The thought that goes into any mating is your breeding program. Some breeding programs develop one litter at a time: “I'll see what happens here, then plan the next mating accordingly.” Long range breeding programs may involve step-wise decisions: “I'll try to achieve these goals in this mating, then breed back to solidify those goals next time.”

Goals should be written down, and prioritized. These may fall under the categories of health, conformation, performance, and behavior. Goals can involve increasing trainability or performance, losing a detrimental gene, or acquiring a conformational characteristic. You should determine which traits you wish to retain, and which traits you wish to acquire in the offspring. The mode of inheritance of traits will determine how quickly you can achieve a goal. The response to selection can occur more rapidly with single gene traits, or may take a few generations for polygenic traits.

Genetic diseases that cause death, discomfort, or those that are not treatable, should have a high priority in genetic disease control. An early goal is to decrease the incidence of affected dogs being born. Disorders with a late age of onset are more difficult to control, as genetically affected dogs can be bred before becoming clinically affected. A reliable early test for identification of affected dogs and carrier dogs leads to better management of genetic disorders.

Breeders should understand the limitations of genetic tests to evaluate their results. This includes the age when the test can be performed, and the accuracy of the test. Breeders should understand that linkage based tests do not identify the defective gene, but a marker that lies close on the chromosome. If a crossover occurs between the marker and the defective gene during reproduction, false positive and false negative results will occur.

Individual breeders can use genetic tests to; identify carriers, work to breed away from the defective gene(s), and ensure that the defective gene(s) is not reintroduced in future matings. Each breeder will have their own rate of progress, depending on the frequency of the defective gene(s) in their own breeding dogs, and which desirable dogs are carriers.

With reliable tests for carriers, you can breed quality carrier dogs to normal dogs. Normal testing offspring who display desirable traits should replace carriers for future breeding stock. This may not occur in one generation. As more breeders work away from the defective gene(s), the problem for the breed as a whole diminishes.

A mistake of some breeders is to think that selection against carriers is unnecessary, as long as affected dogs are not produced. You should never select more carrier offspring in the next generation than the average frequency of carriers in the population. By not selecting against carriers in breeding stock, you are selecting for a carrier frequency of 50 percent; much higher than most breed averages. This almost guarantees that half the quality dogs in your next generation will be carriers.

If a quality, normal testing dog has not been produced after a number of matings, a different method can be used. We can look to the common experience when a top performer does not reproduce itself well, but a littermate produces far better than itself. When left without quality, genetically normal breeding stock, breeding to an average, but genetically normal littermate may ultimately provide the desirable offspring you want.

If a direct test of the genotype is available, the results of the proposed mates will be all that is necessary. If a phenotypic test for polygenic disease is available (such as hip radiographs or CERF examinations), then the results of the proposed mates, their full-sibs (littermates or repeat breedings), and the results of the grandparents and their full-sibs are important. With polygenic disease, the breadth of pedigree (full-sibs) is as important, if not more important than depth of pedigree (parents and grandparents) in visualizing the spectrum of genes that can be passed on. Normal breeding dogs from mostly normal litters are the best candidates for breeding.

If there is no test for carriers, relative risk assessment can be used for genetic counseling. This technique is useful in autosomal or x-linked recessive disorders. It is based on pedigree analysis and knowledge of the known affected and carrier individuals in the pedigree. The downside of this technique is that it applies selective pressure against all relatives with involved pedigrees. Therefore, genetically normal individuals will be selected against. This can adversely impact the gene pool with widely dispersed genes, or in small breeding populations.

Without genetic tests, breeders can still reduce the carrier risk in their matings. If a valuable breeding animal is determined to be a carrier, he or she can be retired from breeding and be replaced with a quality offspring. The genes of the retired dog can be preserved through the selected offspring, but the carrier risk can be cut in half. To further limit the spread of the defective gene, the offspring should only be used in a limited number of carefully planned matings, and should also be replaced with one or two representative offspring. In this way, you are maintaining the good genes of the line, reducing the carrier risk with each generation, and replacing, not adding to the overall carrier risk in the breeding population.

If gene tests are not available, the storage of frozen semen is important for quality dogs with high-risk pedigrees. If tests evolve that can differentiate carrier from genetically normal dogs, offspring from frozen semen matings can be reintroduced into the gene pool. Both DNA (from blood or cheek swabs) and semen should be stored to utilize this method.

The proper use of genetic tests is not one that continually multiplies carriers in a breeding program. It should be geared toward producing quality, genetically normal dogs. The total elimination of defective genes will probably be impossible for most breeds. With an established testing program, the breed can monitor the frequency of the defective gene in the breeding population, and work to decrease the percentage of carriers.