Do you REALLY need to take a genetics course to be a dog breeder?

In the "good ol' days" probably not, but dogs are in a bit of a bind right now. Decades of breeding in closed gene pools (because of closed stud books) means that our once healthy breeds have lost genetic diversity and concentrated the nasty mutations, with the result that it takes some serious match-making and a wad of cash for DNA tests to produce healthy puppies, and still you could be unlucky. Trying to purge the gene pool of the mutations is doomed to fail, so breeders will need to start breeding in a way that allows mutations to remain in the gene pool without causing trouble. This is something breeders of other domestic animals figured out how to do long ago out of necessity, because if they don't have healthy animals they can't stay in business. But dog breeding has lagged far behind, and we have some catching up to do.

How many of you reading this are involved in using assessments of genomic diversity to inform breeding decisions? Or if you aren't, is your breed club doing this? According to the canine geneticists and veterinarians, this is what we need to be doing, and if we could have a show of hands I suspect we would find that mostly we are not. But this definitely will be in your future and there will be a learning curve, so if you're not on it already now is a good time to take a little peek at what lies ahead.

Take a quick look at this list of the tools you will be using to understand the genetics of your breed in the not-too-distant future: inbreeding coefficient, effective population size, effective number of founders, effective number of ancestors, relationship coefficient, kinship coefficient, single nucleotide polymorphisms (SNP), multi-locus heterozygosity, Hardy-Weinberg, linkage-disequilibrium, and runs of homozygosity. These are not obscure scientific terms; they are as fundamental to population genetics as dominant and recessive are to Mendelian genetics. If you continue to breed for very long, these terms will be rolling off your tongue and part of your standard vocabulary when you're planning for your next litter.

My point is that The Future is here. There are more and more papers like this one coming out, which is terrific for dog breeders. This is information you can use to solve genetic problems in your breed and plan breeding strategies that will produce the healthier dogs in the future. If you're a lucky Bullmastiff breeder, you should grab a copy of this paper and sit down with your fellow breeders to absorb the gold mine of information. If this isn't your breed, you will still benefit from reading this because the tools and concepts will be the same for all breeds.

​And I'll put in a little plug here, and remind you that ICB teaches courses designed for dog breeders that are a great place to start the next phase of your education as a breeder. (See the info below.)

​What was the bottom line for Bullmastiffs?

Mortlock S-A, MS Khatkar, & P Williamson. 2016. Comparative analysis of genome diversity in Bullmastiff dogs. PLoS ONE | DOI:10.1371/journal.pone.0147941 January 29, 2016. (download pdf)

In an ideal world, studbooks would be open to the introduction of new dogs that could benefit the gene pool, and there are a few kennel clubs that are now permitting and even encouraging this. But whether the gene pool is open or closed, producing healthy animals requires a healthy gene pool, and for this breeders need to practice sound strategies for genetic management. In an open gene pool, this will prevent the development of problems, and in a closed one it will reduce the incidence of genetic disorders and the rate of genetic decline.

Here are three basic principles of sound genetic management that breeders can adopt to reduce the frequency of genetic disorders in their breed.

1) Increase the number of breeding animals
Smaller populations become inbred more quickly, so the simplest way to reduce the rate that inbreeding is to maintain a larger population of breeding animals. The easiest way to do this without producing an oversupply of puppies is to increase the number of different sires being used in breeding. Instead of a few individuals producing most of the next generation, limit the number of breedings per individual and make use of more dogs.

2) Eliminate popular sires
Popular sires are a double whammy on the gene pool. Not only do they reduce the number of male dogs contributing to the next generation by doing more than their fair share of breeding (see #1 above), they also distribute dozens or even hundreds of copies of their mutations (and ALL dogs have mutations!) in the puppies that they produce. The pups might all be healthy because they got only one copy of a mutation, but a generation or two down the road, those mutations will start showing up in pairs and suddenly breeders will find themselves dealing with a new genetic disease that seemingly came out of nowhere. In fact, the new genetic problem is the completely predictable result of a breeding strategy that creates many copies of a particular dog's mutations. Blaming the dog ("We didn't have this awful problem until Fido introduced it to the breed!") is only an effort to deflect responsibility, because every breeder that used him as a sire participated in creating the resulting genetic problem. (For more about this, read The pox of popular sires.)

