Tuesday 18 February 2020

Registries and Parentage

Last year, the Kennel Club announced that from 2022 it would limit assignment of 'hereditary clear' DNA status of dogs it registers. What does this mean?

Modern DNA tests are now available for medical conditions that can occur in many breeds. These tests are of great benefit to breeds, as they enable breeders in many cases to avoid ever producing a puppy that will be affected with these conditions. Most such conditions are autosomal recessive, which means that in order to express the condition, an individual must inherit two 'copies' of the causative allele, one from each parent. All one needs to do to prevent such a condition from expressing is to ensure at least one parent in every breeding is tested 'clear' -- i.e. both alleles are the one not associated with the disease. 'Carrier' (one allele) and 'affected' or 'at risk' (two alleles, depending on the onset and severity of the particular condition) can be safely bred to 'clear' partners.

What follows from this is that where someone breeds two animals who are both DNA tested as 'clear', it's possible to declare the offspring also to be clear, as there is nowhere for any other allele to come from. Such animals are currently recorded by the KC as 'hereditary clear'. It's likewise possible to declare all the offspring from an affected/clear breeding as 'hereditary carrier', or in theory, if someone was stupid and uncaring enough to breed two affected animals together, to declare the offspring 'hereditary affected'. However, when a clear and a carrier parent are mated, the genetic combination of the offspring can't be inferred and they have to be tested, as statistically each has a 50:50 chance of being a carrier or a clear.

Of course, it then also follows that two 'hereditary clear' animals bred together should also produce 'hereditary clear' offspring. And in practice, assuming parentage is accurate, this is the case. Mutation rates make it extremely unlikely that a mutation will spontaneously occur in any given locus, and this method of determining the genetic status of individuals should be reliable for many generations.

Following the publication of a research paper, the Kennel Club have decided to limit the number of generations animals will be recorded as being hereditary clear in this way. Unfortunately, the research paper found that the recorded pedigrees of animals might not always be reliable, and for this reason this decision was made. There are only really two reasons why an animal's pedigree might be incorrect:

1. An accidental mating or sexual contact with a male other than the one intended. The risk of this is probably low since dogs do not usually mate silently and a mating usually involves a tie that lasts several minutes, so unless the dogs were left unattended together, this would probably be noticed. And if a responsible owner is aware that a bitch in season was unattended with an entire dog, the owner would normally be aware of this risk and do a parentage test. It's also possible, although unlikely, that someone might have two litters born at a similar time (which again, most responsible people won't normally do unless there's a very specific reason) and managed to confuse which pups came from which bitch, and again in this case the decent thing to do would be to DNA test the pups once they were microchipped to determine accurate parentage.

2. Fraudulent behaviour from irresponsible people. Unregisterable dogs being registered with whatever pedigree information the registerer has access to so they can be used for breeding. Dead animals' pedigrees being recycled to avoid paying a nominal fee to register others. Puppy farms might appear on paper to own several sisters from the same litter, whereas in reality there is only one bitch and she is bred every season and the false sisters used as registered mothers, allowing this unfortunate bitch to have more than the four permitted litters.

Unfortunately, if incorrect pedigrees are a problem, the issue of  'hereditary clear' animals should be the least of a registry's worries. If pedigrees are inaccurate, COI calculations and other factors to consider when breeding together animals are also likely to be inaccurate, and animals could end up being more inbred than their pedigree suggests. Testable genetic diseases are the tip of a very large iceberg: a microscope that allows us to see diseases that are otherwise invisible and untraceable unless we're unfortunate enough to combine two carriers and have some offspring express them. Understandably, animals who are not closely related in the case of most conditions, do not frequently share the same testable mutation that causes a problem. DNA tests are rarely an impediment for the choice of a mating partner in a breed unless the potential mating partners happen to be closely related. It's easy to forget the huge number of potential genetic diseases that can't be tested for, and that accurate assessments of relatedness such as COI are one of our only defences against these problems.

So limiting the recording of 'hereditary clear' animals is not the solution to this problem. The problem is that the pedigrees of some animals appear to be inaccurate. The only truly acceptable solution to this as I see it is to insist that pedigrees ARE accurate using DNA testing to confirm the parentage of all puppies at registration. This isn't something that's horrendously expensive, and is something that responsible people will routinely do if there is any doubt, however small, that the parents are the ones intended. It is not too much to ask any respectable breeder.

Meanwhile, the British Alpaca Society also made an announcement last year, that they were phasing in compulsory DNA identification of males intended for breeding at the point of registration, possibly because of anecdotes I've heard about problems with a particular individual or individuals and deliberate fraud, although I've no idea if this is true. I'm not sure what effect this will have, as alpacas don't currently have any DNA tests for diseases that affect them, and pedigrees in alpacas are a lot simpler than in dogs, as the foundation stock is often within 5 generations. Compared with the costs and income from breeding alpacas, and the fact that each female only has one offspring a year, the cost of testing both parents and an offspring in this case is proportionally more and might deter people from registering and using males if they only breed on a small scale and the male is only likely to sire a few offspring. This in turn could worsen popular sire issues in alpacas, with the numbers of males available for breeding being limited.