Selective breeding

Selective breeding in domesticated animals is the process of developing a cultivated breed over time.

In general, the owners of the animals use three strategies to refine local populations:

Selective Breeding Methods

Isolation. There must be a period in which the members of the group are relatively fixed, so that no new genetic material comes in. Without genetic isolation of the group, the differentiation that creates a new breed cannot take place.
Artificial selection. Breeders must prevent random mating from coming about, and limit mating to those individuals who exhibit desired characteristics. One logical consequence of this isolation is the next characteristic: inbreeding.
Inbreeding. Ordinarily those who are controlling the artificial breeding will find it necessary at some stage to employ a degree of linebreeding (mating within one bloodline, or strain) or inbreeding (mating closely related individuals), to facilitate the weeding-out of undesired characteristics and the fixation of desired traits. Inbreeding and linebreeding are controversial aspects of artificial selection, but have been practiced for centuries.

The Appaloosa horse, which was developed by the Nez Perce Indians in the Northwest United States, provides an example. The Spanish colonists had established horse breeding in what is now New Mexico by about 1600, and the Spaniards of that era were known to have horses with spotted coats. By 1806 (when they are mentioned in journals kept by the Lewis and Clark expedition) the Nez Perce were observed to have developed strong, hardy, spotted horses.

It is not known if the Nez Perce practiced inbreeding, but they were reputed to geld stallions judged unsuitable for breeding, and to trade away mares likewise unsuitable for breeding, which accomplishes the goals of isolation and artificial selection.

Closed vs. open studbook

A studbook is the official registry of approved individuals of a given breed kept by a breed association. It is said to be "closed" if individuals can be added only if their parents were both registered. It is said to be "open" if individuals can be added without their parents being registered, such as by inspection.

Studbooks have been kept for centuries; the concept of the breed associations and clubs is more recent. Most of the "purebred horses" have open studbooks. For example, a "purebred" Arabian mare can be "examined" by the Trakehner authorities; if she is found acceptable, her offspring can be registered as Trakehner. By contrast, the studbooks of purebred dogs only remain open if the breed is under development or if there is deemed to be an insufficient genepool.

Crossbreeding and backbreeding

In some registries, breeders may apply for permission to crossbreed other breeds into the line to emphasize certain traits, to keep the breed from extinction or to alleviate problems caused in the breed by inbreeding from a limited set of animals. A related preservation method is backbreeding, used by some equine and canine registries, in which crossbred individuals are mated back to purebreds to eliminate undesirable traits acquired through the crossbreeding.

Some horse societies accept crossbreds who meet certain criteria onto the breed registry.

Purebred Cats, Dogs and the Debate over 'Breed Purity'

Most purebred cats and dogs of breeds recognized by all-breed club registries are controlled by "closed studbooks".
In a number of modern breeds recognized by the kennel clubs, there are high incidences of specific genetic diseases or disorders and sometimes increased susceptibility to other diseases, reduced litter sizes, reduced lifespan, inability to conceive naturally, etc. This came about because:

Many breeds have been established with too few foundation dogs or ones that were already too closely related, or both

There was artificial isolation: the registries (stud books) are closed for most breeds; therefore one cannot introduce diversity from outside the existing population.

Most selective breeding practices have the effect of reducing the diversity further. In addition, in the show world, breeding specimens are often selected on the basis of aesthetic criteria only, without regard for soundness.

Even if the foundation dogs were sufficiently diverse genetically, almost no one knows how their genetic contributions are distributed among the present day population, consequently, breeding is done without regard to conserving these contributions, which may be of value to the general health and survival of the breed.

Purebreds

The very idea of 'breed purity' often strikes an unpleasant chord with modern animal fanciers because it is reminiscent of nineteenth-century eugenics notions of the "superior strain" which were supposedly exemplified by human aristocracies and thoroughbred horses. The application of theories of eugenics has had far-reaching consequences for human beings, and the observable phenomenon of hybrid vigor stands in sharp contrast.

The idea of the superior strain was that by "breeding the best to the best," employing sustained inbreeding and selection for "superior" qualities, one would develop a bloodline superior in every way to the unrefined, base stock which was the best that nature could produce. Naturally the purified line must then be preserved from dilution and debasement by base-born stock. This theory was never completely borne out. It can be said that when the ideal of the purified lineage or aesthetic type is seen as an end in itself, the breed suffers over time. The same issues are raised in the world of purebred cats.

His claim that selective breeding had been successful in producing change over time was one of the key arguments proposed by Charles Darwin to support his theory of natural selection in his acclaimed yet controversial work Origin of Species.