From a few percentage of the DNA we know its function: it are genes responsible for the production of proteins. From large amounts of DNA, situated between genes, we do not know the function. Nevertheless we are able to establish in the lab differences in the composition of this DNA. Several molecular genetic techniques are used to find genetic markers on the chromosomes.
Sometimes a genetic marker is an allele of a gene producing a protein. It is called a functional marker that affects directly the function of the protein. However, in most cases the genetic marker is a piece of DNA from which we do not know the function. It is situated on a chromosome close to a gene and therefore related to one of the alleles of this gene. From the start of the molecular genetic work in animals, animal geneticists have done a lot of work to find genetic markers. Before that start, they only knew that a sire and a dam passed one of their two alleles to their offspring, but they did not known which ones. With genetic markers, it is possible to trace which allele of a sire and which allele of a dam is passed to the offspring.