Line-breeding versus Outcrossing
A very liberally edited version of an article by Jerold S. Bell, D.V.M. that appeared in the September 1992 American Kennel Club Gazette, "The Ins and Outs of Pedigree Analysis, Genetic Diversity, and Genetic Disease Control" ... followed by some personal observations.
Without exception all breeds of dogs are the result of line-breeding. Line-breeding has either occurred through natural selection among a small isolated population (i.e. the dingo) or through the influence of man, breeding selected animals to derive specific traits. Either way intensive line-breeding is responsible for setting enough of the dominant traits that the resulting group breeds true to type. At which point a population of dogs can be said to be a breed.
Dogs actually have more genes than humans. Tens of thousands of genes interact to produce a single dog. All genes are inherited in pairs, one from the sire and one from the dam. If the inherited genes from both parents are identical they are said to be homozygous. If the pair of inherited genes are not similar, they are said to be heterozygous. The gene pairs that make a German Shorthair breed true to type are obviously homozygous. However, variable gene pairs like those that control coat color, size, scenting ability, etc. are still heterozygous within the breed as a whole.
Line-breeding concentrates the genes of a specific ancestor or ancestors through their appearance multiple times in a pedigree. When a specific ancestor, appears more than once behind at least one ancestor on both the sire's side and yet another on the dam's side, homozygosity for that ancestor's traits is possible.
However, if this specific ancestor appears only through a particular offspring of the ancestor in question, then the breeder is actually breeding on the offspring of the ancestor, rather than on the ancestor itself. This is why having many "uncovered crosses" to a specific ancestor (those that come through different offspring of the specific ancestor) gives the breeder the greatest chance of making the desired traits, of the specific ancestor homozygous.
Homozygosity greatly improves the chances that the resulting pups, will in turn pass on the desired traits of the specific ancestor, to their pups. When selecting pups from a line-bred litter the breeder must choose pups that display the desired traits of the specific ancestor, or they have accomplished little. In fact, if these traits are not present in a line-bred pup, it is very likely that it inherited its genes from the remaining part of its pedigree and will be unable to reproduce the desired traits.
Line-breeding significantly increases homozygosity and therefore uniformity within a litter. One of the best methods of evaluating how successful a line-breeding has produced, is to gauge the similarity of the littermates as compared with pups of other litters, with similar pedigrees. Considerable similarity among littermates tells the breeder the genes have paired together as anticipated. The resulting pups will likely be able to pass those genes onto the next generation.
Undesirable recessive genes are always masked by a dominant gene. Through line-breeding, a rare recessive gene can be passed from a common ancestor, on both the sire and the dam's side, creating a homozygous recessive offspring. The resulting offspring actually displays the trait, neither of their parents displayed, even though both of them carried it.
Line-breeding does not cause good genes to somehow mutate - it only increases the likelihood that existing genes will be displayed - allowing the breeder the chance to eliminate what had previously been unseen in their particular line, although it was always present.
Too many breeders outcross as soon as an undesirable trait appears, blaming the problem on breeding "too close." Nothing could be further from the truth. In fact out-crossing insures that the undesirable trait will be carried, generation after generation, in a heterozygous recessive state; only to reappear again and again. Therefore the breeder who turns away from line-breeding, is simply passing a known problem onto successive generations and future breeders.
When an undesirable trait is exposed, the breeder who does his breed a real service, is the one that stays with his line long enough to rid it of the undesirable trait. By controlling which specimens within his line are used for breeding, he can eliminate the undesirable trait. Once the recessive gene is removed, it can no longer affect the breeder's line.
Novice breeders don't realize that individual dogs may share desirable traits, but inherit them differently. This is especially true of polygenic traits, such as ear set, bite, or length of forearm. Many breeders fail to understand that breeding dogs which are phenotypically similar, but genotypically unrelated, won't produce the desired traits in the current litter; and will actually reduce the chance of these traits being reproducible in successive generations.
Line-breeding must be made on a combination of performance, appearance and ancestry. If a breeder is going to be successful in solidifying a certain trait, they must rigorously select their breeding specimens, which display the desired trait. In doing so, the breeder has a chance of making this desired trait homozygous over time. This is the key to successful line-breeding that is most often missed by unsuccessful breeders.