When the DNA has been collected and extracted you need to make a choice between the methods to ‘read’ the DNA. This depends on the intended purpose. Do you need to know the DNA composition on a limited amount of places in the genome or the complete sequence of the DNA on all chromosomes?
The DNA composition at a specific place in the DNA can be measured as a genetic marker. A genetic marker has a known location in the genome. In addition, the composition of the genetic marker can differ between animals, and even between homologues chromosomes within an animal. You can detect and compare the alleles of a genetic marker. Animals can thus be homozygous or heterozygous for the marker. Here we will discuss only the two markers that are most commonly used in animal breeding related fields. These two are the microsatellite marker and the single nucleotide polymorphism (the SNP).