Diversity

What Is Genetic Diversity?

The canine species has a collection of genetic material, which when you consider all the genes available in the entire dog population (purebred and mixed-breed alike), is called the gene "pool". Mankind, starting in the Victorian era and continuing today, has further carved the canine gene pool up into much smaller collections of genetic material, known as breeds. A gene pool should not be confused with a population number. The two are not synonymous. A breed of dogs can have a large number of individuals, but because these individuals have a large proportion of their DNA in common with each other, the breed's gene pool is actually very small, and that breed lacks genetic diversity.

On the other hand, a breed can be numerically quite small, but because breeders have allowed for a wide range of correct types within the breed, genetic diversity can be quite large. To some extent, we have managed this in the Chesapeake Bay Retriever breed. Our standard allows for quite a large range in sizes, coats, and colors. There is a wide range of hunting conditions in the US. The Chesapeake Bay Retriever standard has been written to allow breeders to breed a style of dog for every hunting condition that exists, and still breed a dog that is correct within the standard. This has allowed breeders to continue on with a particular strain which suits their hunting conditions, while other breeders can develop a style of Chesapeake which is more suitable for other hunting conditions.

Since the 1940's, AKC and most other purebred dog registries worldwide, operate as "closed" registries. That means new dogs are not allowed to be registered unless their parents are also registered. In practical terms, this means that only descendents of dogs registered in the latter part of the 1940s are registered today. In all breeds, this means there is a generation-on-generation rise in COI values and a corresponding loss in diversity. We still have a good deal of genetic diversity within our breed, but are at risk of losing it unless conservation measures are taken.

Risks to Chesapeake Bay Retriever Diversity

Currently, the healthy Chesapeake gene pool is in jeopardy. This threat comes from many directions, but there are two that are the main risks to maintaining the breed in its present, healthy state. One is the rapid drop in population we are currently seeing. The other is the incorrect use of DNA tests when selecting breeding stock. Each of these risk factors will be examined in turn.

The first is registrations. AKC is the primary registering body of Chesapeake Bay Retrievers in the world. More Chessies live in and are bred in the US than in any other country. The largest genetic diversity exists in the US. Canada is the second-largest registered population, with the UK and Scandanavia making up the third largest pool. Anything which threatens the AKC-registered population damages the breed as a whole. We have seen, in recent years, a dramatic drop in new registrations, and in new dogs entering the Stud Book. AKC only publishes a dog in its Stud Book the very first time the dog sires or produces a litter. So, dogs that are published in the Stud Book represent the sires and dams of future generations. Unregistered dogs cannot produce registered offspring, and most puppy buyers look for registered pups.

Below is a chart diagramming AKC Stud Book entries for the years 2005-2011, month-by-month. It is plain to see that registrations continue to trend downward. Not only do the numbers trend downward, but the individuals appearing in the Stud Books are from similarly-bred bloodlines. We are starting to lose the working gundog lines which have always existed in the breed, and have made up a significant source of outcrosses and genetic diversity; "fresh blood" for breeders to tap into, when they feel it is needed. Many of these outcross lines are being lost.

Much of this can be laid at the economy's doorstep. Many people have decided to forego breeding their dogs for many reasons. As can be seen on the chart, there is a definite trend downward from late 2008 onward, with the 2011 numbers being the lowest yet. Total registration numbers for the breed (all dogs registered, not just the breedable ones) are less than half what they are in a typical year. What this means in plain terms is that we have lost roughly half or more of our breeding population in the past five years. The breeding animals that are left are more closely related than in years past. This can cause a loss in diversity and a rapid rise in COI numbers; much faster than can normally be expected.

The second main factor affecting diversity is how we are using health test information. Health tests should be used as a means of gleaning information and insights into a dog's personal genetics. No dog will pass every test; conversely, there are many factors, positive and negative, for which there is no gene test. Therefore, we should always consider the whole dog and the balance of positive and negative points that dog represents, when deciding to breed, and who to breed him or her to.

Most of the health problems that affect Chesapeake Bay Retrievers are polygenic in inheritance. We have a few tests for polygenic diseases, and these need to be examined. Let's suppose that a particular hereditary disease has five genes that, collectively, contribute to development of the disease. For simplicity's sake, we'll call them A, B, C, D, & E. A capital letter, as always, signifies the dominant allele of a pair, while a small letter is the recessive. In developing a DNA test for a polygenic disease, often the test only identifies one allele of the ten possible (ten dominant, ten recessive, for this one disease). This means that we are blinkered; we are only allowed to see one tiny slice of that dog's genes regarding that one disease.

