The ambiguous role of DNA-testing in dog breeding: What breeders want is not always what they need

The use of DNA testing in dog breeding has significantly enhanced the health status of many breeds suffering from Mendelian inherited diseases. Notably it has within certain breeding programs helped address the challenge of late clinical onset and enabled the identification of carriers. However, many dog breeders tend to see the use of DNA tests as a magic bullet to deal with all heritable diseases at the cost of other more traditional breeding tools, which often are needed to solve the problems. Here we use Intervertebral Disc Disease (IVDD) as an example to discuss this challenge.
IVDD is a painful, and potentially fatal condition which currently affects one out of five Dachshunds. The risk is correlated with the number of calcified intervertebral discs, which is highly heritable. In Denmark, a breeding program based on a radiographic evaluation of the number of calcified discs supplemented with Estimated Breeding Values (EBVs) has been running for around 20 years with good results especially in wire-haired Dachshunds. In 2017, an insertion of an FGF4 retrogene on CFA12 was identified as responsible for the chondrodystrophic phenotype and associated with the risk of developing disc herniation in chondrodystrophic breeds, and a commercially available DNA test was developed. Many breeders are in favor of using this DNA test instead of the more laborious alternative, but this could potentially have serious deleterious effects on the breed.
The frequency of the FGF4 risk allele is extremely high in the Danish long- and smooth-haired populations and a significant association between the FGF4 retrogene insertion and the disc calcification status has only been demonstrated in the wire-haired population. Considering this, it can be argued that, at least in Denmark, the FGF4 retrogene insertion on CFA12 cannot stand alone as a risk indicator. Relying on the DNA test will have an irreversible effect on the Dachshund breed, excluding far too many healthy dogs from breeding. Thus, using a combination of calcification status and Estimated Breeding Values remains the most reliable breeding scheme for disc herniation in Dachshunds, despite many breeders wanting to use DNA tests as a quick fix.