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1/1/2020

The messy science of assessing working ability in dogs

2/14/2019

By Carol Beuchat PhD

Dealing with the behavioral issues of dogs is a big business. Trainers and therapists abound, as do the professional suffixes tagged after the names of those who took some sort of course or were accredited by an organization.

I have no idea whether the majority of these people know what they're doing. I can tell you, though, that the scientific literature about behavior in dogs is a morass of tangled, insufficient, and often contradictory studies. In fact, in the field of canine behavior, science is marching forward very slowly, even as the ranks of lay behaviorists swell and practitioners claim to become ever more authoritative and confident of their expertise.

How reliable are behavioral assessments of dogs? Are they repeatable, meaningful, and verifiable? This especially matters when dogs are being assessed for working ability, as in breeding programs for service, police, and other types of working dogs. Breeding and training these dogs is time consuming and expensive, and being able to accurately assess the usefulness of a potential working animal is the differences between success and failure.

A recent study evaluated the reliability and validity of various behavioral tests that are used to assess the traits of working dogs (Brady et al 2018). What the researchers found should give pause to anybody that professes to have a deep and true understanding of canine behavior.

The aim of this study was to assess the reliability and predictive validity of tests designed to assess relevant traits of working dogs. They reviewed many published, peer-reviewed studies and proceeded to evaluate only those that met strict criteria for focus, design, methods, and analysis. Of the thousands of behavior studies they reviewed, 16 were judged to meet the requirements of their analysis.

For the selected studies, they evaluated the reliability, repeatability, and predictive validity of the behavioral tests, both within and among "raters" (the individuals conducting the evaluation). They had an assortment of problems to deal with, like the use of different terminology for the same trait. More seriously, they found that data were often inadequately reported, statistical analyses were misinterpreted, and there was an overall lack of concordance in the various methods used for assessment.

Ultimately, they concluded that there is "a widespread lack of information relating to the reliability and validity of measures to assess behaviour and inconsistencies in terminologies, study parameters and indices of success...This review indicates that we are still not addressing concerns over the lack of standardisation (sic) amongst research on dog behavioural tests".

What this means is that we are probably not as good at assessing behavioral traits as we think we are or, at the very least, it's hard to tell how good we are because of limitations of the studies and the lack of standardization in terminology and protocol. Certainly, it should give pause to anybody relying on "experts" for advice, most of whom cannot lean on published studies to support claims about the validity and reliability of their assessments.

Buyer beware.

You can download a copy of the study below.

REFERENCES

Brady, K., N. Cracknell, H. Zulch, and D.S. Mills. 2018. A systematic review of the reliability and validity of behavioural tests used to assess behavioural characteristics important in working dogs. Frontiers in Veterinary Science 5(103);doi: 10.3389/fvets.2018.00103.

Are you interested in dog behavior?

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The Genetics of Behavior & Performance
Online course starts 4 March 2019
10 weeks, $125

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A new ICB course that will use the DNA data from YOUR dog!

2/5/2019

By Carol Beuchat PhD

Have you ever wondered how scientists figure out the genetic basis of a particular trait? This is especially difficult if the trait is polygenic and many genes plus environmental effects might be involved.

These are called "continuous" or quantitative traits; most of the traits under selection by dog breeders are of this type. For most of us, the process of identifying the markers associated with particular traits is a "black box" from which information mysteriously emerges from huge files of cryptic genotype data. How are scientists able to identify which of the many of thousands of markers play a role in the expression of a specific trait?

In ICB's has a new course, The Genetics of Continuous Traits, we'll take the lid off the box and show you how scientists get from genotype to phenotype using DNA data you provide for your own dogs! For a learning example, we will study the genetics of body size, which is a trait that varies widely and continuously among breeds and mixed-breed dogs.

We will use the raw DNA data file provided by Embark for your own dog, together with information about the size of your dog that you will provide. If we get data for enough dogs of a single breed, we can also explore the genetic basis of variation within a breed, also for a variety of mixed-breed dogs.

We will review some published studies for comparison with our own results, so you will also get to make comparisons with "real world" information.

This course is a great opportunity for you explore "under the hood" and learn how scientists go from a table of data to new information extracted from the data for your own dog!

Don't miss this great learning opportunity and the chance to analyze the data for your dog!

This unique online course is $125 and lasts 10 weeks, with students free to work along with the class or at their own pace. There are no prerequisites and a scientific background is not required - just your keen interest in dogs!

Class starts 11 February. Register now to join us!

The Genetics of Continuous Traits

Check out the information for the course and register here

https://www.instituteofcaninebiology.org/continuous_traits.html

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How to breed dogs that are better than their parents: the genetics of continuous traits

1/19/2019

By Carol Beuchat PhD

The quantitative genetics of continuous traits

Through a series of clever experiments, Mendel opened the black box that held the secret of the gene, which he concluded was responsible for the inheritance of traits in plants and animals. Knowing this, breeders could do some simple breeding experiments to reveal whether the genes for particular traits were dominant or recessive, which allowed them to design breedings that produced predictable traits.

While this took some of the mystery out of breeding for many traits, for other traits prediction remained elusive, and breeders realized that in some cases the genetics of a trait must be more complex. The problem, of course, was that some traits are determined by many genes. How could breeders do selective breeding on these so-called polygenic traits to reliably produce particular traits?

The puzzle was finally solved by a university geneticist named Jay Lush. In the 1930s, Lush realized that, for many traits, there could be lots of variation from individual to individual in a trait. That is, some traits were not "binary".

For instance, there could be a range of size in a population of cows from small to large and everything in between, and not just two (binary) sizes of large and small. He realized that this was the case for many traits and began to think about how genetics could account for this. What Lush had stumbled upon was the key to selective breeding for traits that can vary continuously - genetic variation.

He described this in his groundbreaking book, Animal Breeding Plans.

"Variation - differences between individuals - is the raw material on which the breeder works. It is not necessary that the animals vary widely enough that the breeder can at the very start find some perfect ones to select, but they must vary enough that some of them will be closer to his ideal than others are... The effects of a combination of genes in the individual equal the sum of the average effects of those genes." (Lush 1937)

Here, Lush is making the two observations that transformed animal breeding in the mid-1900s: 1) that genetic variation provides the raw material for selection, and 2) that some of this variation was "additive". Put another way, the effects of multiple genes acting on the same trait can be added. One large dog bred to another large dog could produce offspring larger than either parent.

This is what he is alluding to when he says that it's not necessary for a breeder to find the exact traits desired in a potential breeding animal, because genetic variation can be used to create a new mix of genes that will produce a trait not present in the current population.

Lush's observation launched a new field of genetics, called "quantitative genetics", that was based in mathematics and statistics and applied specifically to traits that vary continuously. The advances in our understanding of quantitative genetics subsequently revolutionized animal breeding and was the basis of the spectacular improvements in production that became the modern system of commercial breeding of livestock and other animals.

One of the best examples of the gains that could be achieved by understanding the basis of additive genetic variation is for milk production in cattle. At the beginning of the 1900s, average milk yield was about 2,000 kg per year.There were no cows to be found anywhere that could produce 8,000 kg of milk per year. However, with the application of selection based on quantitative genetics in the 1940s, milk production soared and by 2000 it averaged more than 8,000 kg of milk per year - a four-fold increase in milk production over a period of about 50 years. Gains in production were made incrementally, a bit more each generation, and the basis for progress was finding advantageous combinations of genes that, added together, would push a trait in the desired direction. Breeders used the genetic variation in the animal population to create new combinations of genes in the next generation, then selected from among those animals the ones that improved on the trait over their parents.

There was one critical thing that was absolutely necessary for this to work: there needed to be genetic variation in the population. Breeders had to protect the genetic variation in their breeding stock, because without it new combinations of genes would not be possible and there would be nothing to select for.

The realization that selective breeding could produce animals that were superior to both parents revolutionized animal breeding. The use of additive genetic variation to produce animals with traits not present in the original breeding stock became the fundamental process of selective breeding in domestic animals.

Commercial breeders have leveraged additive genetic variation to produce chickens that grow faster, are larger as adults, and lay more eggs than the ancestral jungle fowl from which the modern chicken was domesticated.

Continuous variation in dogs

Of course, dogs provide many examples of traits that have been shaped by selective breeding that takes advantage of additive genetic variation.

Body size is an obvious one. Researchers have identified multiple genes that can be associated with variation in body size in dogs. Some of these have a large effect, accounting for a significant fraction of the variation in size. But there is still much variation that is not yet accounted for genetically, and there might be dozens or even hundreds of other genes that have tiny effects individually but collectively account for differences among individuals.

Let's look at another example.

People probably started racing dogs thousands of years ago, and it's fair to suspect that over this time there has been selection to improve speed.

These are data for 1,000 racing dogs in Ireland over a distance of 480 meters (Taubert & Agena). Most dogs cover the distance in 29-30 seconds. But there is also much variation among individuals, from the slowest that took about 32.5 seconds, to the fastest at about 28 seconds.

There could be many reasons for this variation, including motivation, condition of the track on the day, and other enviromental factors. But at least some of this variation might be attributed to genetics.

How could breeders use selection to breed faster dogs?

Results of 1000 dogs, shown in 1/10th of a second difference. The height of each bar shows the number of dogs belonging to the time below it.

One option would be to breed only the best to the best. Identify the sire and bitch with the fastest racing times and breed them together. Will some of the offspring be faster than either parent? Perhaps. Might some be slower? Perhaps. So what do we do from here?

We could mate the fastest male in the litter with the fastest female, and again select the fastest of their progeny.

We might end up with dogs faster than the first two parents, but over the generations of inbreeding and strong selection (breeding only "best to best"), progress will start to level off. We will have eliminated much of the original genetic diversity in the dogs of the first generation. In fact, the puppies in each litter will share a larger and larger fraction of the same genes every generation. We are not going to get faster and faster dogs forever. Why? Apart from the deleterious effects of inbreeding, we have tossed out the genetic variation necessary to produce improvement in a continuous trait by exploiting additive genetic variation. We have bred ourselves into a dead end.

So how can you produce faster dogs from selective breeding and not run into this problem of a genetic dead end?

Redefine what you mean by "best". We do definitely want to select the best animals to breed, but we need to think of it in terms of the genetics of the population. To improve on a polygenic trait, we need genetic variation to select for. Instead of selecting a single best dog, we can select a subpopulation of dogs that are all faster than average. We will then use the genetic variation in those dogs, and the random inheritance of that variation in the offspring, to push racing performance in the direction of higher speed.

Taubert & Agena

Can we keep producing faster and faster dogs forever? Probably not. If we don't run out of genetic variation, at some point we will run up against the limits of design and physiology. But we can definitely use selective breeding in this way to improve most traits that are polygenic in dogs.

So think about this. What traits do you strive for that are polygenic? Size. Temperament. Working ability. Coat quality. Ear length. Muzzle length. Shoulder angulation. Intelligence. The list is long.

Note that there is another issue here that breeding in this way addresses. The phenotype of polygenic traits is likely to be a reflection not just of genetics, but also of a roster of non-genetic factors, some of which might be known but most will not. When you select only the "best" individual to breed, you are selecting for the combination of genes and environment that produced what you perceive to be best. But you really only want to be selecting based on genes, because only that part of a trait can be inherited. Maybe the fourth "best" dog has great genes for the trait you want but was raised in a less than ideal situation. That dog's genes will get tossed if you only select the single best animal. By breeding a subpopulation of the top performing dogs, you preserve the genetic variation you need for selection and also reduce the influence of non-genetic factors in your choice.

