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Do you REALLY need to take a genetics course?

1/31/2016

 
By Carol Beuchat PhD
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.
If you're not sure what you need to know that you don't already, have a look at this paper published this week about the genetics of Bullmastiffs in Australia (Mortlock et al 2016). This might not be your breed, but you should have a look at it anyway, because sooner or later there will be a paper like this for your breed and you're going to need to understand it. 
Here's what Mortlock and colleagues have to say:
"Management and preservation of genomic diversity in dog breeds is a major objective for maintaining health...Concerns about the potential effects of inbreeding and reduced diversity on health
and welfare within breeds, has also led to a call for improved genetic management practices. Hence, managing diversity has become a major focus for dog breeders and oversight authorities. National breed clubs are now assessing methods for evaluating genomic diversity to inform breeding decisions and reduce the incidence of disease, while maintaining positive breed traits and diversity."
(Mortlock et al 2016)
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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?
"...Bullmastiffs generally have a level of genetic diversity that is mid-range when compared with other breeds, but a relatively low effective population size, and a rate of inbreeding that slightly greater than that the level required for avoiding the effects of inbreeding depression. This evaluation provides information that may influence decisions to maintain genetic diversity within the breed. Any decisions that affect the breed as a whole would be most effectively implemented through the collaborative efforts of breed clubs that maintain data records of registered dogs, and can provide information to their members. There are many examples where breed clubs have implemented registration policies and provided the best available advice to reduce the incidence of inherited diseases and deleterious alleles, and promote breed health...The results of the present study show evidence of ancestral inbreeding in Bullmastiffs, and unequal founder contributions during breed establishment. A relatively small effective population size may be improved by utilising the available genetic diversity in systematic manner."

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)

Ready to learn?
​

You can learn about effective founders, Hardy-Weinberg, kinship coefficients, and all the rest in the ICB course Managing Genetics for the Future.

​The next class starts Monday, 1 February.
Learn more about the course and sign up HERE.
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Three key strategies to reduce genetic disorders in dogs

1/27/2016

 
By Carol Beuchat PhD
In many breeds, dodging genetic disorders is becoming a significant problem because troublesome recessive mutations can be widespread in the population. The need to avoid producing dogs that are homozygous for a particular mutation drives the search for the gene and subsequent development of a genetic test. In many cases, these efforts are funded by breeders who believe that "identify-and-eliminate" is the best strategy for dealing with the problem. (See Managing genetic disorders: "Just eliminate the bad gene".)
Unfortunately, because there can be dozens or even hundreds of disease-causing mutations in every dog, there will always be another genetic problem waiting in the wings to suddenly pop up in a breed. If we had tests for all the mutations found in purebred dogs, both the ones we know about and the ones that have not yet been identified, it would become impossible to breed if breeders wanted to avoid every risk.

​You can appreciate the futility of this search-and-destroy strategy when you see that even now, the number of known disorders in dogs outstrips the available tests. This is genetic whack-a-mole, and it will be no more successful in eliminating genetic disorders in dogs than the strategy of trying to rid your yard of moles by shooting just the ones that stick their heads out of a hole.
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Claiming that a dog is "health tested" and therefore a good candidate for breeding is wholly misleading when there might be 5 available tests for a breed, but there are also dozens of known disorders without tests and more appearing every day (What does "health tested" really mean?). 
We are trying to eliminate lung cancer without giving up cigarettes. We can spend millions on research and testing to battle genetic diseases in dogs, but we cannot win this fight unless we change the breeding strategies that produce the problems in the first place. Most genetic disorders in dogs are caused by recessive mutations that have been lurking harmlessly in the gene pool for hundreds of generations. They suddenly become a problem because of the way we breed purebred dogs, by inbreeding in a closed gene pool. The level of inbreeding in a closed population will increase relentlessly, and as homozygosity increases so will the expression of disease-causing mutations. This is not just predictable, but inevitable.
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.)
​
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. 




​You can learn more about the basics of sound genetic management of breeds and populations in the courses offered by the Institute of Canine Biology. The next course, Managing Genetics for the Future, starts Monday, 1 February.
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Is it Nuture or Nature?

