What experience and science can tell us about dog breeding
Breeders assess the problems they see in the breed and take action to solve them based on what they know from their breeding experience.
When you get a cough, you pull out the medicine you usually use and wait for it to go away. But if that cough is tuberculosis and not a common cold, your medicine won't solve the problem and the consequences can be serious. You need to see a doctor and you need to take the right medicine. Breeders are aware of their breed's problems. They respond to them using the tools they know from breeding and which typically include culling dogs affected by a genetic problem and breeding away from dogs suspected of being carriers of genes assumed to cause the health problem. The cough is thus treated as if it were a common cold. In reality, it's not mutations that cause genetic disorders. If you focus on mutations instead of solving the real problem, you'll never win.
Every dog has mutations, you know about some and you don't know about many until they become a problem. Trying to improve health by focusing on them one by one is a genetic game of whack-a-mole that you'll never win. We don't win because we're not focusing on the source of the problems.
So what is the source of the problem? Animals in closed populations can only breed with their relatives. All purebred breeding is inbreeding. Inbreeding creates homozygosity - two copies of the same allele at a locus. This is good for genes for type. It's bad for genes that are broken. A genetic disorder is not caused by mutational bombs that you can simply remove and restore health. A genetic disorder is what happens when a dog doesn't inherit a copy of the allele necessary for proper function. So we have some loci that have two copies of a good allele; but for all loci that have two copies of a broken allele, something will be functionally disrupted.
By throwing mutations out of the gene pool, we try to produce healthy dogs. However, it's a closed, finite gene pool; we'll eventually throw out all the genes. In fact, animals in closed populations die out.
Let me repeat. Animals in closed populations - aka closed gene pools - die out.
There is no "breeding magic" to prevent this. There is no "scientific magic" to prevent this. Animals in closed gene pools die out. Some sooner, some later, but inbreeding will relentlessly increase over time and diversity will decline until so much is broken that the animals can no longer reproduce and survive.
All the other things that breeders usually discuss are really not relevant to solving this overarching, inevitable problem. Should we care about hip scores, or is longevity more important? What about an eye problem that has a late onset? What about mutations with only mild consequences? There's a lot to talk about, and the discussions go on... for years.
But here's the only problem to talk about: inbreeding and loss of genetic diversity.
Solve this problem and you'll have healthy dogs. If you start with a population of healthy dogs and randomly remove 40% of the alleles the breed started with, you're sure to break something. The average inbreeding of this breed is more than 40%; if half of that (20%) is homozygosity for good genes, then 20% of that is homozygosity for bad genes. That's a lot of broken things.
You can't select your way out of this problem; remember, selection removes alleles and the problem is lost alleles. Some lost genetic diversity could be restored by strategically using less related dogs in breeding. Genetic analyses can reveal if this is possible.
Today we have much better tools for making breeding decisions than just looking at a pile of pedigrees and comparing health problems. At the very least, you should be using them. You should know the heritability of all traits and disorders that are the subject of selection (0.06? 0.33? 0.89?). You should know the size of your gene pool (is it 57, 18, or 6?). You should know the effective population size of the breed (504? 92? 4?). You should know the pairwise relatedness of breeding dogs in the population; inbreeding data suggests that dogs are on average as closely related as you would get from 3 or 4 consecutive crosses of full siblings. Would you ever do 3 or 4 purebred crosses????. Genetically, that's what you have. You need to know which dogs in the breeding population have the highest genetic value so you can be sure to breed those, and which have the lowest value so you can cull them. You should know how much improvement in all these things is possible if the existing genetic diversity in the breed is used in the most strategic way. If this proves insufficient to restore the health of the breed, you need to evaluate strategies that will enable it.
These are things you won't learn in 20 or 30 years of breeding. You probably don't know anything about effective population size or relatedness coefficients or founder genome equivalents. These are things you don't learn by breeding. They come from the science of population genetics, which has been developed over the last 100 years by studying thousands and thousands of breeding programs in domestic and wild animals. These are tools used by breeders of other domestic animals. They are used in genetically managed working dog breeding programs; they work in dogs just as well as in other animals.
To solve the problems of this breed and purebred dogs, we will need to correctly identify the cause of the problem (inbreeding and loss of genetic diversity), determine the best strategies for solving the problem, and design a breeding strategy that effectively and efficiently restores the health of the breed. We have the tools and expertise to do this. We could be doing it NOW.