Most breeds have closed gene pools, meaning that breeding individuals must have confirmed pedigrees of ancestry from the existing
breed. No new genes can be introduced into the breed, and genes can be lost to the gene pool by selective breeding (or not breeding) of
individuals. The problem with limited genetic diversity in purebred populations stems from the effects of deleterious genes. If a breed has
a high frequency of a deleterious gene, then the breed will have issues with that disorder. Deleterious genes can cause increased neonatal
death and smaller litter size, specific genetic diseases, or impaired immunity. In some cases, selection for a specific phenotype has brought
a defective gene along with it at a high frequency. The most extreme example is the linkage of spotting in Dalmatians with the autosomal
recessive gene for abnormal purine metabolism (hyperuricosuria). All Dalmatians are homozygous recessive for this defective gene, which
can predispose to bladder stones and a skin condition.
Breeds with genetic diversity issues need to determine how they can best improve their situations. Is there enough diversity of normal genes to maintain the health and vitality of the breed? Is there a way to breed away from high frequency defective genes without losing valuable normal genes in the process? Some breeders discourage linebreeding and promote outbreeding in an attempt to protect genetic diversity in their breed. It is not the type of matings utilized (linebreeding or outbreeding) that causes the loss of genes from a breed gene pool. Rather, loss of genes occurs through selection: the use and non-use of offspring. If a breed starts narrowing their focus to breeding stock from a limited number of lines, then a loss of genetic diversity will occur.
The process of maintaining healthy lines, with many breeders crossing between lines and breeding back as they see fit, maintains diversity in the gene pool. If some breeders outbreed, and some linebreed to certain individuals that they favor while others linebreed to others that they favor, then breed-wide genetic diversity is maintained. It is the varied opinion of breeders as to what constitutes the ideal dog or cat, and their selection of breeding stock based on their opinions that maintains breed diversity.
The most important factor for diminished genetic diversity in breeds is the popular sire syndrome. The overuse of a popular sire beyond a reasonable contribution through frequent breedings significantly skews the gene pool in his direction, and reduces the diversity of the gene pool. Any genes that he possesses - whether positive or negative - will increase in frequency. The insidious effect of the popular sire syndrome is the loss of genetic contribution from quality, unrelated males who are not used for breeding. The loss of other quality breeding lines causes a significant loss of breed genetic diversity. The popular sire syndrome is a significant factor in both populous breeds and breeds with small populations.
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