Let's say that a test is developed that identifies the recessive b gene at the B locus. This gene has been identified as being associated with development of a disease (this is very similar to the situation we have currently with the DM test). A dog that tests BB is certified "clear", a dog Bb is a "carrier" and a dog bb is "at risk" to develop the disease. Why do we say "at risk"? This is because we are only able to see that one allele of that one locus. We do not know what is happening on the other four loci, A,C,D, & E. The genes on these loci may have significant effect on whether a dog actually develops disease. When we use a DNA test for a polygenic disease, we always have to remember that we do not have the whole picture. DNA tests for polygenic diseases should not be used to eliminate ANY dog from breeding. Here's why.

Again for simplicity's sake, we'll assume that dominant alleles are for the non-disease state, while recessive ones indicate risk for disease. Let's say a dog's DNA makeup for the five gene loci in question is AA bb CC DD EE. While this dog tested "at risk" using the one-gene test, in truth, this dog has a strong, healthy grouping of alleles for this disease. He would contribute many genes that prevent development of this disease. But because we have no test for those other four genes, we cannot know this. Eliminating this dog from the gene pool would also mean removing all the good alleles it can contribute.

Let's look at another example, and one that may explain why some dogs that have tested as "clear" actually have developed symptoms. Remember, in a polygenic disease, it is a cumulative effect of all the genes responsible for development of disease, not just one gene. A dog may test BB (clear), but its actual genetic makeup for the disease might be aa BB cc dd ee, or in other words, other than the two dominant, non-disease alleles, this dog has a preponderance of recessive, disease-causing alleles. So while this dog has a "clear" status, it might even develop symptoms of the disease, and certainly has the likelihood of passing on a multiple of disease-causing alleles to its offspring. This is why breeders must be cautious not to apply the same rules to DM testing as we do with the PRA gene test. PRA is a single-gene recessive. DM, cataracts, hip dysplasia, and many other disorders of our breed are polygenic; a single-gene test for a polygenic disease does not give a clear enough picture of any dog's genetic makeup with respect to what he/she will pass on to their offspring.

Health Clearances - By The Numbers

Health clearances need to be viewed in context. When looked at individually, it is easy to say that all dogs should be clear for a particular test. But when looked at with the bigger picture in mind, as more and more tests are developed, fewer and fewer dogs will pass them all. We have reached the point in the Chesapeake breed where breeders must be willing to compromise in some things in order to continue breeding quality animals, or even to continue the breed at all. Let's look at the numbers.

As of writing this article, the number of dogs either tested clear or Clear By Parentage for DM is 739. This is worldwide. Obviously, we cannot insist on breeding only DM-tested "clear" animals, as 739 is not enough to keep the breed going. When we stand back and look at the dogs' health status as a whole, the numbers become even more telling:

• 739 with a DM Clear status; of these:
• 441 have some kind of hip clearance; of these:
• 303 have an eye clearance

And on it goes. Breeders will need to learn how to juggle these many test results in a way that is meaningful, all the while remembering that many of the most valuable traits we bred for (temperament, structure, working qualities) there is no gene test for! Now more than ever, we need to remember to keep the whole dog in mind when making breeding choices. Test results need to be looked at as faults, just as any other traits we consider when selecting breeding pairs. Test results should not be used to weed out which dogs should not be bred, they should be used to determine which dogs should be bred to each other, however.

What Can Be Done?

Breeders should continue to test their stock, as this is information which aids in breeding quality dogs. However, breeders should not remove quality animals from a breeding program based solely on a single test result. The dog's entire potential contribution of both positive and negative traits needs to be weighed.

To maintain breed numbers, we should also consider registering whole litters before sending them to their new homes. This accomplishes two things: it creates a permanent record of the dog which the breeder can use to track pups, and possibly use them in breeding programs in later years. It also gives a clearer picture of just how many Chesapeakes there are, currently. AKC is the only major registry which does not require whole litter registration. Because of this, and because AKC is our primary registering body, it is very difficult to determine just how many Cgesapeake Bay Retrievers there are, and which bloodlines are still present in the country.