You have no doubt noticed that this method of breeding, where the "best" is defined as a subpopulation of individuals instead of a single dog, is not the way dog breeders usually breed. We usually choose to breed only the dog we perceive to be the "best", ignoring the possible effects of environment on our assessment of the other apparently-inferior dogs. Doing this, we narrow the gene pool and increase inbreeding every generation, both of which will limit our ability to continue to improve traits. This applies to health as well as physical and behavioral traits. We can't "breed around" health issues if the necessary genetic variation no longer exists in the population of breeding animals.

Can we breed better dogs by taking advantage of additive genetic variation? Yes, by changing the way we define "best" during selection. The improvement we can achieve might be significant - in health, in physical traits of importance, in temperament, and many other traits that we care about.

Let's breed better, healthier dogs. Learn about the quantitative genetics of continuous traits and how you can use this knowledge to your advantage in your breeding program.

Ready to get started? Check out ICBs newest course, The Genetics of Continuous Traits, which starts on 7 February 2019. Join us!

REFERENCES
Taubert H & D Agena. Quantitative Traits. (no date, no publisher)
Lush, J.L. 1937. Animal Breeding Plans.

New ICB Online Course

The Genetics of Continuous Traits

Online course starts 6 February 2019
10 weeks, $125

LEARN MORE

The right - and wrong - way to use DNA tests

1/7/2019

By Carol Beuchat PhD

Since tests for specific mutations have become available in the last few years, the mantra of breeders is that their puppies are from "health tested" parents. To breed without first doing the available DNA tests is considered the height of irresponsibility in the fancy. But there is a right way to use DNA test results and also a wrong way.

If you are reading this, you probably consider yourself to be a responsible breeder. Let's do some cyber dog breeding using some information from DNA testing and see how you do! All you need is a pen and paper along with your expertise as a responsible breeder.

Okay, we have a bitch we want to breed, and we have selected seven possible sires (S1 to S7). We have ranked these according to how well we think they fit what we're looking for in a sire in terms of conformation, temperament, health, longevity, working ability, or whatever criteria are important to you. We have given three green starts to the dogs we rank the highest and one green star to the dogs ranked lowest. However, we would be willing to breed to any of them. Assume we have done the relevant phenotype tests (e.g., hips, elbows, eyes, heart, etc.) and the results for all of those were acceptable.

The first thing we need to do is run the appropriate DNA tests for the recessive mutations known to be in the breed. In this case there is one, for the "red circle" trait. Our bitch is carrier, as are two of the sires. I have identified the carriers with a red X on the chart, and the dogs that were clear have blue check marks.

Now we have our health-tested dogs from which we are going to select the perfect sire for our bitch. Using your rankings for overall quality, together with your information from health testing, rank the sires with 1 being your first choice and 7 your last choice.

On your piece of paper, make columns for S1 through S7, and in the first row below that write your ranks for each of the potential sires.

Let's say you went to a little more trouble before making your breeding decision and you were able to get the predicted average inbreeding coefficient of the litters that would be produced from our bitch and each of the seven sires. (You can get this information from the kinship coefficient, which is an index of the relatedness of a pair of dogs and can be determined either from pedigree or DNA information. The kinship coefficient of a pair of dogs is equal to the inbreeding coefficient of their potential offspring.)

Let's add the predicted litter COI to our table. With this information to consider as well, again rank the sires from 1 to 7 and add these data to the next row of your table. (Did this alter your first set of ranks?)

This is usually as much information as a breeder has about the dogs they want to breed.

You did the testing for the "red circle" mutation in our potential parents and discovered that two of the sires were carriers. For both of them, there would be a 25% risk of producing puppies that are homozygous for the red circle mutation. You probably chose to eliminate those two sires from breeding consideration, which reduced the risk of producing affected pups in this litter from 25% to 0%.

You breed using your top-ranked sire and your bitch produces a beautiful litter of puppies. You advertise your pups as being from health-tested parents, keep a lovely pup for your breeding program, and send the rest off to pet homes. Sometime later one of the pet owners contacts you with the report that their puppy has a serious inherited blood disorder, and they ask how this could be if you claimed your pups were from health tested parents?

Indeed. How can this be???

We only know what we can know. We can know if a dog possesses a mutation if we have a test for it. We did our tests so we knew about the status of the red circle mutation in all of the potential parents.

But most dogs have many recessive mutations lurking in their genome for which there is no DNA test, and we have no way to know they are there if they are not expressed. Clearly, there was a mutation in your parents that you didn't know about. You feel horrible, offer to replace the puppy, and bury yourself in pedigrees trying to figure out how you could have produced a puppy with a genetic disease after being so careful.

If there is no DNA test for a recessive mutation, a disease can suddenly appear out of the blue that you have never seen in your lines if you happen to pair two carriers. This is why, if somebody claims that they only breed within their own kennel because they "know what's in their lines", you know that either they don't understand genetics, or they are being dishonest. It is not possible to know what recessive mutations are in your lines if you have no way to detect them.

So this leaves you in a pickle. All dogs have recessive mutations, and there are always going to be some that you don't know about. How do you avoid them? This is like tip-toeing across a mine field in which there are 3 mines that you can't see but are flagged, but you know that there are 28 more hiding out there somewhere. One wrong step and you will meet your maker. If these are mutations hiding in your dogs, this is a pretty hectic way to breed.

What if there were two mine-fields, but you can choose which one to cross. The first minefield has 3 mines you know about and can avoid and 28 that are hidden. The second mine field also has 3 that are flagged, but only 6 more that are hidden. If you're not ready to start your after-life, you would logically decide to cross the second mine field, where the risk of getting blown up is only 25% of the risk in the other one.

How does this apply to dog breeding? Let's pull back the curtain and reveal the unseen mutations in the dogs in our breeding program.

Now we can see the problem. Our bitch has not one but three mutations that are also found in our "health tested" sires. Have a look at your last set of sire rankings. Now that you can see these other mutations, are you still happy with those ranks? If you would like to change your rankings, add another row to your table with these new assessments.

Great, you say. But in the real world, if we don't have tests for those unknown mutations, there is no way for us to avoid them, right?

Actually, there is. You just need one piece of information that in fact you already have - the predicted inbreeding coefficient of the litter.

Remember that inbreeding is defined as the probability of inheriting two copies of the same allele from an ancestor. By definition, then, inbreeding is homozygosity. If the inbreeding coefficient of a dog is 25%, then the probability of inheriting two copies of the same allele from an ancestor is 25%. If that allele happens to be a recessive mutation, then the risk of producing a genetic disorder caused by that recessive mutation is also 25%. Likewise, if the inbreeding coefficient is 10%, then the risk of a genetic disorder produced by a recessive mutation is also 10%.

Think about this. You did mutation testing to eliminate the 25% risk of producing a recessive genetic disorder from two carrier parents. But we just explained that the inbreeding coefficient tells us the risk of producing a genetic disorder from ANY recessive mutation, the ones we know about as well as the ones we don't.

So, we can be clever about this. We can control the risk of genetic disease from all recessive mutations by controlling the inbreeding coefficient of the litter. If we test for red circle and eliminated the carrier sires, it would be dumb to then breed to sire #1. We have paid to eliminate the 25% risk from the known mutation then done a breeding with a 31% risk of producing a disorder from some other mutation we don't know about.

Let's read that again.

We tested, eliminated the carrier sires so there is no chance of producing affected puppies from the known mutation, then we bred to a "clear" dog with a 31% risk of producing puppies with a disorder from some other mutation we don't know about.

You might be breeding "health tested" dogs, but you are still producing puppies with a significant risk of genetic diseases from recessive mutations.

Go back to what we know about the inbreeding coefficient. If our litter has a predicted COI of 10%, then the risk of ANY mutation causing a problem is only 10%, including the one we paid to test for. This is because parents with a kinship coefficient of 10% are less similar genetically than parents with a kinship coefficient of 25%. If the parents have fewer genes in common, there is a lower chance of a puppy getting two of the same mutation from both.

So it's simple. Reduce the risk of genetic disorders in your puppies by reducing the predicted inbreeding coefficient of the litter.

If you've never thought about this before, this should be your light-bulb moment. All this "health testing" is a waste of time and money if we choose parents that produce a litter with an inbreeding level of 38%.

This is the WRONG WAY to use DNA testing. The breeder believes they are doing everything they can to produce puppies that will live long, healthy lives. But in fact they mark the known land mines with flags then assume the coast is clear without considering the risk produced by the many unseen explosives.

To produce healthy dogs, we need to get the risk of problems caused by ALL recessive mutations as low as possible, the ones we know about as well as the ones we don't. You can estimate this risk from the kinship coefficients of the potential parents. These numbers can be computed from a pedigree database, or (even better) they can be determined from the genotype data produced by DNA testing.

Don't waste your money on DNA tests then breed in a way that has a high risk of producing disease. Use those tests to eliminate all risk from mutations we can test for, then use kinship coefficients to make sure we have reduced as much as possible the risk from the unknown mutations hiding out in the genome of every dog.

We CAN reduce the risk of genetic disease in dogs

Learn how in ICB's online course

Managing Genetics for the Future

The next class starts the week of 7 January 2019

We hope to see you there!

Are breeding restrictions putting your breed at risk?

1/6/2019

By Carol Beuchat PhD

There might be thousands of dogs in your breed, but the ones that are bred and pass their genes to the next generation are the only ones that really count in terms of genetics.

In most breeds, only 20-30% of the dogs produced are used for breeding. The rest go to pet homes, usually with a contract that stipulates that the dog cannot be bred or offspring cannot be registered. These dogs join the ranks of the spayed and neutered. This means that the number of dogs producing offspring in a breed is much less than the census number. This has significant consequences for the genetics of the breed.

Let's Simulate!

There are some fun tools we can use to explore the effects on genetics of changes to some of the properties of a population. This is one that we use in my population genetics courses to help students understand how genetics can be affected by changes in various properties of a population such as size or addition of new individuals.

One of these is an online population simulator called Red Lynx. It's easy to use, and if you have access to the internet you can take it for a test drive.

Go the the Red Lynx website at http://scit.us/redlynx/.

On the landing page, click on the button to start the Red Lynx simulator.

This will take you to the simulator and you should see the screen below.

Red Lynx simulates the "behavior" of a single allele, "A1", in populations with various properties. There are two alleles at every locus, so actually A1 has a pair (lets call it A2). But we only need to simulate one allele, because if the frequency of allele A1 in a population is going up, the frequency of A2 must go down. If we model the behavior of A1, we know that A2 will be responding as a mirror image. So, we will run our simulations using only a single allele at a locus.

On the simulation page, you will see a graph, and below that a series of parameters that you can change using some simple sliders. We are only going to play with the first three: number of generations, population size, and initial allele frequency (green arrows). You can change these either by using the slider or just type the number you want in the box. You can ignore the rest of the sliders on the page.

Okay, let's see what this does. Let's start with the default values when you first go to the page, which are 2000 generations, population size of 800, and initial frequency of A1 as 50% (so we know that the frequency of A2 will also be 50%). Click on "Run Simulation" (red arrow). A line will appear on the graph.

This line is the predicted behavior of the allele A1 in this population over time, assuming a 50/50 chance of inheriting the allele at each generation in a population under "ideal" conditions - no selection, no migration of A1 alleles in or out of the population, and no mutation. You can see that the initial frequency is 50%, and from there it change in frequency in the population with each generation.

Now, without clearing the graph, do a few more simulations. Each of these lines will be different because the role of chance in inheritance at each generation. If you do enough of these, you might see one of the lines go either all the way to 0% and flat-line (red arrow), or to 100% and stay there (green line). In the first case, all copies of the red allele have been lost from the population; for the green arrow, the alternative allele (A2) has been lost completely, leaving only A1, a situation we call "fixed" for that allele.

So what?

I hear you say "That's cool, but so what?".

