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Genetic diversity is the set of differences between species, breeds within species, and individuals within breeds expressed as a consequence of differences in their DNA.

In farm animals, the variation between breeds in performance is important in the start of a breeding program or farm activities. What will be the best breed given the production circumstances and which breed fits the best to our defined breeding goal? The concentration worldwide on a limited number of breeds leads to an increasing number of breeds being considered unprofitable and consequently leads to risk of extinction, reducing the variation between breeds.

The variation between breeds is the result of random drift, migration, selection and mutation. Standardized breeds were created out of Landrace breeds and selection lines out of standardized breeds, based on crossbreeding and subsequent selection.

The in vivo conservation of a breed requires a well-designed breeding program that accounts for the small number of animals and that is strictly followed by the breeders and evaluated frequently. The main objective for in vivo conservation is to facilitate the use of the breeds in the rural area for 1) nature management, 2) production of regional products with a high additive value and 3) the maintenance of cultural historic activities.

In vivo and in vitro conservation is complementary: when you do both, you guarantee flexibility of breeding programs by safeguarding rare breeds and have the possibility to use them for present activities. Gene banks can have an important role in the support of small rare breeds and can help to make these populations viable again.

A major source of the reliable information on the genetic variation in a breed is the pedigree, i.e. a record of sire and dam for each individual, accumulated over generations. There is a need to identify these relationships through recording the pedigrees of animals, at least in sufficient depth to identify sires and dams that are responsible for these relationships among individual animals. The deeper the pedigree, the better the true relatedness can be calculated.Informative DNA markers can help the measurement of genetic diversity in two ways. The first way is to overcome the problem that in some species it may be impossible or very costly to observe pedigree directly. By genotyping a small number of polymorph markers on all offspring and all possible parents, it is possible to identify the sires and dams of almost all the offspring. The second involves the extensive genotyping across all chromosomes of the genome in order to estimate the actual proportion of DNA shared by sibs or other relatives more precisely than simply using the expectation for sharing DNA between relatives that is provided by the pedigree

Nowadays, DNA information of cryo-conserved sires and from animals in the living populations becomes available. The combination of their DNA information can be used to realize three opportunities: 1) to make the gene bank a more complete archive of genetic diversity, 2) to determine the history of the genetic diversity from the living populations and 3) to improve the performance and the genetic diversity of living populations.

Breeding populations should be monitored for population size, the rate of inbreeding and the generation interval.

The rate of inbreeding can be decreased by expansion of the size of the effective population, restrictions in the number of offspring per parent and mating schemes to control and manage relationships. An outcross is very effective in this respect.

For small populations gene banks offer the opportunity to use sires again when the initial use did not (accidently) result  in offspring that can be used for further breeding.