From the moment a breed is founded and the stud book is closed, loss of genetic diversity over time is inevitable and relentless.
You cannot remove just a single gene from a population. You must remove an entire dog and all the genes it has.
You cannot select for or against a single gene, because genes tent to move in groups with other genes ( this is called "linkage"). If you
select for (or against) one, you select for(or against) them all.
Breeding for homozygosity of some traits breeds for homozygosity of all traits. Homozygosity is the kiss of death to the immune
system. And by the way, as genetic variability decreases, so does the ability of the breeder to improve a breed through selection,
because selection requires variability.
The consequences of inbreeding (in all animals) are insidious but obvious if you look-decreased fertility, difficulty whelping, smaller
litters,higher puppy mortality, puppies that don't thrive, shorter lifespan, etc. Genetically healthy dogs should get pregnant if mated.
They should have large litters of robust puppies, with low pup mortality. Animals cannot produce viable offspring are removed by
Mutations of dominant genes are removed from the population if they reduce fitness. Mutations of recessive alleles have no effect
unless they are homozygous. So rare alleles are not removed, they are inherited from one generation to the next, and every animal
has them. Lot's of 'em.
If you create a bunch of puppies from you favorite sire, you are making dozens of copies of all the bad alleles in that dog (which were
never a problem before because they were recessive) and spewing them out into the population. Now, a (previously) rare mutation will
be become common, its frequently in the population increases, and the chance go up that some puppy will be produced that is
homozygous (has two copies of that bad allele)- and homozygous recessive alleles are no longer silent.
Genetic disorders caused by recessive alleles don't "suddenly appear"in a breed. The defective gene was probably there all along.
Make a zillion copies, and you have a diseases.
Using DNA testing to try to remove disease genes from the breed will not make dog healthier.
The breed will continue to lose genes every generation (by chance or selection) until the gene pool no longer has the genes necessary
to build a healthy dog.
At this point the breed might look wonderful (because of the selection for type) but it will suffer from the ill effects of genetic
impoverishment-inbreeding depression, diseases causes by recessive alleles, increased risk for cancer etc.
The health of an individual dogs cannot be improving the genetic health of the breed. The only way to improve the genetic health of
the breed is to manage the health of the breeds gene pool.
Population genetics provides tools for genetic management of breeds or other groups of animals. Breeders can improve the health of
dogs they breed if they understand and use them.
The Institute of Canine Biology