which may be used in genotyping. Furthermore, genetic markers may help the identification of quantitative trait loci (QTL) which are regions in the genome that may be associated with certain phenotypic traits.

Microsatellites go by a few names such as ‘microsats’ or short tandem repeats (STRs). Due to microsatellites being one of the earlier common technologies to genotype animals, it is often referred to as a ‘DNA profile’ however, there are now other technologies that can also be used to obtain a DNA profile of an animal. Microsatellites are regions of DNA that have tandem repeats. In other words, it consists ofshort DNA sequences that repeat after each other at specific loci in the genome. Microsatellites are often used for parent verification in livestock species.

SNPs, commonly pronounced ‘snips’, differ from microsatellites in that they are a known single nucleotide in the genome rather than a segment of DNA and they have a greater density. In other words, more SNPs can be found throughout the genome compared to microsatellites. Due to the large coverage of SNPs throughout the genome, SNPs may provide a plethora of information regarding genetics at the molecular level. SNPs can also be used for parent verification and of recent importance, are enabling the establishment and continual updating of reference populations which may contribute towards genomically enhance estimated breeding values (GEBVs), also referred to as ‘single-step’.

So, what are the genotyping requirements of the Simbra Cattle Breeders’ Society of Southern Africa?

The society requires that:

  • All registered males must have sire verification. Sire verification may be done using either microsatellite genotype profiles or SNP genotype profiles.
  • The sire of all registered animals born from 1 September 2022 must have a SNP genotype profile.

While it is not required, it should be noted that a Cum F0 female may be upgraded to a Cum F1 should the animal be sire verified.

Full parent verification (both dam and sire) is not a requirement however, one may be encouraged by the potential of having correct pedigree information. Parent verification is possible using both microsatellite genotype profiles and SNP genotype profiles, depending on the service provider. For parent verification, microsatellite profiles are not compatible with SNP profiles however, SNP profiles of different densities (50K, 100K, 150K, etc.) are compatible with one another.

For more information on the Simbra DNA pipeline, please contact the Simbra office on