3) Use strategic outcrossing to reduce inbreeding
In many breeds, there are genetically-distinct subpopulations of dogs. They might represent bench versus field lines, color or coat varieties, geographic areas, size, or some other factor. Because they carry genes that will be less common in other groups, they can be used to reduce the level of inbreeding in a litter of puppies. The number of loci that are homozygous (with two copies of the same allele) will be reduced, and therefore the risk of expressing a recessive mutation will be less. An outcross every now and then can be sufficient to reset the inbreeding to a healthier level.

​By the way, you will hear some breeders claim that outcrossing will introduce new genetic disorders to your dogs. But if you understand how recessive genes work and you practice good genetic management, those new mutations are no different than the ones already in your lines - they won't cause any problems unless you create puppies that inherit two copies in the same one. New mutations will have low frequencies in the population, and sound genetic management will keep it that way. (See Using inbreeding to manage inbreeding.)
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Three key strategies to reduce genetic disorders
Every dog - in fact, every animal - has mutations that could potentially cause disease, and don't let anybody try to claim that their dogs are any different. The key to producing healthier dogs is breeding in a way that reduces the chance that an animal will inherit two copies of the same mutation. Doing the available DNA tests for a breed then producing a litter with an inbreeding coefficient of 20% is self-defeating and just asking for trouble.

Money to identify mutations, develop tests, and screen potential breeding stock is all for naught if we are using breeding strategies that are specifically designed to increase homozygosity of the genes for desirable traits, because homozygosity of mutations will necessarily increase as well. You cannot do one without the other.

If we're serious about reducing genetic disorders in dogs, the things we must do are simple and clear. It is responsible breeders, not researchers and DNA tests, that will reduce the burden of genetic disease in dogs. 

By Carol Beuchat PhD

Every litter of puppies you breed is a genetics experiment. You are trying to combine the genes in a male and a female dog in a way that is likely to produce offspring with a particular set of traits. You often hear people say that breeding dogs is a "crap shoot", implying that a breeder has no way to predict what traits will appear in the offspring of a breeding.

Many traits, however, are affected by dozens or even hundreds of genes that can influence a trait directly and also by epistasis, which results from the interactions among genes and will depend on which particular combination of alleles an animal happened to inherit. Traits with complex genetics are far less predictable, but they include many characteristics breeders care about like size and personality, as well as disease conditions like hip and elbow dysplasia.

Making this even more complicated is the fact that non-genetic factors can affect the traits of interest as well. Size is clearly genetic, but the ultimate size of a dog as an adult will also depend on its nutrition as a puppy. For example, Labrador Retriever puppies that were fed 25% less than a matched littermate from 8 weeks old also weighed about 25% less as adults (you can read about that experiment here). This non-genetic factor (food consumption in this case) is referred to as an "environmental" effect. These two factors - genetics and environment - are what we are referring to when we talk about "nature vs nurture".

This is where things get tricky for the breeder. If you're trying to select for a particular trait, how can you predict what you are going to get in a litter when there might be hundreds of unknown, interacting genes involved as well as a host of environmental factors, both known and unknown? It might seem to the breeder like there are too many unknowns and too much complexity to predict what you will get from a breeding. Yep, it can indeed seem like a crap shoot.

Fortunately, there are a few tools available to help us with this problem, and if we understand what they mean and how to use them, we can improve our ability to produce puppies with the traits we want.

One of these tools is something called heritability. You will probably hear this term used by other breeders, but most use it incorrectly and don't understand what it means. To be fair, it's a simple concept but is a bit tricky to explain. Here's a basic definition:

The heritability of a trait is the fraction of the variation in phenotype among animals in a population that can be attributed to genetics.

I've highlighted two words, "variation" and "population", because these are key to understanding heritability. You can't talk about the heritability of a trait if it has no variation, and you can't talk about the heritability of a trait in reference to one particular individual. By definition, heritability involves variation in a trait within a population of animals, and it specifically refers to the part of that variation that is the result of genes.