Let's say the A1 allele was for something like the ability to smell a particular scent. If this isn't something you would be selecting for, this simulation suggests that there is a chance it could be lost from the population just by chance, a phenomenon called "genetic drift". Maybe this scent wasn't important to you, but if it was to the dog (e.g., a pheromone), it would have consequences that might affect some aspect of the physiology or behavior of the dog. Perhaps it is an allele that prevents fearfulness; losing it from the breed would definitely have consequences for the welfare of the dog. Or maybe it is an allele at a locus that is most beneficial when heterozygous - that is, the genotype A1A2 is more beneficial to the dog than either A1A1 or A2A2, something called "over-dominance". If one of the alleles is inadvertently lost from the population, all individuals will be homozygous for the other allele, and beneficial effects of heterozygosity will be unavailable.

So now let's do the fun stuff.

Let's make the number of generations in the simulation 100 so it will be more relevant to dog breeding. Change the population size to 50, and leave the allele frequency at 50%. Use the button to clear the graph, and run some simulations.

You should find that the frequency of A1 goes to one extreme or the other (0% or 100%) in many of these simulations.

Now run some simulations with different population sizes, perhaps 100 and 25. How does this affect the graph?

This simulator makes it easy to explore the effect of population size on the behavior of alleles in the population that you aren't paying any attention (because they are not under selection). Clearly, the genetic stability of a population is sensitive to the number of individuals.

Why does this matter to your breed?

How big is your breed? What fraction of the puppies produced are used for breeding? Remember, only reproducing animals count when we're considering genetics. What are the effects of breeding contracts or spay/neuter policies on the population genetics of your breed? How stable is it genetically to the chance loss of alleles by genetic drift?

These changes in allele frequency occur in all populations. If a population is divided into closed subpopulations, the same phenomenon will occur in each of them. This will cause them to drift apart genetically over time. Breeders can take advantage of these differences as outcrosses that can restore alleles that might have been reduced to very low frequency of lost entirely. You can simulate this using the slider for "migration". If breeders can work together to tend these subpopulations in a breed, they can reduce the loss of genetic diversity, slow the increase in inbreeding, and benefit from the hybrid vigor produced by an outcross. Similarly, is the population of your breed stable, or is it one of the many with registrations dropping off and fewer active breeders than there used to be?

The simplest thing you can do to reduce the chance loss of important genetic diversity from your breed is to use more of the dogs produced in the breeding program. If the usual fraction is 20%, increase it to 40% or more. Don't send so many puppies off with contracts that prohibit breeding, or breed once before spaying or neutering. How much of a difference will it make? You can check it out using the Red Lynx simulator. Just remember that the simulator assumes a population with no selection, no migration, and no mutation (unless you stipulate conditions for these using the sliders). Certainly a purebred population will be under selection for the traits for type, but you can assume there is no selection for the "neutral" alleles that have no effect on type.

This simulator can also have a very practical use. Let's say your breed is discussing separating various colors in the breed into separate populations that would not interbreed. Or perhaps it is different sizes, or some feature of phenotype. If the groups are prevented from interbreeding, what will the consequences be for the genetic stability of the resulting smaller populations? There are many examples of breeds being split in the past - Norwich and Norfolk were separated based on ears, Toy and Standard Manchester were separated by size, the Belgian Shepherds are separated in the US based on color (but not in Europe), and perhaps you know of others. Splitting a breed WILL have consequences to the genetics of the separate populations, as you can see here effects of genetic drift on allele frequency. There will also be changes in other genetic properties of the populations such as the rate of inbreeding, and breeders should carefully consider these before deciding to make any changes in the breed.

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More on "Simple strategies to reduce genetic disorders in dogs"

12/30/2018

By Carol Beuchat PhD

In a previous post, I showed how inbreeding and strong selection increase the risk of genetic disease (via increased expression of deleterious mutations) and diminish overall health (via inbreeding depression). I also explained how we could improve health and reduce the risk of genetic disorders by making some simple changes in the way we breed. I showed why these things happen using a simple path diagram.

(If you didn't read my previous post, you should do that first and return here: Simple strategies to reduce genetic disorders in dogs)

There are other consequences of inbreeding that might be less familiar to the dog breeder but can ultimately be more important because they also feed into the same cycle of "inbreeding -----> genetic disease".

Below is the figure from my previous blog post, to which I have added another loop (in green). (I have collapsed the loop that was to the left of health consequences and simply replaced it with the word "health".)

Once again we start with inbreeding in a population of dogs. Mating related dogs produces inbreeding, in which a puppy gets identical copies of an allele from both parents, increasing the fraction of genes that are homozygous. To here, we are following the same steps as we reviewed before.

At this point, we will add a new detail to our path diagram. The homozygosity produced by inbreeding might be scattered over the chromosomes, or it can be in blocks of adjacent genes on a chromosome.

Blocks of homozygosity on the chromosomes are called "runs of homozygosity" (ROH), and they have two important properties.

a) the blocks of homozygous alleles tend to get longer and longer with inbreeding;

b) linkage disequilibrium increases with inbreeding.

We need to define "linkage disequilibrium". We usually think of inheritance as one of the two alleles at a loci that are passed on to a descendant by random chance. This is a simple and useful way to think about inheritance, but in reality it can be more complicated. In fact, the regions of homozygous loci that form runs of homozygosity tend to be inherited together as a block. This non-random inheritance at adjacent loci in a run of homozygosity is called "linkage disequilibrium".

So, follow along using the chart below -

1) inbreeding produces homozygosity

2) "runs" of homozygosity (ROH) increase

3) linkage disequilibrium increases

4) deleterious mutations get trapped in blocks of homozygosity

In step 4, why do mutations get trapped in blocks of homozygosity? Inbreeding removes genetic variation. To breed "away" from a deleterious allele, the alternative (i.e., normal) allele must replace it. When there is inbreeding to increase homozygosity for genes for type, as well as selection to reduce genetic variation, the normal allele can become rare. Homozygosity of the mutation within ROHs will increase. Now it becomes difficult or impossible to remove or even avoid a mutation, and over time the number of mutations that are "trapped" increases.

5) mutation trapping increases the "genetic load", the number of deleterious alleles in the gene pool

6) the expression of recessive mutations increases

This path now joins the main pathway that we discussed previously.

You can see that the breeder is now trapped. We are trying to improve type and reduce genetic diseases at the same time as we lose the genetic variation needed for improvement. We are also making it more and more difficult or even impossible to breed away from genetic issues because of linkage disequilibrium. Of course, we continue to select strongly for type, which insures that the blocks containing those genes remain homozygous. The mutations in these blocks are trapped forever.

Now this path feeds back into the larger pathway, where we remove affected dogs or entire lines in an effort to get rid of the genes causing problems. But this reduces the size of the gene pool and throws out valuable genetic variation.

And so it goes, round and round, the quality of the gene pool deteriorating a bit more with every generation.

This is a real pickle if you're a breeder. What all this means is that the more effort you put into breeding for improved health using the usual strategies of inbreeding and strong selection, the bigger the problem gets. This is where we are.

How do we fix this?

If we breed a very inbred dog to one that is not closely related, we can reduce homozygosity (inbreeding) in the puppies. Less inbreeding means smaller blocks of homozygosity, so linkage disequilibrium is reduced. Mutations and other unwanted genes that were trapped in runs of homozygosity are now "set free", so you can breed away from them. There is also new variation that you can make use for improvement of phenotype, so selection will be more effective.

Note that the most useful dogs for an outcross will likely be the ones that are not what you would choose to breed to on the basis of phenotype. The dogs you gravitate to with good type are likely to have all the same ROH you are battling with already, and there will be little to gain. Paradoxically, dogs with more phenotypic variation, especially as it varies away from the extremes in type, will have the most to offer you in terms of escaping from the feedback loop illustrated above. You probably won't get stunning puppies out of a breeding with a dog with mediocre type, but you will escape the loop that is strangling your breeding program and sending purebred dogs towards the cliff.

I can hear a bunch of people complaining that outcrossing will introduce new mutations to your line. Yep, it might. You would probably know about the dominant mutations in a dog you're breeding to, so the new mutations are likely to be recessive. Look again at the feedback loop and you will see that those recessive mutations are completely harmless as long as you don't breed dogs together that have the same ones. And if you keep inbreeding low, you can eliminate those mutations through selection because they aren't trapped in those blocks of homozygosity. Also put your foot down on popular sires; the last thing you want is to produce dozens of puppies that each carry half the mutations found in the favorite dog. Remember, inbreeding is how we ended up with the current problem in the first place. The solution is simple: don't put two copies of the same mutation together in a puppy.

You can fix this problem. You can eliminate health problems in a generation. You can use selection more efficiently. You can add the variation necessary to produce better dogs than you have now. Lives will get longer. Vet bills will go down. Breeding will get easier. Litter sizes will increase. The health and welfare of dogs will improve.

The secret to improving the health of dogs is not more DNA tests, but sound genetic management. We know what is causing the high burden of genetic disorders in dogs, and we know how to prevent this. Trying to eliminate problems by chasing down pesky mutations will not get us out of the feedback loop that is causing the problem. Breeding ever more selectively won't help either. These things make the problem worse.

The solution is genetic management. Understand how the problems are created. Understand the critical importance of genetic variation and reduced inbreeding for improving health. And breed in a way that will be sustainable into the future.

If you learned something useful from this article, there is much more information out there that will improve the health of dogs and make your breeding program more successful. The best way to increase your knowledge and understanding is through one of the courses offered through ICB. These courses are specifically designed for breeders and they truly are the best way for breeders to learn what they need to know to improve the health and well-being of dogs.

The next course is Managing Genetics for the Future and starts 7 January 2019. You can learn more about it and register here -

https://www.instituteofcaninebiology.org/managing_genetics.html

I hope to see you there!

Simple strategies to reduce genetic disorders in dogs

12/29/2018

By Carol Beuchat PhD

Over the last few decades, the number of genetic disorders in dogs has been increasing at an alarming rate. This is despite the diligent efforts of breeders to breed healthy dogs. Why is this happening?

I have created a very basic flow chart to illustrate how a breeding strategy to reduce genetic disorders in a population will actually have the opposite effect. I will go through each of the steps in the process, and you can follow along on the picture.

1) Let's start with a population of dogs in a closed gene pool like the one in the left circle below. Because all the dogs in the population come from a small number of founders, they are all related. Breeding two together is likely to produce offspring that are homozygous for some loci; that is, they inherit two copies of an allele that originated in a common ancestor of both parents. In the flow chart, the inbreeding step results on average in an increase in homozygosity in the offspring.

2) Every dog carries dozens or even hundreds of recessive mutations cause no problems if there is only a single copy of the mutation and the other allele at the locus is normal. But if two copies of the mutation are inherited, there is no copy of the normal allele, so homozygosity increases the expression of these recessive mutations.

3) Homozygosity also has more general detrimental effects on function such as reduced fertility, smaller litters, higher puppy mortality, shorter lifespan, etc., which we collectively call "inbreeding depression". Inbreeding also increases the incidence of polygenic disorders such cancer, epilepsy, immune system disorders, heart and kidney issues, and others.

4) Dogs with genetic disorders are usually removed from the breeding population.

5) Removing dogs from the breeding population reduces the size of the gene pool.

6) Smaller gene pools have less genetic diversity.

7) With less genetic variation in the population, the genetic differences among individuals are reduced and their similarity and relatedness increases.

8) Breeding related animals is inbreeding, so once again this step results in an increase in homozygosity.

From here, we now have a negative feedback loop that goes back to the top of the list of steps. Again, the increased homozygosity increases inbreeding depression, the risk of cancer, epilepsy, and other polygenic disorders, and the expression of recessive mutations.

