There are four ways to strengthen the breed population:
Enlarging the population.
Managing diversity - breeding most distantly related dogs together and outcrossing.
Health testing breeding dogs.
Establishing a store of cryo-conserved genetic material (frozen semen to reinfuse back into the genepool).
We know that loss of genetic variation has adverse consequences for canine health and fertility, specifically the high prevalence of recessive genetic disorders. What occurs when dog breeds suffer too much inbreeding is decreased fertility, difficulty whelping, smaller litters, higher puppy mortality, puppies that don't thrive, and a shorter lifespan.
In the dog breeding world, action to maintain or increase genetic diversity should be a high priority in the interests of the health of purebred dogs. Possible remedial action includes limits on the use of popular sires, encouragement of breedings of lesser used and most distantly related dogs, and outcrossing.
The health of individual dogs cannot be improved without 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 breed's gene pool. Which leads me to the following discussion:
The number of puppies that grow up to be bred from a breeding pair, determines how much of the parents’ genes gets transferred into the collective genomes of the puppies and carried onto the next generation. The higher the number of puppies that go on to breed, the more transferred, the lower the number of puppies that go on to breed, the higher percentage of genes lost.
So, out of a breeding pair, you have 1 puppy that goes on to breed, that puppy will retain 50% of each parent to contribute back into the genepool. If you have 2 puppies, the percentage transferred back in is 75%, 3 puppies will bring 87.5%, 4 puppies will bring 93.75%, 5 puppies will retain 96.875% of the parents genes.
Here is how: We know each parent contributes 50% of his or her genes to each puppy. If 1 puppy goes on to breed, it would preserve 50% of each parent. It is unlikely that a 2nd puppy would get the other half of the genes that the 1st puppy didn’t, so you expect that the 2nd puppy to get half of what the 1st got (25%), and the 3rd puppy would get half of what the 2nd puppy got (12.5%), and so forth, down to the 5th puppy (3.125%).
1st puppy -50%
2nd puppy - 25%
3rd puppy - 12.5%
4th puppy - 6.25%
5th puppy - 3.125%
TOTAL with 5 puppies going back into the genepool, you retain 96.875% or roughly 97% of the genes from the parents.
The reverse is true. If you look at what you lose when no puppies go on to breed, from your breeding pair, you lose 100% of the parents’ genetics. If you have only 1 puppy go on to breed, you lose 50%, 2 puppies go on to breed you lose 25%, 3 puppies go on to breed, you lose 12.5% of the genes from the parents.
Bottom line, each breeder needs to think about one, their own breeding program and the long term consequences to losing genetics in their line, by keeping only one or even petting out the entire litter. But two, thinking strategically about the loss of genetic diversity in our entire genepool, when we lose these genes, we cannot get them back. Ideally, it would be great to place 2 to 3 puppies into homes where they could be bred and contribute to the genepool, to retain 75 to 87.5% of their parents genes.
Information for this article comes from Carol Beuchat, PhD Scientific Director, Institute of Canine Biology