The best way to become comfortable with the concept of heritability is to think through some simple examples. Here are some great videos that start with the very basics and do a good job of explaining the concept and what it means. The first one starts with DNA and chromosomes and, even if that's all old hat for you, watch it through to the end because the second video picks up where that one left off, and if you don't watch the first one you won't understand why he's talking about "tea bags" in the second one. The third video gets into the nitty-gritty, and I think you'll benefit from watching it a few time, so don't hesitate to hit the replay button. In all of these, you can think about dogs and dog traits (like temperament or hip dysplasia) instead of the human examples, because the concepts all apply regardless of the animal.

• After you get through these videos, you should understand how nature (genetics) and nurture (environment) can both affect the phenotype of a trait.
  
  
• You should also understand what is meant when somebody says that the heritability of trait like size (or temperament or hip dysplasia) is a particular value like 23%.​

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• You will know why it is incorrect to say something like "Hip dysplasia is 23% genetics and 80% environment". In fact, the acid test will be whether you can explain to another breeder what is wrong with that statement. Give it a try!

This video is licensed under a Creative Commons Attribution-Share Alike 3.0 Unported license.

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​By Carol Beuchat PhD
​
We often talk about hip dysplasia as if it is a discrete disorder, and a dog either has it or doesn't. In fact, the word "dysplasia" is a general term in medicine that refers to an abnormality in form or development. In dogs, hip dysplasia is a process with no fixed endpoint. A dog can have "normal" hips (loosely defined), or the hips are not normal and are therefore considered dysplastic, with degrees of variation from slight to severe.

The hips of all puppies are normal at birth. (We have previously discussed this here.) At birth, there are no signs of dysplasia or abnormalities of bone or cartilage that would indicate which puppies will go on to develop hip dysplasia and which won't. Sometime between birth and when the puppies are about 4 weeks old, there are changes in the tissues of the hip joint that affect how tightly the head of the femur is held in the socket. This is the development of joint laxity, and it is the prerequisite to the processes that result in deformation of the hip. Unfortunately, we haven't figured out how to prevent the development of joint laxity because we don't know if it's an issue of genetics, environment, or both. ​
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Although we don't yet know how to prevent the development of joint laxity, we do know about some of the factors we can control that will affect the risk of developingof hip dysplasia. If we add them to the map of potential paths hip development can take over the life of a dog, we can see where we might intervene to change the course or the severity of developmental dysplasia. Instead of doing a breeding then crossing your fingers for the next 12 or 24 months, waiting for a dog to be old enough for a hip evaluation, the breeder can play a critical role in making sure their careful breeding selection isn't foiled by failure to control the environmental factors that we know can have a large effect on hip development.

​The thing that becomes clear when you look at our developmental map, however, is that the time period when a lot is likely to go wrong is after the puppies go to their permanent homes at 6 to 8 weeks. If you look at that list of risk factors, you will see that too many of them are the very sorts of things that are quite likely to happen in the puppy's new home. Over-feeding, changes in diet (e.g., yummy scraps from the table, lots of cookies for the cute puppy), inappropriate exercise, stairs - all can turn a little hip laxity into a lifetime of painful dysplasia. A little too much love can go a long, long way.

These are things a new puppy owner needs to be educated about. Puppies seem tough and resilient, but an x-ray clearly reveals the immaturity of the skeleton. This image of a 2 month old Bernese Mountain Dog shows the locations of cartilage as open gaps between bones because the joints have not yet ossified. The skeleton will not reach adult size until the puppy is 5 or 6 months old (older for large breeds), and it will not be fully ossified until the puppy about 1 a year old. ​

​Scientists have been trying to solve the puzzle of hip dysplasia for decades. Have they been looking for answers in the wrong places? 

ICB is organizing a Citizen Science project to study hip dysplasia in dogs. If you're planning on having a litter of puppies in the near future, you can join us! We will be recording the weight of the puppies, how much they eat, how fast they grow, and a few other things might provide the information we need to figure out how to reduce or even eliminate hip dysplasia in dogs. We will need a lot of data for many different breeds, both large and small, so we need your help!

We will need all of the study participants to be up to speed on what is already known about hip dysplasia from previous studies. To do this, we have organized a course that all of the participants need to enroll in calledUnderstanding Hip & Elbow Dysplasia. The course starts on 4 January 2016 and will last about 10 weeks.

You will learn about anatomy, development, genetics, biomechanics, and much more to lay the foundation for the project. After the course is over we will continue working with those participating in the study to organize the protocol for data collection.

The course is open to everyone whether you are participating in the study or not.