The result of this negative feedback loop is the steady deterioration in health of the population over the generations unless there is appropriate intervention.s

Let's have a look at the cycle for the population of dogs in the circle on the right in the illustration.

a) Breeders are very selective about which dogs are used for breeding. In general, about 25% of the purebred puppies produced are bred, and typically this is only one or two puppies per litter.

b) Of course, this means that 75% of the puppies are not bred. Removing them and any unique genes they may carry from the breeding population reduces the size of the gene pool.

c) Smaller gene pools have less genetic diversity.

d) If there is less genetic diversity, the dogs in the population are more similar to each other genetically.

e) Breeding dogs that are similar genetically will produce homozygosity in the offspring.

f) Homozygosity increases the expression of deleterious mutations.

Ultimately, the path feeds into the steps we have already described that form a negative feedback loop that increases the incidence of genetic disease.

The goal of selective breeding is to produce quality dogs. The two breeding strategies we have just described, breeding of related dogs (inbreeding) and breeding "the best to the best", do not result in improvement except in the short term. In the long term, the loss of genetic diversity limits the possibility of genetic improvement because the population has lost the genetic variation needed for selection. Inbreeding depression and increased incidence of genetic disease reduce the quality of the breeding stock, and improvement - or just maintaining quality - becomes more and more difficult. Without intervention, animal populations bred this way go extinct.

If you understand the downstream consequences of breeding decisions, which are depicted as steps in these flow charts, you can prevent this cycle of genetic deterioration. For example, the simplest action to take is to be less restrictive about which animals are bred. Breeding 50% instead of 25% of the puppies produced will reduced the depletion of the gene pool. Breeding dogs that are less closely related will reduce the risk of producing genetic disorders in the puppies as well as inbreeding depression. Replacing genes lost from a population through outcross to another population (i.e., through a plan of rotation breeding) or introduction via a cross-breeding program will broaden the gene pool and mitigate the effects of selective breeding.

DNA testing is a valuable tool but not the holy grail. By itself, it will not result in healthy dogs. Ultimately, to improve the health of the purebred dog we need to understand basic population genetics and follow a sound strategy for genetic management. Solving the problem requires understanding the cause how some simple changes in the way we breed can dramatically improve the quality of the dogs we produce.

Continue to read Part 2 of this article:
"MORE ON "Simple strategies to reduce genetic disorders in dogs"

Celebrating the Preservation Breeders!

12/24/2018

By Carol Beuchat PhD

There are more than 1,000 known breeds of dogs, only a few hundred of which are "recognized" by a kennel club. By any measure, this is a spectacular level of structural, physiological, and behavioral diversity to see in a single species, and we owe a large measure of the development of human civilization to the dogs that have helped along the way.

There is growing awareness now that many of these breeds are becoming rare and run the risk of disappearing entirely. The UK Kennel Club recognized this possibility a few years ago and created a list of native breeds that are vulnerable to extinction because of declining numbers. In some breeds, the numbers haven't moved much or continue to decline, but in others the heightened visibility has resulted in an increase in the number of puppies produced.

The Dandie Dinmont Terrier is one of the breeds on the vulnerable list, with numbers produced per year hovering between about 80 and 150 per year since 2010. So the birth of a litter of 5 adorable little pups just in time for the holidays is cause for celebration and noteworthy enough to make the news.

Also celebrating are the folks at the Mongolian Bankhar Dog Project. While all is bleak and frigid on the Mongolian plateau, they are welcoming the arrival of 11 new puppies that will be placed in about 2 months with one of Mongolia's nomadic herders. Each will puppy be introduced to the livestock, grow up as a hoof-less member of the herd, and serve as their protector for the next decade or more. The Bankhar Project is bringing these dogs back from the brink of extinction by replacing guns with these traditional Mongolian livestock guarding dogs, allowing the herders to coexist peacefully with the snow leopard, wolves, and other native predators. By the way, that whelping box is not in a cozy abode in the middle of the spare room. It's a hut outside and it's bitter cold. These pups are coming into the world as they have for thousands of years, ready for the weather and with no expectation of napping on the sofa. I haven't verified this yet, but I'm betting that the "fog" you see puffing in the video is the condensation of the warm breath coming from behind the video camera.

Also in the frozen north, the Norwegian Lundehund Club is readying for the production of the first backcross generation in their breeding program to save the Lundehund from extinction. The dam is Lundhund x Buhund cross and the sire is a Lundehund. The F1 dogs were healthy and very much resembled Lundehunds, retaining almost all of the unique anatomical features of the breed (polydactyly, ability to close the ears, extreme flexibility). The progeny of the backcross should produce pups that are even closer to breed type.

We celebrate these preservation breeders! They are doing the hard work of making sure that the precious genes in the few remaining dogs of these breeds are preserved - duplicated, recombined, and packaged into a new generation of puppies that will carry the breed forward. Each tiny new nose, while appearing in the depths of winter, holds the promise of a brighter future for a breed.

On preserving the purebred dog

11/27/2018

By Carol Beuchat PhD

In 2015, the UK Kennel Club published a basic genetic analysis of pedigree breeds based on the data in their stud books. This analysis showed that, for many breeds, there were high levels of inbreeding and low effective population sizes. Subsequently, to address concerns that some of their native breeds might be at risk of extinction because of declining numbers, they created a listing of breeds that were vulnerable or at risk. They have subsequently monitored registrations of these breeds and annually update the statistics online.

Although AKC would have the records for yearly registrations, they don't make those statistics available. Unless breeders or breed clubs compile these records themselves, there is no way to track breed population sizes in the US. Based on pedigree records of a few breeds that I happen to have, however, there is good reason to be concerned.

I have pedigree databases for a number of breeds that were compiled by breeders and provided to me for genetic analysis. These include the Irish Wolfhound, Afghan Hound, Belgian Tervuren, Rhodesian Ridgeback, and Portuguese Water Dog. I have compiled the information for number of dogs born per year as reflected in the pedigree database, and in some cases I have also recorded the number of litters recorded per year.

For the odd assortment of breeds I have data for, there is a consistent and very disturbing trend. Since about 2000, registrations are crashing. (Note that the decline in Afghans dates to the 1970s but since about 2000, registrations are dropping even more rapidly.)

These are not slow declines; they are crashes. And if you extrapolate the lines, the trajectories of these breeds will hit zero in just a few years - less than a decade for some. I'm sure there are breeds with steady or even increasing registrations, but we don't have the data to know. In the UK, registrations of many breeds are also dropping, but at the same time the numbers of Pugs and French Bulldogs are going stratospheric. Perhaps that is the case in the US as well.

Population crashes have consequences. Genetic diversity is lost, and the rate of inbreeding necessarily goes up as effective and census population sizes go down. We can expect the incidence and number of genetic disorders to increase. Health will decline and interventions by breeders will become increasingly ineffective. It's not a good situation.

What are we doing about this? Nothing. If AKC is monitoring breed populations, they are not making that information available. Unlike kennel clubs elsewhere in the world that have geneticists on staff to provide guidance to breeders about genetic management, or organizations like the Animal Health Trust with expertise and research capabilities that are available to breeders, in the US it's every breeder for themself. Breed clubs and their health committees make decisions about breeding strategies in the absence of relevant expertise, and more often than not the general strategy is to remove dogs from the breeding population that are afflicted with disorders for which there are no tests (e.g., epilepsy, cancer, immune system disorders, etc).

I am not aware of any plans to address these problems, by the kennel club, breed clubs, or smaller groups of breeders. In fact, breeders might not even be generally aware of their dire situation. For the breeds with data below, time for action has nearly run out.

I have argued before that dogs have high value as a genetic resource. Dogs shaped the development of civilization. In many places in the world they are still essential for the special abilities they have for management of livestock, not to mention their roles as service animals, detection of everything from invasive plants to cancer, military and police service, and companions that improve our own health and longevity while they enrich our lives.

There is plenty of evidence that purebred dogs are not doing well. And we also know that in many cases we are not doing what we can (as for the Doberman). Breeds are about to disappear. Are we going to just let this happen?

Irish Wolfhound

Number of Dogs

Number of litters

Afghan Hound

Number of litters

Belgian Tervuren

Number of Dogs

Rhodesian Ridgeback

Number of Dogs

Portuguese Water Dog

Number of Dogs

Is the Ky allele in Wirehaired Pointing Griffons evidence of cross-breeding?

11/23/2018

By Carol Beuchat

Is the Ky allele in Wirehaired Pointing Griffons evidence of cross-breeding?

This has apparently been a burning question in the Griff community for several years and the cause of rifts among lovers of the breeds on various sides of the argument.

In short, every now and then somebody produces a Griff puppy with tan points resulting from Ky. This has been taken by some to be evidence of a deliberate or accidental cross-breeding in the past, punctuated by the assertion that the dogs carrying this allele are thus not "pure" WPGs and should not be allowed to breed.

The first point here is that there is no way to know what specific genes were present in the founder lines more than a century ago. Each dog added to the mix would add another spoonful of genes from the large, diverse genetic stew available among dogs at that time. Certainly, it is fair to expect that the original gene pool was very diverse.

Could the Ky allele have been present in that original gene pool? That would depend on how common it was and how it was distributed among dogs, recognized breed or otherwise.

Eduard Korthals developed the breed in the Netherlands in the late 1800s, with the aim of producing a gun dog that was versatile, hardy, and devoted to its master. To do this he crossed a variety of dogs, some of unknown lineage but carrying some of the traits he wished to produce in the breed. Among those of various types were probably spaniels, retrievers, pointers, and otterhounds. The breed was created as many others have been, as "blender breeds" that borrowed a bit of this from one breed and a bit of that from another to produce a new breed of dog well-suited to a particular purpose in the eyes of its creator.

So here are the crucial bits of information for this discussion of the Ky allele as evidence of genetic contamination.

1) The Ky allele is the ancestral form of the K allele. It is found in all wolves. It is thus likely to have been in the earliest dogs.

2) How common is the Ky allele in dogs? To answer this question, I contacted two highly-regarded canine geneticists with access to large databases of dog DNA data, including alleles for color: Dr Adam Boyko (Cornell University and Embark Vet) and Dr Jonas Donner (Genoscoper and MyDogDNA). They both confirmed first that the Ky allele is the ancestral K allele that is found in wolves. They also both said that the Ky allele is very widespread among breeds and dogs in general. Boyko said "I think it's in more breeds than not...even some black breeds like Schipperke and Belgian Sheepdog." Donner said that "Ky/Ky is the fixed genotype in the modern wolves we have tested, so yes it is the ancestral allele...The frequency of the ky allele in dogs overall is about 70%".

Not only is the presence of the Ky allele not evidence of a cross-breeding event, it would be surprising to NOT find it in a modern dog breed created by crossing various breeds as well as dogs of ambiguous lineage. Ky is recessive to other K alleles, so it can be present in a population for many generations without being expressed. Having a few tan point dogs pop up in a long line of dogs where this has never been seen is proof of nothing more than the roles of chance and allele frequency in the expression of recessive alleles.

There is no scientific or even rational basis for the claim that Griffs carrying the Ky allele are not "purebred" or "true" Korthals. The policy of some groups to purge all the "contaminated" dogs carrying the Ky allele from breeding populations is both wrong-headed and detrimental to the breed because it reduces the size of an already limited gene pool and unnecessarily removes quality dogs for a cosmetic trait that won't even be expressed if a dog is just a carrier. Those claiming that the "pure" or "true" Korthals does not carry this gene and that dogs that do are "just mutts" do a true disservice to the breed for the apparent purpose of elevating their own dogs to a higher status than others. This is not to better the breed, and it doesn't. It is nothing less than a shameless scam.

The data to disprove the fallacy of the claim that dogs carrying the Ky allele are descendants of cross-breeding are abundant and readily-available. There is no evidence that it is associated with any detrimental or undesirable trait in this breed (which has also been claimed) or any other. Remember: this is the K allele found in wolves. In fact, the K allele is not a "color allele". The K gene is otherwise known as the β-defensin gene, and as the name implies it plays a role in the synthesis of peptides with antimicrobial activity in the skin, assisting in its role as a barrier to infection. (Candile et al 2007, Hedrick 2009, Leonard et al 2012).

