Here is some food for thought.
Dogs have 78 chromosomal strings, as opposed to the 46 humans have. This accounts for their resistance to sustained in-breeding as well as their great plasticity in the formation of variety--the Great Dane to the Chihuahua--but in the German Shepherd we are now beginning a second century of in-breeding, and we are building on a mountain of back-massing that permeates the entire breed.
Line-breeding, the breeding of first, second and third cousins is in-breeding one or two generations removed.
In (short for incest) breeding is the breeding of mother to son, father to daughter, brother to sister and uncle to niece.
In-breeding and line-breeding are used in the formation of breeds to 'set type' and create uniformity by limiting the gene pool.
Limiting the gene pool is done to make it more likely that the breeder will score the particular characteristics desired in the cosmic lottery of gene selection when the genes from a male and female are combined. It also makes it more likely that perhaps unwanted recessives will occur.
An example of the occurrence of recessives--the color black. Originated with a dog named Roland v Starkenburg (the first black GSD born 1902). Virtually all black GSDs come from Roland. Because black is a recessive allele, in order for a black pup to be born, he must receive the allele from both parents, ie, mom must add the black recessive allele and dad must also add the black recessive allele, so that the pup has no other color 'choice'. Pup is black. Again, because black is recessive, a black and tan or sable bred to a black individual may very well produce an all black and tan or all sable litter of pups. This is common. As a result of this, one fine day, a sable is bred to a sable, or a black and tan, and whoopsie! one or two or even half the litter is born black.
The recessive alleles have traveled down through the years and the generations, maybe 40 years, maybe 7 or 8 generations, only to suddenly appear. Often, no one knew they were there.
Somebody who wants black dogs then in-breeds black to related black, in order to produce blacks on a consistent basis. Sophisticated breeders know this method will work.
BUT. Here's the kicker. Many, many genetic 'disorders' travel the same way, unseen, and until recently, undetectable, until in-breeding brings them to the fore. The same 'uniformity' that makes the 'black and red' dog in the German High Line, the sable in the German working line, black dogs and white dogs, serves to increase the odds that two or more (EPI is not completely understood yet, genetically, but so far we know that 3 recessive alleles are involved) recessive alleles will wind up in the same pup at the same time.
Some people insist that we go ahead and line/in-breed and then simply test the pups (result) and eliminate the undesired results. Now, never mind the culling controversy--what do we do with the undesired result? how many disorders can we eliminate only to find others cropping up? or do we start making judgments--this disorder is not so bad but that one is?
Here are some of the disorders currently appearing:
vWildebrands (Canine Hemophilia)
juvenile renal dysplasia
At this time, while many of these disorders are associated with specific 'lines' while others, like EPI, are distributed widely through-out the breed.
'Out' breeding 'buries' the disorder but does not eliminate it. It can still crop up here and there but becomes far less common.
Some people advocate eliminating any dog that carries the disorder from the gene pool. If done rigorously enough, this will result in the elimination of that disorder, but in many of the instances where this method has been tried, something even worse has emerged, brought to the fore and made more common by the in-breeding and the narrowing of the gene pool used to find and eliminate a less lethal allele.
And so it goes. khawh