Screening for genetic markers of disease: what do we tell our clients?

Genomic tools make it relatively simple for a scientist to discover the molecular basis for a hereditary disease. So far we have tests for at least 20 simple, Mendelian disease genes and information about the heredity of more complex diseases such as developmental bone diseases. If these disease genes are the most important considerations in horse breeding, we can use the tests to eliminate the genes in a generation. Simply test all horses for these genes and cull the carriers. However, this approach is probably not in the best interest of breeders who are most interested in selecting for performance.
Breeders have selected horses for generations to craft breeds and individuals with unique and valued attributes including stature, gait, colour, racing performance, jumping ability and conformation. From genome studies, we know that horses have approximately 21,000 genes and it seems foolish to suddenly abandon selection from among all 21,000 genes and attach supreme importance to a single gene, especially one that does not enhance performance. The point is to prevent that gene from having an impact on the breeding programme.
Mendelian recessive disease genes are frightening for breeders. These genes often have their effect by producing defective proteins. A single defective gene may not affect the horse since they will have 2 copies, one inherited from the dam and one from the sire. The problem occurs when 2 carriers are mated and their offspring inherit the defective gene from both parents. There is no possibility to produce a functional protein and the result is embryonic loss or birth of a foal with a hereditary disease. Inbreeding increases the risk of a foal having a recessive genetic disease because it increases the chance of mating carriers to carriers.
Genetic tests allow breeders to identify carriers and keep them in their breeding programmes, as long as they never mate carrier to carrier. As long as carriers are never bred to carriers, affected offspring will never be produced. The frequency of the gene will not increase in the population. Breeders can select livestock and apply culling based on the performance characteristics they value. Genetic progress will be more rapid than if they were to cull animals with desirable genes because of the presence of a single gene defect.
The point is that breeders should select for the genes they want to have in their livestock and use genetics to avoid pitfalls. Breeders are expert at designing perfect matings. However, a pair of recessive disease genes can destroy success. We have the tools to allow breeders to apply positive selection but avoid hereditary diseases due to a recessive disease gene.