While breeders are struggling to manage a number of emerging health issues in this wonderful breed, it should be a matter of policy that the loss of genetic diversity for any reason should be minimized to the fullest extent possible. A genetic management plan that strategically prioritizes retaining genetic diversity through the breeding of dogs carrying less common alleles should be encouraged by the custodians of the breeds, and breeders that do this should be supported.

There are some other important things breeders can do to improve the future of this breed. It would be useful to do a breed-wide survey of genetic diversity using a genotyping service like Embark. This will provide information on both breed-wide and genomic inbreeding, the size of the gene pool, distribution and frequency of alleles for known mutations and traits (including color), and the potential presence of lineages of differing genetic composition that can be managed in a way to support retention of the genetic diversity currently available in the breed. These data can produce much information that would assist breeders interested in developing breeding plans that will improve the health of the breed as well as its highly valued qualities as a working dog and a companion. You can see examples of these types of analyses for a number of breeds using the ICB Breeder Tool at http://bit.ly/2OE88by, and ICB can assist you with this.

It would also be extremely useful to do a genetic analysis of a pedigree database. This will provide wealth of information about history that might not otherwise be known through other records. It can also reveal current breeding practices that are detrimental to the preservation of genetic diversity, allowing breeders to take steps that will provide more genetic stability and facilitate management of existing health issues. You can see an example of this type of analysis here (The amazing secrets hiding in your pedigree database). This analysis is for Afghan hounds, but it provides a good model of the wealth of information that can (and should) be extracted from a pedigree database with the appropriate software and expertise. ICB can provide this type of analysis, and it would be very worthwhile to do for this breed.

I have been asked to weigh in on the "Ky debate" many times over the last 10 years or so, and I hope this will put the final nail in the coffin of this debacle that has probably done great damage to the gene pool and therefore the future of the breed. Breeders should consult with scientists that have the appropriate expertise to address critical issues of genetic management instead of trying to do this "in house". There is first the issue of bias interfering with judgement, in the same way that a surgeon should not operate on a member of their own family. But most especially, genetic management of small populations of highly inbred dogs is very difficult; a policy decision to address one problem can have an unanticipated effect on something that was not considered. Here, what appeared to be a simple policy decision about a "color" allele probably did lasting damage to an already small gene pool; certainly it strained relationships among breeders and has fostered the development of cliques that have divided what should be a family of breeders that collectively support the best interests of the breed. I would encourage breeders to heal the wounds, get some factual information about the current genetic status of the breed, and work together to solve problems and insure a bright future for the breed.

REFERENCES

Cadille SI, CB, Kaelin, BM Cattanach and others. 2007. A β-defensin mutation causes black coat color in Domestic dogs. Science 318: 1418-1423.

Hedrick PW. Wolf of a different color. Heredity 103: 435-436.

Leonard, B. C., Marks, S. L., Outerbridge, C. A., Affolter, V. K., Kananurak, A., Young, A., ... Bevins, C. L. (2012). Activity, expression and genetic variation of canine β-defensin 103: A multifunctional antimicrobial peptide in the skin of domestic dogs. Journal of Innate Immunity, 4(3), 248-259. https://doi.org/10.1159/000334566

Cool tricks with Kinship Coefficients, part 4: "How closely related are the dogs in my breed?"

9/7/2018

By Carol Beuchat PhD

One of the problems with strong selection in a closed gene pool is that the dogs become progressively more and more similar genetically. Although selective breeding in purebred dogs results in consistency, it also has the downside that a breed can find itself stuck in a genetic cul-de-sac from which it can't escape. If you need to change the direction of selection, for example to breed towards a different trait or away from a genetic disorder, you need to find dogs with the genetic diversity necessary to support selection in a different direction. Genetic diversity is the raw material for selection; you can't change anything without it.

How much genetic diversity is there in your breed? How can you find the dogs that might have the genetic variation that you're looking for?

There are several different ways to determine how much genetic diversity there is in your breed, but let's look at one that uses the kinship coefficients that we have already been talking about (see Parts 1, 2, and 3 in this series; links at the bottom).

Let's say that we have a population of animals that are not closely. If we compare the genes in each dog with those in every other dog in the population, we can compute each dog's mean kinship, which I explained in a previous post. Since we know the dogs in our population are relatively unrelated, we know that the values for mean kinship will be low (they can range from 0 to 1). If we graph the mean kinship of all of the dogs in the population, we might get a chart that looks like the first one on the left below for Labrador Retrievers, in which all of the values are less than about 0.06. On the other hand, if we have a population of closely related dogs, we might get a graph like the last one on the right below for Irish Wolfhounds, in which most of the values are greater than 0.3. If you scan the graphs for the other breeds depicted below, you will see that the distribution of values for mean kinship can vary considerably.

What do these graphs tell us about genetic diversity?

Remember that mean kinship is the average relatedness of a dog to all others in the population. The Labrador Retriever is one of the most popular breeds in the world so numbers are very high, and there are populations of show dogs, hunting dogs, personal pets that will all be a bit different from each other genetically, and populations in different countries will probably be different from each other as well. This is a breed with a LOT of genetic diversity, and the mean kinship values are mostly low. But if you were to make another graph with just the show dogs, the distribution would probably be skewed towards higher values because those dogs would be more closely related to each other than they are to field line dogs.

When you compare Labradors with Irish Wolfhounds, the graph is skewed strongly towards much higher values. This indicates in this population of over 200 dogs, the average relatedness was very high. The exception is a few dogs that fall far below the pack and are not closely related to the bulk of the population. This indicates that most of the dogs are closely related to each other.

Because the kinship coefficient is based on genes that are the same because they are inherited from the same ancestors, we can interpret these graphs in terms of relatedness. If you breed two first cousins from parents that are not inbred, the predicted inbreeding coefficient of their offspring is 0.0625, or 6.25%. Looking at the graph at the top for Labrador Retrievers, we can see that most of the values of mean kinship are lower than 0.06. So we can say for this population that on average, the Labradors are less related than first cousins.

You can do the same thing for the graphs for other breeds, using this chart for the kinship coefficients for each level of relatedness.

So, looking at the chart for Irish Wolfhounds (bottom right), you can see that most of the dogs have a mean kinship > 0.25; that is, on average most of these dogs are more closely related to each other than full siblings. Imagine a family reunion with a few aunts, uncles, and cousins, and 134 of your siblings. This is a breed with a very high level of average relatedness to each other. Likewise for Cavalier King Charles Spaniels. In the small sample of Havanese, there two clusters of dogs, one with a relatively high level of relatedness to each other, and another with rather low relatedness.

There are several different ways to understand the genetic diversity in your breed. Here, we show you how you can use the kinship coefficient to provide information about the average levels of relatedness in a population of dogs. This is another tool you can add to your genetic toolbox!

We can provide genetic analyses like these for any breed from both
pedigree and DNA data using the ICB Breeder Tool.

Are you interested in using the ICB Breeder Tool with your breed?
Contact us to get started!

Cool tricks with Kinship Coefficients, part 3: "How can I manage a disease without a DNA test?"

9/6/2018

By Carol Beuchat PhD

This is part 3 of "Cool tricks with kinship coefficients". Check out "Part 1: Is this dog really an outcross?" and "Part 2: Should I breed this dog?"

About 80% of the genetics diseases we know about in dogs are caused by a single recessive mutation. Using modern DNA technology that enables us to scan thousands or millions of markers in a dog's genome, we can usually find these broken alleles and develop a test that breeders can use to screen their dogs.

Many disorders, however, are not the result of a single mutation. For these, there might be dozens or even hundreds of genes involved. Creation of a test that will identify an affected dog with no symptoms, one likely to produce affected offspring, is not likely to happen for most of these. This is a huge problem for breeders, because many of these diseases, like cancer, epilepsy, autoimmune dysfunction are very serious and becoming more and more common. Yet they do seem to run in related dogs, so we know genetics is important. How can we manage these diseases if we don't have a DNA test? We can use kinship coefficients. Watch this.

Kinship coefficients provide information about the relatedness of dogs by assessing pairwise genetic similarity. A statistical technique called cluster analysis can use the kinship data to construct a dendrogram - a genomic pedigree - that groups dogs together that are closely related and also indicates the relationships among groups. If a trait or disease has a genetic component, we should expect that clusters of closely related dogs are more likely to share traits than unrelated dogs because they share many of the same genes.

This is a dendrogram constructed using kinship coefficients computed from DNA data for 211 Irish Wolfhounds. The upper figure is the right to the right blown up so you can see a bit easier, and the lower chart is the entire dendrogram.

Let's take a little tour of the lower chart. You can see that the population of dogs has been separated into two smaller groups at the arrow labeled "A". If we follow the branch that comes off point A to the right, we come to a second branch at the arrow B that creates two subgroups. If we follow that branch at B to the left, we come to branch C that again splits the dogs into two groups. You can see now that is called a dendrogram because it is a picture of a structure that branches like a tree.

Dendrograms are a bit tricky to read properly and getting good at it takes some practice. You need to remember that branches can rotate around any branching point. So for instance, the very top branch that divides at A can be rotated around the junction at A so that the green group on the far left is moved to the far right to sit nest to the turquoise group. Clearly, that green group is not most closely related to the red group that was right next to it at when it was at the left end of the chart. For that matter, we can rotate the two groups on the far right (at arrow D) so the green group is now right next to the red group. So there are actually many different ways to arrange the clusters that don't change their relationships to each other. This is because relatedness is indicated by the length of the lines that connect groups or dogs. Dogs connected by very short lines are closely related, and dogs that are more distantly related are connected by longer lines. When we swivel groups around branching points, the length of the connecting lines is not changed so the information about relatedness is not changed. (Check out How to read a dendrogram)

Now we have a picture of the genetic relationships among all of the 211 dogs in this sample. We also have information about which of these dogs has been diagnosed with epilepsy. This is indicated by the three asterisks ("***") at the tip of the branch for each dog. For dogs without asterisks, this could be because they have never reported epilepsy or we have no information. So this chart can't be taken as a representation of which dogs have epilepsy and which do not. It only tells us which dogs have reported a diagnosis of epilepsy.

So, what does this graph tell us? We can see that affected dogs tend to cluster together by family groups, which likely reflects a genetic component to disease risk. Unfortunately, there are no large groups where epilepsy is completely absent. This tells you that the genetic predisposition to epilepsy is widely, but possibly not uniformly, distributed throughout this population of dogs. With some good record-keeping and the addition of data to the database, we might be able to come up with a clearer picture of the patterns of risk that can be used to make breeding choices that will reduce the number of affected dogs.

There are many breeds battling to control genetic disorders for which there are no DNA tests, or the test is unreliable for identifying dogs that will develop the disease (e.g., degenerative myelopathy). For these, kinship analysis could provide very useful information to breeders about risk of disease. Of course, the same technique described here could also be used for diseases caused by single mutations. If incidence of all genetic disorders was mapped on a dendrogram and kept up to date, breeders could notice a problem developing long before it becomes widespread in the breed and difficult to manage because of the high frequency of carriers.

One caveat about dendrograms from kinship coefficients. The cluster analysis uses the information for all dogs in a sample population to construct a tree that is most likely to reflect their true relationship. If more dogs are added to the population, the groups might be sorted differently because the relationships among them are changed. So to be useful, data for kinship should be updated regularly and needs to accurately represent the genetic breadth of the population of interest. This would be true

We can produce kinship coefficient from both pedigree and DNA databases. There is some advantage to the DNA data because it will distinguish differences in relatedness among siblings whereas pedigree data does not. On the other hand, the pedigree information is invaluable because it doesn't require collecting a DNA sample and the cost of analysis. If you aren't trying to compare siblings, you need to run only one or maybe two dogs in a litter, which can reduce the expense considerably.

