Rummaging through my reprint collection looking for a particular paper, I ran into one published several years ago about the link between inbreeding and genetic disease. It was written by John Woolliams, a very highly regarded animal geneticist, whose research over the decades has done much to improve the science of animal breeding. The paper is for veterinarians, but most of the language is clear enough that it should be accessible to the lay animal breeder.
As he points out, the examples are from livestock breeding, but the principles apply to any animal. When I skimmed through it again, I found him saying many of the same things we talk about in discussions of breeding dogs, so while the diseases he talks about are different, there are ready parallels that you probably know about in the dog world. You will notice that he doesn't talk much about the breeding of individual animals, as dog breeders usually do, because the genetics that matter for health are those of the entire population - the gene pool that comprises the genetic resources of the breed.
Woolliams J. 2012. Influence of genetics and inbreeding on disease. In Practice 34: 196-203.
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