Why We Use the UC Davis Canine Genetic Diversity Test

For the years since we’ve been offering our services to breeders, there has been widespread discussion as to the efficacy of the canine diversity test we use, a DNA test developed by Dr Niels Pedersen and his team at the UC Davis Veterinary Genetics Lab.

It’s a more old-fashioned kind of test that came out at a time when the popularity of a newer kind of DNA testing was really becoming more available and affordable, and canine researchers all over were very excited about the possibilities the new testing offered. It also happened to come out at the same time as some other companies started offering large panel testing for identified genetic mutations, which offered breeders and owners a “one-stop shop” for results for DNA health testing. As a result, there was a full scale marketing effort to compete with the new UC Davis test, on the basis that the new kind of testing used many thousands more markers. That’s a compelling comparison on the surface, since more is more, right? Except the comparison was apples and oranges.

We were prepared to be wrong, and we waited for other companies to develop applications for their kind of testing that would service breeders in the ways breeders need. Those companies had far deeper pockets and some big name researchers. We could really only wait. And since we got into this project as a way to help dogs, not to become a tech company, our stance was that if the other guys provided a better, more effective product, then all power to them.

It’s been nearly 10 years, and to date there is no more effective product using the newer kind of DNA testing to help manage the genetic diversity in purebred dogs and their various lines. No one has gleaned more useful, applicable information that we have by using the UC Davis test, and there are factual reasons for this. We thought so early on, but were open to being wrong.

Here are some reasons why.

First, we must look at the goal of testing purebred dogs for diversity and health.

There are two uses for DNA: one is to find potential mutations that affect health and appearance. This is the one that most breeders are familiar with, and the one the newer kind of testing, called SNPs, can offer with more precision than the old kind, called STRs. Both have limitations for this applications, though STRs have more limitations.

The other use for DNA is to establish identity and relatedness, like paternity or kinship. This makes it particularly useful for studying population genetics in various species, because that often involves assessing how related, or genetically alike, all the individuals in a population are. It also makes a very useful test to predict how inbred offspring will be. Both SNPs and STRs can be used for this, but in this case STRs have more limitations in creating an interface for breeders that offers them practical information. STRs have proven to be very good for this application.

So why is this? Because of the way both tests were developed and the nature of domestic breeds. The widely used canine DNA tests are expansions of the first tests, which were done by decoding the DNA of some very inbred dogs. This was necessary, in order to identify the areas of the DNA that control certain important functions. These areas can be identified because those dogs inherited the same genes from both parents, which is what happens in both inbreeding and selective breeding, natural or artificial. In selective breeding for certain traits, humans figured out how to breed two dogs with the same desired traits to create more puppies with those same desired traits. So in this way, we humans created breeds with all spots, or all curly hair, or all brown coats and noses. These areas of the DNA have been shown to be the same areas where common disease mutations in breeds are found, and so they are good areas for research. These tests are also very good at differentiating a Vizsla from a Dalmatian, which is why they can do a good job of identifying breeds in a mixed breed dog’s ancestry, but they are not very good for differentiating two Vizslas from one another or two Dalmatians from one another.

By comparison, testing for identification and kinship is best done by looking at the parts of the DNA where individuals are more likely to inherit different genes from both mother and father. That way, if a dog does in fact inherit the same DNA, we know it’s more likely due to inbreeding, and not selection for a trait. STR markers are ones that have been used widely for decades, but they are not all equal. In order to develop a useful test for accurate identification and kinship assessment, the right ones should be used, and to pick which ones requires some rigorous selection and statistical analysis. Because UC Davis is the leader in forensic DNA research for identification in the world, they used the same level of scrutiny for the STRs they selected for their canine diversity test as researchers do when identifying human DNA for paternity or criminal court cases.

It is also the nature of the markers tested that SNPs mutate relatively slowly and STRs mutate relatively quickly in evolutionary terms. Therefore, SNPs are better for assessing ancient relatedness, and STRs are better for assessing more recent relatedness. Because purebred dogs are more of a modern phenomenon, the way to preserve their existing DNA requires breeders to find the dogs that are least related within the context of their own breed in order to avoid unseen inbreeding or loss of existing diversity. There are strategies by which breeders can make decisions that will preserve more diversity, so that all the dogs do not become too genetically alike, but to do that, they have to be able to “see” how different or alike each dog is to one another. Carefully selected STRs offer a much more detailed and robust method of doing that. SNPs largely see all the dogs within a purebred breed as more or less the same.

There is no useful competition between these two tools. Both are necessary and useful and should be applied appropriately where they offer the most benefit.

Our goal at BetterBred is to offer insights to breeders that will help they preserve their breeds. We strongly encourage DNA health testing for known mutations so that breeders can make informed decisions. However, it is not enough to know the status of a few known genes in dogs that have over 19,000 genes and to try to “breed those out”. We will never be able to “purify” a canine genome through testing and selection, because there are always new ones. But we can, by maintaining existing diversity in various ways, keep the frequency of disease genes lower in each gene pool. This results in more healthy, happy puppies and longer longevity for both each dog and each breed. The best tool we have for what we do is the UC Davis Canine Genetic Diversity test.