Since the passage of the Wild and Free-Roaming Horse and Burro Act in 1971, the Bureau of Land Management (BLM) has been charged with managing wild horse populations on public lands. The management policy must often obtain a balance between preserving the horse herds and maintaining the often delicate ecosystems in which the horses live. To maintain this balance, horse population sizes must be kept at levels low enough to prevent the herds from damaging the public lands.

Since horses have few natural predators this means periodic removal of horses. However, population sizes small enough to prevent ecological damage may pose problems to the long-term health of the horse herds. Small population size is directly related to the loss of genetic variability and an increase in inbreeding, and both processes can have deleterious consequences. Modern techniques of genetic marker analysis can be used to develop management plans that can help maintain genetic variation in small populations. The Equine Blood Typing Research Laboratory (EBTRL) of the Veterinary Science Department of the University of Kentucky has been involved in such studies of feral horse populations for a number of years.

Genetic marker analysis has several uses that relate to the development of management strategies. The primary use is to give an estimate of the level of genetic variation present in the currant population. The type of management decisions that can be made will be different for populations that have relatively high variation compared to those that already have low genetic variability.

Another use is to determine if there is population substructure. It is easier to preserve genetic variation in a naturally subdivided population than in one that is not subdivided. This is because each different subdivision will maintain different sets of the total genic diversity of the total population. Genetic markers also can identify populations that would be most suitable as a source of immigrants if a population has low variation and needs an infusion of new genes to restore variation and reverse inbreeding