Think about the valuable information analysis of kinship coefficients could provide to inform your breeding decisions and managing the genetic diversity of the breed. If you have a pedigree database or genotype analysis from high density SNPs, it would be well worth doing.

Cool tricks with Kinship Coefficients, part 2: "Should I breed this dog?"

9/5/2018

By Carol Beuchat PhD

This is part 2 of "Cool tricks with kinship coefficients". Check out "Part 1: Is this dog really an outcross?"

One of the major ways genetic diversity is lost from a breed is through selection. In wild animal populations, most animals produce offspring and pass their genes to a new generation. The progeny that inherit the best combinations of genes survive and reproduce themselves, and those that were not as lucky are culled by natural selection.

In dogs, we often breed only one or two puppies from a litter, selecting those that we feel best suit the goals of the breeder and are good representatives of the breed. But if you started with a sire and dam that you felt were quality dogs, all of those puppies should have "quality" genes but in different combinations, some of which make for a "better" puppy than others. When the pups judged to be less suitable are not bred, we risk losing from the gene pool some of the genes that produced the good quality in the parents. We limit our future breeding options when we lose those genes, and we also remove the opportunity of tossing them together with a mix of genes from another parent dog to perhaps produce something wonderful. You can't breed every dog, and not every dog is worth breeding.

If you breed for both quality (on whatever scale) and health (and of course you so), you should be concerned about the inadvertent loss of genetic diversity that results from selective breeding because eroding the genetic base of the breed will have consequences down the line. But how do you determine which dogs are important for preserving genetic diversity? You can use the kinship coefficient.

The kinship coefficient (K) is an estimate of the genetic similarity of two animals that are related by ancestry. As I explained in Part 1 of this series (Cool tricks with kinship coefficients, part 1: Is this dog really an outcross?), the kinship coefficient of the sire and dam determines the inbreeding coefficient of their litter. Put another way, the inbreeding coefficient of a dog is the kinship coefficient of its parents. (And remember from part 1 that K must always be a comparison of two individuals.) We are going to see how you can use the kinship coefficient to assess the genetic value of a dog to the breed.

Below is the same kinship matrix we talked about in my previous post about kinship coefficients. Again, the white squares on the diagonal are each dog compared to itself (so K = 1), and the other squares are color-
coded to make it easy to spot combinations that are less (or more) related to each other.

We can use the color coding indicated in the three squares in the upper left corner on the matrix to easily spot dogs that are closely related to other dogs (i.e., green, yellow, and red). If you follow across the rows of dogs 6 and 7 from left to right (or follow down the columns for these two dogs if you prefer), you will see that there are lots of red, orange, and yellow squares, indicating dogs as closely related to 6 and 7 as half-siblings (K = 0.125) to full siblings (K = 0.25). This means that the genes in dogs 6 and 7 are also found in other dogs in the population because they share ancestry.

Now do the same thing for dogs 3 and 4. You will find that most of the squares are green, indicating that they are not closely related to most of the dogs in this group. Interestingly, 3 is as related as a full sibling to 9 and 10 (K = 0.25), which are likewise closely related to each other; similarly, 4 is closely related to 11 and 12, which are likewise as related as full siblings. It would be interesting to look at the genealogical relationships among these four dogs from pedigrees.

If dogs 6 and 7 have many relatives in the population and dogs 3 and 4 have very few, then the latter pair are genetically more valuable because they carry genes that are not common among these dogs. It is fairly easy to identify the genetically important dogs in this small example population, but how can we do it with a large population of dogs with complicated patterns of relationship?

The easiest way is by computing the mean (average) of all of the kinship coefficients for each animal. In the figure below, have added a column on the right labeled mK, for "mean kinship". It is easily computed by adding up all the values in a row and dividing by the number of dogs. (The kinship coefficient of each dog with itself is included in the calculation.) Now we have a column of numbers in which it is easy to see which dogs, by the bright yellow squares, are most genetically different from the rest. Although on average, they are as related as half-siblings to the rest of the population, we know that it includes dogs with little or no relatedness, and you should keep this in mind when you are comparing the values for different dogs. It is always worth examining the kinship matrix to see whether a dog with K = 0.125 is closely related to everybody, or instead is unrelated to most of the dogs but closely related to a few that drive up the average (as here).

Now we can use the data for mean kinship to quickly identify the dogs that are genetically most valuable in a large population. The simple bar graph organizes the dogs by rank, with the lowest values of K to the left - the dogs with the highest genetic value - and high values to the right (the dogs with lowest genetic value). In this population, there are a few dogs with high genetic value, but most of the rest of the population is closely related.

We should be using kinship coefficients much more than we are, and that is to the detriment of maintaining genetic diversity in our breeds. Breeders should know which dogs are genetically valuable, even if they aren't the top winners in competition, because the genetic variation they carry is the raw material for breed improvement in the future. Lines lost are lost forever. Perhaps breed clubs should have a genetic diversity committee that is responsible for monitoring the population to prevent loss of variation, or this could fall to the health committee because diversity and health go hand in hand. Note that if everybody rushes to breed to the least related dogs, their genes will become common and intermixed in a way that prevents them from being used strategically to manage genetic diversity. Diversity should be exploited strategically. (For the same reason, there should be a "popular sire" monitor, whose job it is to keep an eye out for sires producing more than their fair share of puppies.)

Learn how to use the kinship coefficient to take some of the guesswork out of decisions about genetic relatedness or uniqueness when you are considering your future breeding plans. This simple tool can provide you with a wealth of valuable information!

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Cool tricks with Kinship Coefficients, part 1: "Is this dog really an outcross?"

9/3/2018

By Carol Beuchat PhD

Every few generations, it's a good idea to cross out to a relatively unrelated dog to bring in some new genetic diversity and freshen up your lines. But finding the right dog to do this with can be tricky. A dog that doesn't share any ancestors with the dog you want to breed in the last 5 or 6 generations might have enough shared ancestors farther back in the pedigree to provide a lot of relatedness. Or even worse, maybe you don't have a decent pedigree database so you really have no idea how closely two dogs might be related. This is an especially irksome problem if you're contemplating bringing in an expensive import. You really don't want to get it wrong.

So what do you do? How can you identify a dog that will be a good outcross for your breeding program?

How related are these two dogs?

Conservation genetics has the perfect tool for this. It's called the "kinship coefficient" (K), and it measures the genetic similarity between two individuals (Li et al 2011).

In particular, the kinship coefficient tells you how much of the genomes of two dogs are the shared because they were inherited from a common ancestor. (You will also see the kinship coefficient referred to as the "coancestry coefficient"; they are the same.)

The kinship coefficient reflects shared ancestry (coancestry) in the same way as the coefficient of inbreeding. First cousins will, on average, share 6.25% of their genomes, and K for the pair will be 0.0625. In half-siblings, the prediction of fraction shared is 12.5%, or K = 0.125; and for full siblings K = 0.25, or 25%.

The kinship coefficient is related to the coefficient of inbreeding: the coefficient of inbreeding of a dog is the kinship coefficient of its parents. So, the kinship coefficient between a potential sire and dam is also the predicted inbreeding coefficient of their litter. The kinship coefficient in population genetics uses the Greek symbol phi, as in this figure.

The kinship coefficient can be calculated from a pedigree database, just as inbreeding coefficients are. But it can also be estimated directly from DNA data - in effect, the "realized" kinship coefficient that reflects the actual level of shared ancestry between two dogs based on their DNA.

Let's look at this very simple pedigree containing 14 dogs. Perhaps you were contemplating doing a breeding between dogs 14 and 7, but you are worried that it might be too close. You want to know how closely related - genetically similar - those two dog are. The kinship coefficient will tell you this. Here's how.

The kinship coefficient is always a comparison of two dogs. You can compute the K for each pair of the dogs in the pedigree and display them in the form of a matrix. Each dog is listed down the side and also across the top. The number in the box where the column and row of a pair of dogs intersects is the kinship coefficient of that pair. The white boxes on the diagonal are each dog compared with itself.

For example, we can determine that the kinship coefficient between dog 14 and dog 7 is 0.19, or 19%. This means that if you were to choose one allele at random from the pair of alleles at a particular locus on the DNA of dog 14, and likewise choose an allele at random from that locus for dog 7, the probability of choosing two alleles that are identical because they were inherited from a common ancestor is 0.19, or 19%. To put it another way, the chance that the offspring of this pair of dogs will be homozygous at that allele (have two identical copies of an allele inherited from a common ancestor) is 19%. Furthermore, if these two dogs were to produce a litter, the predicted coefficient of the puppies would average 19%.

Computed from a pedigree, the kinship coefficient is an estimate of the average expected kinship coefficient; that is, the shared genetic relatedness because of shared ancestry. But kinship can also be determined directly from DNA genotyping data, such as is provided by Embark. (As far as I know, this is the only company that will allow dog owners to download the raw data for their dogs.) When based on DNA, these are "realized" rather than predicted estimates of genetic relatedness, and they will be different for every dog in a litter.

Now, here's the beauty of this. Let's say you're looking for a dog that will be an outcross for a bitch you want to breed, and you're willing to import a dog if you have to. You have computed the kinship coefficients from the pedigree database available for your breed, and there are two dogs overseas - litter mates, in fact - that look promising. Would these dogs be a good outcross for your bitch? Would one of these be a better genetic fit to the bitch than the other?

To answer these questions, you can do direct comparisons of the genomes of these two dogs with the bitch you want to breed by calculating the kinship coefficient for both of the sire-dam pairs. Modern DNA analysis using "single nucleotide polymorphisms" (SNPs) can now provide excellent data with very high resolution that you can use to do this. ("Single nucleotide polymorphism" is a fancy term for loci that are highly variable ("polymorphic"); the abbreviation is pronounced "snips".) We can easily and inexpensively compare hundreds of thousands - even millions - of loci on the chromosomes of a pair of dogs, assess whether the alleles at each of those loci are the same or different. Further, using data for allele frequencies in the larger population we can determine if the shared SNPs are copies of the same allele in a common ancestor; that is, they are "identical by descent" (IBD). This is the technique used for establishing the relationships among many breeds of dogs (Dreger et al 2016), and it is also used to identify genetic mutations associated with diseases in genome-wide-association studies (GWAS).

Instead of estimating kinship from a pedigree database, which will only give you one number that applies to the entire litter, you can estimate the actual degree of genetic similarity between two dogs. In fact, using SNPs you can even see which areas on each chromosome are shared. You can use this information to see if blocks of homozygosity overlap in two dogs, in which case all of the offspring would also be homozygous in the same place. (More on this in an upcoming blog post!) You can specifically look at characteristics of the genome of the two litter mates and determine if there are any ways one might be a better match to your bitch than another. And the kinship coefficient will also tell you the estimated inbreeding coefficient of the litter produced by each potential sire.

For the preservation breeder, the genomic kinship coefficient from SNP genotype data provides you with the best, most advanced tool available today for genetic management to improve the quality of your puppies while also protecting genetic diversity for the health of your breed in the future.

We will be learning about kinship coefficients and how to use the kinship matrix in ICB's new course, "Strategies for Preservation Breeding", which starts 10 September 2018. Join other preservation breeders who will be using this powerful tool to improve their breeding program. If you're interested in using genomic kinship coefficients to explore options for your next breeding, contact ICB and we will work with you to set that up.

Watch this space for more Cool Things you can do with kinship coefficients!

