Because most breeds of goats were produced by a process of inbreeding, the breeding of purebred goats is, by definition, a form of inbreeding, although the term is not generally used to refer to matings where a common ancestor does not occur behind sire and dam in a four or five generation pedigree..
In genetic terminology, inbreeding is the breeding of two animals who are related to each other. In its opposite, outcrossing, the two parents are totally unrelated.

LINE BREEDING
The purpose of line breeding is to fix certain traits or the influence of certain ancestors upon the progeny. This procedure varies in degree from intense inbreeding to mild line breeding. While line breeding can result in exposing undesirable characteristics within the offspring, it can also result in true-breeding strains that consistently pass desirable traits along to their offspring. The degree of line breeding depends on the number of common ancestors, how far back in the pedigree they appear, and how often each common ancestor occurs.

From a genetic viewpoint, inbreeding results in an increase of the number of homozygous gene pairs in the offspring. Homozygous refers to a condition where two paired chromosomes have the same allelle (gene type) at a corresponding point. Because two close relatives tend to have more of the same alleles (by virtue of inheritance) than two unrelated individuals, their mating provides a greater chance for identical alleles to be paired within their offspring. This increase in homozygosity is directly related to the appearance of both desirable, undesirable, and even detrimental characteristics that were not necessarily apparent in the sire and dam. When goats are line bred haphazardly, without culling of inferior stock, many undesirable traits may become predominant in their offspring.

Many undesirable genes are recessive. Fortunately, they have no influence in the heterozygous state, since the effect of the recessive allele is completely hidden by the effect of the corresponding dominant allele. Because of the overall effect of line breeding is an increase in homozygosity, it increases the number of homozygous recessives. Hence, the effects of undesirable recessive genes begin to surface. Line breeding does not create undesirable trait, it simply exposes recessive alleles for hidden weaknesses which are present within the sire and dam. Successful line breeding demands the culling of inferior breeding stock over many generations to help eliminate some of the undesirable recessive genes from the herd. The breeder must be objective when the need to cull arises.

Perhaps the greatest advantage of line breeding is that it increases the prepotency of individuals within a herd and consequently helps to create distinct true-breeding strains or families. This prepotency (the ability of a buck or doe to stamp desirable characteristics upon their offspring with a high degree of predictability) is the result of the parent being homozygous for important desirable traits. When such a parent carries two identical alleles on corresponding points of a chromosome pair, they transmit that allele to the same chromosome point within the offspring. If two such parents are mated, the offspring will always possess the same desirable trait. Therefore, as line breeding increases homozygosity, it also enhances prepotency. This is advantageous only if the parents are homozygous for desirable traits.

As mentioned previously, line breeding exposes certain weaknesses within the inbred herd. Uncovering these undesirable traits can be an important tool for the overall improvement within a breeding program. By setting certain selection guidelines, and by carefully eliminating line bred individuals which show inherit weaknesses, the breeder can slowly remove any undesirable recessive genes from their herd. They will find that improved conformation, milking ability, etc., are actually improved when line breeding is accompanied by careful selection. A successful line breeding program requires good foundation stock and severe culling over many years.

The detrimental effects of line breeding are usually exaggerated in a close, or tight, line breeding system, often referred to as inbreeding. This is especially true when average breeding stock are used and little culling has been implemented. Close breeding can produce extremely good, or extremely poor, results. Success and failure depend on factors such as planning, foundation stock, emphasis on culling, and completeness of pedigree and performance records, etc. Haphazard close breeding could be very detrimental to the overall quality of the resulting offspring. To avoid disaster, a careful study of the merits and weaknesses of the breeding stock should precede a close breeding program. Only the most outstanding animals can be used with any degree of safety in a long term close breeding program.

One method of progeny testing a sire is to mate him to a large group of his own daughters. A study of the offspring determines whether he carries undesirable genes hidden in the heterozygous state. After a sire proves that he is of superior gene type, the experienced breeder may choose to continue the close breeding to increase prepotency of future breeding stock.

The most conservative form of line breeding is referred to as loose line breeding. It is usually associated with slower improvement and limited risk of producing undesirable individuals. It can involve matings between closely or distantly related animals, but it does not emphasize continuous sire-daughter, dam-son, or brother-sister matings. The main purpose of line breeding is to transmit a large percentage of one outstanding ancestor's genes from generation to generation without causing an increase in the frequency of undesirable traits often associated with inbreeding.

Because loose line breeding is not based strictly on mating closely related individuals (with very similar gene types), it does not necessarily cause a rapid increase in homozygous gene pairs. Consequently, it will not expose undesirable recessive genes as extensively as close line breeding. For this reason, loose line breeding is generally a safer breeding program for most breeders.

Intensive inbreeding (and the resulting increased homozygosity) is often directly related to an increase in the expression of many undesirable traits. Therefore, the line breeder should carefully study pedigrees for each prospective mating and determine if, and how closely, the buck and doe are related. By following certain guidelines, the breeder can limit inbreeding (and, therefore, homozygosity) within their herd. At the same time, they may increase the influence of a common ancestor upon the entire strain or family.

CROSSBREEDING is the mating of animals from different lines or strains. Crossbreeding may also be used to produce heterosis, the sudden increase in vigor and fertility caused by a sudden increase in heterozygosity. Because goats from separate lines usually carry very different genotypes, crossbreeding causes a more extreme form of heterosis. The possibility of each parent contributing identical alleles to their offspring is remote. Heterosis from crossbreeding often appears as a sudden improvement in physical characteristics, such as size, endurance, disease resistance, etc. Crossbreeding initiates the desired change, while line breeding or inbreeding increase the ability of each generation to breed "true to type".