Breeding in general

In recent times, selective breeding may best explain how continuing processes of domestication often work. Some of the best-known evidence of the power of selective breeding comes from an experiment by Russian scientist, Dmitri K. Belyaev, in the 1950s. His team spent many years breeding the Silver Fox (Vulpes vulpes) and selecting only those individuals that showed the least fear of humans. Eventually, Belyaev's team selected only those that showed the most positive response to humans. He ended up with a population of grey-coloured foxes whose behavior and appearance was significantly changed. They no longer showed any fear of humans and often wagged their tails and licked their human caretakers to show affection. Fascinatingly, these foxes had floppy ears, smaller skulls, rolled tails and other traits commonly found in dogs.

Breeding in domestic animals is assortative breeding primarily. Without the sorting of individuals by trait, a breed could not be established, nor could poor genetic material be removed. Homozygosity is the case where similar or identical alleles combine to express a trait that is not otherwise expressed (recessiveness).

Inbreeding, through homozygosity, exposes recessive alleles. Inbreeding is used to reveal deleterious recessive alleles, which can then be eliminated through assortative breeding or through culling.
Inbreeding is used by breeders of domestic animals to fix desirable genetic traits within a population or to attempt to remove deleterious traits by allowing them to manifest phenotypically from the genotypes. Inbreeding is defined as the use of close relations for breeding such as mother to son, father to daughter, brother to sister.
Breeders must cull unfit breeding suppressed individuals and/or individuals who demonstrate either homozygosity or heterozygosity for genetic based diseases.

Linebreeding is a form of inbreeding. There is no clear distinction between the two terms, but linebreeding may encompass crosses between individuals and their descendants or two cousins. This method can be used to increase a particular animal's contribution to the population. While linebreeding is less likely to cause problems in the first generation than does inbreeding, over time, linebreeding can reduce the genetic diversity of a population and cause problems related to a too-small genepool that may include an increased prevalence of genetic disorders and inbreeding depression.

Outcrossing is where two unrelated individuals have been crossed to produce progeny. In outcrossing, unless there is verifiable genetic information, one may find that all individuals are distantly related to an ancient progenitor. If the trait carries throughout a population, all individuals can have this trait. This is called the founder's effect. In the well established breeds, that are commonly bred,a large gene pool is present. For example, in 2004, over 18,000 Persian cats were registered. A possibility exists for a complete outcross, if no barriers exist between the individuals to breed. However it is not always the case, and a form of distant linebreeding occurs. Again it is up to the assortative breeder to know what sort of traits both positive and negative exist within the diversity of one breeding. This diversity of genetic expression, within even close relatives, increases the variability and diversity of viable stock.

The two dog sites above also point out that in the registered dog population, the onset of large numbers of casual breeders has corresponded with an increase in the number of genetic illnesses of dogs by not understanding how, why and which traits are inherited. The dog sites indicate that the largest percentage of dog breeders in the US are casual breeders. Therefore the investment in a papered animal, with an expected short term profit, motivates some to ignore the practice of culling. Casual breeders in companion animals often ignore breeding restrictions within their contracts with source companion animal breeders. The casual breeders breed the very culls that a genetics based breeder has released as a pet. The casual breeder was also cited in the quotes above on cattle raising.

Text from Wikipedia