REFERENCES

Dreger, DL, M. Rimbault, BW Davis, A Bhatnagar, HG Parker, & EA Ostrander. 2016. Whole-genome sequence, SNP chips and pedigree structure: building demographic profiles in domestic dog breeds to optimize genetic trait mapping. Disease Models and Mechanisms 9: 1445-1460. (pdf)

Hayward, JL, MG Castelhano, KC Olivera, and others. 2016. Complex disease and phenotype mapping in the domestic dog. Nature Communications 7:10460. DOI: 10.1038/ncomms10460. (pdf)

Li, M-H, I Stranden, T Tiirikka, M-J SevonAimonen, & J Kantanen. 2011. A comparison of approaches to estimate the inbreeding coefficient and pairwise relatedness using genomic and pedigree data in a sheep population. PLoS ONE: Nov 2011; Vol 6:11. e26256. (pdf)

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The easy way to understand the inheritance of recessive alleles

8/22/2018

By Carol Beuchat PhD

Most of the genetic disorders in dogs are caused by recessive mutations, a single broken allele. There are now tests for dozens of disorders that can detect whether a dog has inherited one or two copies of the broken version of an allele. With the DNA testing information, we can reduce or eliminate the risk of producing puppies that will be born with a disease caused by one of these recessive mutation.

We can predict the genes likely to be inherited by the puppies if we know the genotypes of both of the parents from DNA testing.

You have probably seen some busy-looking illustrated examples like the one to the right of the phenotypes to expect from the genotypes of the parents.

These are useful for illustration, but most people (well, speaking for myself) can't just memorize the illustration.

In fact, there is an easier way to figure out the phenotypes to expect from particular genotypes and you don't have to memorize a thing.

We can predict the genes likely to be inherited by the puppies if we know the genotypes of both of the parents from DNA testing. There have been some illustrated examples of the genotypes to expect from various combinations of clear (AA), carrier (Aa), and affected parents (aa). These are useful for illustration, but most people can't memorize the illustration. In fact, there is an easier way to figure out the phenotypes to expect from particular genotypes and you don't have to memorize a thing.

To do this, we can use something called a Punnett Square. Reginald Crundall Punnett was a British scientist that finished his degree in 1898 when things on the cutting edge of genetics were really getting hot. Experiments on Mendelian genetic inheritance of simple traits like size and flower color in sweet peas all the rage, and the concepts of recessive and dominant were throwing new light on the understanding of inheritance.

Punnet wanted to work out a simple way to predict the traits - the phenotypes - that would be inherited from parents. Knowing that each individual has paired alleles for a trait, one inherited from each parent, he came up with the Punnet square. Here's how it works.

Draw a square and divide it in half both ways to produce four compartments. Each compartment will represent a puppy (or a pea seedling, or whatever). Above each of the columns, note the genotype of the father for the gene in question, indicating the dominant allele with an upper case letter and the recessive version with lower case. On the left side, label the rows with the alleles present in the mother. In this example, the father is heterozygous for the B gene (Bb) and the mother is homozygous recessive (bb).

Now, to see what we do next, click on this little alien that can't wait to show you the basics -

Knowing how to do a Punnett square, you can figure out the predicted proportions of phenotypes from combinations of parents with any genotype. So you don't need to memorize a busy chart like this one. Just sketch a square with four quadrants on the back of a napkin and work it out in seconds.

If fact, to convince yourself that you've got this, why don't you see if there are any errors in this one that has been circulating on Facebook! Remember to represent "clear" as AA (or whatever letter you want to use), "carrier" as Aa, and "affected" as homozygous recessive, or aa.

Just remember that these are probabilities. If you (OMG) were to have a litter of 100 puppies (or puppies from the matings of many parents with the same genotypes), you can expect to come close to the predictions from your Punnett square. But the alleles inherited by each puppy are random. As you know from flipping a coin, you shouldn't expect to get 5 heads and 5 tails from 10 tosses every time. But flipped 50 times it should be closer to 50:50, and 100 flips is likely to come close.

The Punnett square works just as well for predictions of two traits at a time. Here's an example of a "dihybrid" cross involving two genes in guinea pigs, one for coat color and the other for coat length. The Punnett square makes it easy to map out all 16 possible combinations of inheritance in just a minute or two.

Have a go at checking the red, blue, and greed Ridgebacks and see if you get the same results for each pair of parents on the left. And below are some other examples you can play with. By the time you've worked through these, you'll be a pro!

If you enjoy learning about the genetics of dogs, check out ICB's online courses designed specifically for breeders and dog lovers.

ICB's next online course starts MONDAY, 27 August 2018

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The amazing secrets hiding in your pedigree database

8/10/2018

By Carol Beuchat PhD

I was honored to be asked to do a presentation about the genetics of the Afghan Hound at their World Congress, which was held in August 2018 in Amsterdam. This is a summary of the information presented.

This is also a great example of the amount of useful information that can be extracted from a basic pedigree database. Using tools from population genetics, we can explore the genetic history of the breed from the founders up to the present day. Along the way, we can examine the genetic impact of each of the founders, the consequences of popular sires and bottlenecks, the effects of historical events such as wars, and changes in breed popularity that affected population size. We can see how genetic diversity has been lost over the generations, and determine the current size of the gene pool and the effective ("genetic") population size.

That's a lot of great info and also a good example of how population genetics can help breeders more effectively manage the genetic health of their breed.

Even if the Afghan Hound is not your breed, this should be interesting to you. And if your breed has a pedigree database, it's worth going through this to see some of the amazing things you might be able to learn about the genetic history and present status of your own breed!

A QUICK SUMMARY

The modern Afghan Hound was developed through selective breeding of land race dogs from Afghanistan.
Within 20 years, the composition of the gene pool was fixed and has changed little since.
A single founder dog, Sirdar of Ghanzi, accounts for 30% of the total genetic diversity in the breed today.
The size of the current gene pool is about 9.
The average level of inbreeding is roughly 20% from pedigrees and 30% from DNA.
The average kinship coefficient is less than the inbreeding coefficient, indicating that breeders are preferentially inbreeding.
The number of dogs produced yearly has been dropping for decades.
The effective population size is falling and is currently at a critical level (about 100).
Breeders need to protect the remaining genetic diversity and could improve it through introduction of new founders from the country of origin.
Breeders should reduce multiple breedings and instead try to use multiple puppies from each litter instead of just one.
Breeders should maintain an up to date pedigree database and do regular analyses like this to stay informed about the genetic status of the breed.
Breeders should minimize the overall risk of genetic disease through sound genetic management instead of one mutation at a time through DNA tests.

The original sighthounds of Afghanistan are land race dogs specialized for hunting. There are multiple varieties adapted to different environments and suited for various functions.

The land race dogs can still be found in Afghanistan and surrounding countries. I asked a Facebook friend in Pakistan if he ever sees dogs that look like the original land race Afghan hounds. He told me that in fact he is raising one and sent this photo of an 18 month old bitch. This looks very much like some of the dogs that became the foundation of the modern Afghan Hound.

The dogs that were to become the purebred Afghan were brought back from the area by British soldiers and their families. Aggressive selective breeding programs that emphasized elegance, beauty, and coat quality quickly transformed the land race dog into the modern purebred Afghan Hound.

As with most breeds, today’s Afghan Hound descends from a group of “founder” dogs from countries of origin. These founder dogs contribute the genes that comprise the original gene pool, which contains all of the genetic variation the breed will ever have as long as the stud book remains closed. (As we will see, additional dogs have been added.)

The process of breed development can have a profound effect on the genetic makeup and diversity of the developing breed. Selective breeding refines type to suit the breed standard and the tastes of breeders, and desired traits are locked in using inbreeding.

Who were the founder dogs of the modern Afghan Hound?

There were two main sources of dogs: short-haired dogs from the steppes that were more suited to the desert, and long-coated dogs from mountainous areas.

These two populations of founder dogs and the kennels that promoted them are referred to as the Bell-Murray (B-M) dogs (desert type) and the Amps dogs (mountain type).

In the breed’s first decade, the Bell-Murray dogs dominated the gene pool. By 1929, four B-M dogs accounted for 59% of the gene pool, each contributing more than 10% to the total genetic variation.

In the breed’s second decade, the influence of the B-M founder dogs diminished. The founder dog with the single largest genetic influence was Sirdar of Ghazni, whose contribution to the gene pool amounted to nearly 30%. No other founder dog from either kennel contributed more than 10% to the gene pool.

(Offspring of first generation founder dogs also appear on this chart.)

Based on the pedigree database, the total number of dogs produced between 1917 and 1933 was 718. Sirdar’s offspring accounted for 10% of these, which makes him the breed’s first “popular sire”.

Sirdar of Ghazni, the breed founder that has had the largest impact on the genetics of the breed.

This is a chart of the relative genetic contributions of the most influential ancestors by decade (except for the first period, which is 13 years, 1917-1929).

The two smaller graphs at the top are the ones you saw previously of the founder contributions to the gene pool in the first and second decades. In this stacked bar graph, you can see that by the second decade, Sirdar dominates the gene pool (lowest block in red). His influence continues unchanged to the present day. In fact, the genetic composition of the breed has changed remarkably little in the last 90 years, other than the influence of B-M dogs slowly diminishing over time. The most significant change in the structure of the gene pool is the addition of Shirkhan of Grandeur (in dark blue at the top of the bars) at the end of the 1960s, and his influence has been increasing.

The popularity of the breed began to increase in the mid-1930s, with some significant surges and declines at various times. These can be attributed to cultural events - specifically, three wars - that changed the resources people had to invest in their dogs

There were Afghan Hounds in Great Britain prior to WW I, but by the end of the war they were gone. The dogs at the foundation of the modern breed were introduced after WW II. Popularity of the breed began to increase in the UK and dogs imported to the US established a growing population there. But during WW II there was massive culling of dogs in the UK and the population plummeted. The US population was less dramatically affected. After the war, popularity surged until the Korean war, which took a greater toll on the production of dogs in the US than the UK. Beginning in 1960, there was a huge surge in popularity of the Afghan Hound.

From about 1,000 dogs produced yearly after WW II, breeding increased to 12,000 per year at the height of the breed’s popularity in 1974. Even more rapidly than the breed surged, breeding crashed and by 1985 had dropped to less than 3,000 per year. The pedigree database records 1,241 dogs born in 2010, almost exactly the same number of dogs produced in 1961 at the beginning of the population boom.

Breeding is the process of copying the genes in dogs of one generation and passing them on to the dogs of the next generation. Which genes are copied and how many copies are made determine the genetic composition of the next generation. So, breeding practices - including population explosions and bottlenecks - can profoundly affect the genetics of a breed.

In most purebred breeds, only a fraction of the dogs born produce offspring themselves, usually about 15-40%. This is also true of Afghan Hounds. This graph shows the total number of dogs produced yearly (in blue, as in the previous graph) and also the number born each year that produced offspring (in red). The difference is substantial. The next graph will show the magnitude of that difference.

This graph covers the same period of time as the previous one and displays the percentage of dogs born that produced offspring.

After the early years of breed foundation, the fraction of dogs bred has varied from about 15-50%. There is a peak in 1965 that corresponds to the start of the period of exponential growth. However, while the population was exploding, the fraction of dogs being bred actually declined and didn’t stabilize until about 1975, which corresponds roughly to the peak in the number of dogs produced per year.

Since 1990, the fraction of dogs that produce offspring has been declining from about 25%, and it appears to be dropping rapidly in the last decade. The most recent estimate (for 2013) is only 7%.

As is also typical of most purebred breeds, fewer males were used for breeding than females. Over most of the history of the breed, the ratio has ranged from about 1.5-2 females to males. The ratio of females to males has been declining over about the last decade.

Shirkhan of Grandeur was born in 1954 and profoundly affected the genetics of the breed. In 1957, he was the first Afghan Hound to win Best In Show at the Westminster Kennel Club.

Shirkhan of Grandeur produced a total of 121 offspring in 49 litters out of 42 dams over the 12 years from 1956 to 1968. Of these, 92 produced offspring themselves.