1/17/2016

 
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.
Obviously, that can't be true, because when you breed two dogs you do have a pretty good idea about what the puppies will be like. This is because the traits of the offspring reflect the influence of the genes contributed by each of the parents, and whether the traits of the offspring are predictable knowing the traits of the parents will depend on the simplicity or complexity of the underlying genetics.

Some traits are genetically simple and are the result of one or only a few genes. For example, a long-coated dog that has a particular variant of the autosomal dominant gene KRT71 gene will have a curly coat
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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%.​
​
  • 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!


​You can learn more about heritability and how to use it in your breeding program in the courses offered by ICB.
​Learn more about them here!


http://www.instituteofcaninebiology.org/courses.html
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Managing the risks of hip dysplasia

1/2/2016

 
​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.
Puppies with tight hips do not develop hip dysplasia as adults (Riser 1985). On the other hand, some puppies that have hip laxity develop hip dysplasia while others do not, and the reason for this appears to be biomechanics. If the joint is loose, there will be abnormal forces on the femoral head and acetabulum (the socket) when the joint is "loaded"; i.e., when the puppy is standing or moving. These abnormal forces lead to the malformations of the joint and other degenerative changes that are collectively called hip dysplasia. The trauma to the developing joint tissues also unleashes a cascade of biochemical and inflammatory processes that further degrade the hip joint and can become a vicious cycle of deterioration.
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For the dog breeder, it is important to recognize where in this process steps can be taken that might reduce or prevent the damage that causes hip dysplasia. Certainly, the first place is when the parents of the litter are selected. We know that genes play a role in determining the risk of hip dysplasia, so careful selection of breeding stock is important. 

​But we also know that there are other non-genetic factors that can also affect whether the developing hip joint will be normal or dysplastic.
This graphic breaks down the process of developmental dysplasia of the hip into a few key time periods so we can identify how and when breeders can affect the course of disease development after the birth of the puppy.

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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. ​
​
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.

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​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. ​
The new puppy owner takes over management at a critical time in skeletal development, and many probably don't realize this judging by the number of YouTube videos of puppies falling down stairs, being dropped by little children, feasting on ice cream and fatty beef bones, and skidding across the wood floor to slam into the living room wall. Along with the instructions for feeding, every puppy should go home with a clear list of what it should and should not be doing and at what age.
​
​Probably the single most significant risk for development of hip dysplasia is body weight. I have talked elsewhere about the studies that clearly show that food consumption during puppyhood can make the difference between a life free of joint disease into old age, or the development of painful dysplasia as a puppy.

The gold standard for managing body weight in both adult dogs and puppies is the Body Condition System (BCS) devised by Purina, which provides both descriptions and illustrations depicting the continuum of body condition from emaciation to obesity. (Click on the illustration to download a copy.)
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There's just nothing like a fat, roly-poly puppy with a sweet expression to melt the heart, but every one of those extra pounds increases the magnitude of the abnormal biomechanical forces on the hips (and elbows, too), doing damage that will last a lifetime. And don't forget that an extra pound standing is multiplied when the puppy is in motion, increasing the forces on the hip in proportion to speed, both horizontally and vertically. (If you're not sure how this works, drop an egg on the table from one inch then again from 12 inches high.)

​Keeping the growing puppy lean (at 4 or 5 on the BCS chart) will go a long way to prevent or at least limit the severity of dysplastic hips.
We still have a lot to learn about hip dysplasia, but we do know that there are environmental factors that affect risk. Breeders who help their new puppy owners understand what these are and why they're important will protect the investment in time and effort they have made to produce puppies that will live long, happy lives.

  • Riser WH, WH Rhodes, & CD Newton. 1985. Hip Dysplasia. Ch 83 in Textbook of Small Animal Orthopedics, CD Newton & DM Nunamaker, Eds. 
  • There is much more to learn about hip dysplasia in ICB's online course Understanding Hip & Elbow Dysplasia that starts 4 January 2016.

Join our Citizen Science Project

​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.
Read more about the Citizen Science Project here!
​

You can register from the "Courses" tab on the ICB website
.
We hope to see you there!

Read more about hip dysplasia in dogs in these blog posts:
  • ​Myths and mysteries about hip dysplasia
  • The 10 most important things to understand about hip dysplasia
  • How do hips become dysplastic?

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