The total number of dogs produced between 1956 and 1968 while he was breeding was roughly 22,500. He produced 121 so his contribution in terms of offspring was tiny, only 0.5%. In terms of direct progeny sired, he would not be considered to be a popular sire. In this chart of sires active for 1954-1968, he is far down in the rankings (arrow).

In fact, the most popular sire at that time, and of all time, was Khinjan Lorach, who was born in 1967 and produced a total of 755 offspring from 112 different dams and 127 litters.

Shirkhan of Grandeur’s impact on the gene pool is a consequence of two things:

1) His offspring appear just at the beginning of the population explosion that began in the 1960s;

2) MOST of his early descendents were bred.

Instead of the usual 20-40% of offspring being bred, for the first 2 generations about 70% of his descendents also produced offspring, and over the next two generations the percentage was more than 40%. His inbreeding coefficient was 8%, so he passed some genetic diversity to his offspring.

Shirkhan of Grandeur came just as the popularity of Afghan Hounds was increasing in the 1960s, so although he was not an especially prolific sire, his descendants contributed significantly to the increase in numbers during that time.

The graph on the left shows the number of offspring he produced from 1956 to 1968. The graph on the right is the cumulative number of his descendants over the next dozen generations. After 10 generations, he had > 130,000 descendants. The total number of dogs in the pedigree database between 1955 and 2017 is 197,214.

These are graphs of the genetic composition of the entire breed in 1954 (larger graph), the year Shirkhan of Grandeur was born, compared to his own genetic profile (smaller graph inset).

There are just three evident differences - Shirkhan of Grandeur had less genetic contribution from Rani of Ghazni and Zorawar than was present in the population as a whole, and more from Danenda of Ghazni.

Historically, purebred dogs have had closed stud books; every dog must be from registered parents, and all dogs in the registry go back to the same (few) founder dogs. The exceptions would be dogs from outside the breed that are specifically approved to be registered.

Because every dog must have registered parents and all share the same founders, ALL breeding of purebred dogs is to related dogs. This is the definition of “inbreeding”. Breeding related dogs creates homozygosity because related dogs share some of the same genes. Homozygosity refers to the inheritance from an ancestor of the same allele from both parents. There can be close inbreeding (e.g., siblings) or distant inbreeding (third cousins), but it’s all inbreeding - it produces homozygosity.

There are advantages and disadvantages to inbreeding. Inbreeding reduces variation among animals and increases predictability in breeding. It also increases prepotency, so parents produce offspring that share their traits.

But there are also significant disadvantages to inbreeding, mostly related to health. Inbred animals are less fertile and produce fewer offspring, and they are more likely to express diseases caused by recessive mutations.
Because the disadvantages of inbreeding affect the success of your breeding program, we tend to worry a lot about inbreeding.

When the small number of founder dogs for a breed is low, there is no way to avoid early inbreeding.

This chart contains the inbreeding coefficient of every dog in the pedigree database for which one can be calculated. The very low or zero values that you see represent dogs with missing ancestors or parents; these values will be underestimates of actual inbreeding so they are an artifact of the data.

You can see that over the history of the breed, most dogs have inbreeding coefficients higher than 0.05, or 5%. Most dogs fall in the range of 10-30% (0.1 to 0.3).

These are the data for inbreeding again, this time plotted as just the mean (red) and maximum (blue) values each year over the history of the breed.

Since about 1935, the average level of inbreeding has gradually increased from about 8% to the current level of about 20%. This is what you would expect for a population with a closed gene pool.

There have also been dogs produced that had extraordinarily high levels of inbreeding. Since about 1950, inbreeding higher than 40% has been common. Since about 2000, the average inbreeding has been stable and the maximum values dropping (but still very high).

What do these values for inbreeding mean? What value would be considered “high”?

This is the same graph you just saw. I have added some colored lines for particular levels of inbreeding.

The lines are for inbreeding that would result from crossing full sibs (25%; red), half sibs (12.5%; yellow), and first cousins (6.25%; green). (These assume the parents in each case are not inbred; otherwise these values will be higher.)

Since 1940, the average inbreeding has been greater than expected for a half-sib cross (12.5%). This means that regardless of the apparent degree of (un)relatedness on a pedigree, most breedings were the genetic equivalent of a half-sibling cross or closer.

This graph shows the level of inbreeding in the current population of dogs. It includes all of the dogs born from 2010 to the present.

Most dogs have an inbreeding coefficient of less than 25%, but there are many higher than 25% and even a few over 40%. Remember that these data are based on analysis of a pedigree database, and we know that missing data will result in underestimation of actual of inbreeding. So these data suggest that inbreeding in general is high in the breed.

Note: The pedigree database I used is not complete. Recent dogs are less likely to be entered, and I looked for the top 40 dogs in the US right now and found only 2, so some countries might less complete than others.

This graph is similar to the one you just looked at for inbreeding, except it is for something called the “kinship coefficient”.

The kinship coefficient (K) is an index of the relatedness (or genetic similarity) of two animals. It is always a comparison of two individuals. The kinship coefficient is related to the inbreeding coefficient: the inbreeding coefficient of a dog is equal to the kinship coefficient of its parents. Similarly, the kinship coefficient of two dogs is the average inbreeding coefficient of their offspring.

We can use the average (mean) kinship coefficient of the animals in a population (mK) to assess how closely related they are to each other. If the mean kinship coefficient is high, then the dogs are, on average, very similar to each other genetically; if the mean kinship coefficient is low, then on average the dogs are less similar genetically.

The graph shows the distribution of mean kinship values that would result if the current population of Afghan Hounds was breeding randomly.

(Remember that just as for the inbreeding coefficient, missing data will underestimate this value.)

These are the graphs you just saw - of inbreeding coefficients on the left, and mean kinship coefficients on the right.

We can learn something about the breeding strategies being used in a population by comparing the data in these two graphs.

Looking at the graph on the right, we can see that if Afghan hounds were breeding randomly, mean kinship coefficients would be relatively low, ranging from 10% to 15%.

From the graph on the left for inbreeding coefficient, we can see that while many dogs fall in the range of 10-15%, most are higher than this.

When the inbreeding coefficient is higher than mean kinship, this indicates that breeders are preferentially mating dogs that are more closely related to each other than the average relatedness in the population. That is, even though most of the dogs in this population are already more closely related than half-sibslings, breeders are still choosing mates that are even more closely related than this.

This also means that with proper mate selection, breeders could reduce the level of inbreeding in their litters by choosing pairs with a lower kinship coefficient.

We are always hearing about the high level of inbreeding in dogs. How high - or low - is inbreeding in dogs?

This chart shows the average inbreeding coefficient of a large sample of dog breeds based on DNA data instead of pedigrees. The breed names are probably too small to read, but the Afghan Hound is indicated by the arrow. The inbreeding levels are marked by horizontal lines as before, with red (25%) for a full sib cross, yellow (12.5%) for a half-sib cross, and green (6.25%) for a cross of first cousins.

The average inbreeding coefficient of the Afghan Hound estimated from DNA analysis is about 30%. This is about the “middle of the pack” for the breeds that have been studied.

This compares to about 20% based on pedigree data. Remember, however, that incomplete pedigree data will underestimate actual inbreeding.

Is 20% or 30% inbreeding “high”? We can compare dogs to other domestic animals.

The graph at the bottom is the one you just saw for dogs, with Afghan Hound marked with the arrow. The chart at the top is average inbreeding based on DNA for horse breeds, with the same colored lines to mark levels of inbreeding.

Only one breed, the Clydesdale, has an average inbreeding > 25%, and more than half of these breeds are less than 12.5%. In fact, about a dozen breeds average about 6% or less.

Inbreeding in purebred dogs is far higher than in horses, and indeed higher than is typical of other purebred domestic animals. Certainly it is the case that high inbreeding levels are not a requirement of either domestication or of maintaining the traits that make each breed unique.

The founder dogs of a breed, both as original breeding stock and also unrelated dogs introduced into the population later, determine the size of the gene pool. Except for genes added to the gene pool by dogs introduced later, the size of the gene pool will decline over time.

All of the genetic variation the breed will ever have is present in these founder dogs.

Genetic diversity is lost during breed formation due to selective breeding for development of type and concentration of the genes for those features. Dogs in the current population retain the genes for type, but will have lost genes for other traits and functions over the generations.

How do you measure the “size” of the gene pool?

This is a graph of how the size of the Afghan Hound gene pool has changed over time. The triangles along the x-axis indicate unrelated dogs (i.e., new “founders”) added to the population after 1925.

Just look at the blue line for now. This is the line for the “effective number of founders” (fe) - specifically, the number of unrelated dogs that would contain the same amount of genetic diversity as the actual population at a particular time. The highest value, fe = 16.5, occured while the breed is being founded.

By 1930, genetic diversity had declined to fa = 9.5. In another decade, fa is reduced and after that it averages about 9.

Additional unrelated dogs occasionally introduced through the 1970s prevented a reduction in the size of the gene pool.

The size of the current gene pool is about 9.

Selective breeding affects the composition of the gene pool.

Genetic diversity can be lost from the gene pool because of selection - some dogs are bred and some are not.

Also, some animals have a disproportionate number of offspring, and their genes become over-represented. The best example of this is the “popular sire”.

Popular sires reduce the size of the gene pool because they deprive other males of reproductive opportunities. They also drive up the average level of relatedness in the population because of the number of siblings and half-siblings that share a sire.

Popular sires are also the most significant cause of genetic disorders in dogs. Most disorders in dogs are caused by recessive mutations that originate with a popular sire. Here’s how this happens.

Every dog (every animal, even you!) carries recessive mutations that are harmless if there is only one copy of the defective gene. In this little population of dogs, each has a different mutation (in red) at the arrows. (We’ll pretend each has only one.)

Let’s say that Hank (with crown!) wins the big dog show. He’s on TV, he goes on tour, and suddenly he is in huge demand as a stud dog.

Hank passes all of his health testing - eyes, hips, and the DNA tests available for the breed.

He produces dozens of lovely, healthy puppies. Many other potential sires are not used, and their contribution to the gene pool declines or might be lost completely.

Each puppy inherits half of its genes from its dam and half from Hank. By random chance, half of the puppies produced by Hank will carry one copy of his recessive mutation. They are not affected by it, because they inherited a normal copy of the gene from their dam.

Everyone is thrilled with the stunning, healthy puppies sired by Hank.

A generation later, some people have bred half siblings that share Hank as a sire. Some of those puppies inherited a copy of Hank’s mutation from both of their carrier parents, making them homozygous for the bad gene.

In this generation, a few puppies are produced with a genetic disorder, but not enough to sound an alarm.

In the next generation, however, Hanks mutation has now spread widely through the breed population, and there are many puppies suffering from this new genetic disorder.

After reviewing their pedigrees, breeders trace the source of the mutation to Hank.

Hank is villified, his owner shunned, and people start breeding around the disorder by avoiding his descendants. Thousands of dollars are invested in a research study, the mutation is identified, and a new test is added to the list of “health tests” every dog is expected to have before breeding.

Of course, this isn’t Hank’s fault. Genetic disorders from recessive mutations result when rare mutations become common in a population. Popular sires produce many copies of their mutations and the result will be genetic disorders for the descendants that get two copies.

Usually, it is forgotten that Hank’s mutation became a problem because he was a popular sire.

The next big winner will probably also become the next popular sire, and his unique mutation will be passed to dozens or even hundreds of puppies. The cycle will continue, and a new genetic disorder will probably be produced.

We can completely prevent genetic disorders caused by recessive mutations. Don’t create popular sires.

We noted earlier that genetic diversity is lost from the gene pool because of selection.

The other way diversity is lost from the gene pool is “just by chance” - called genetic drift.

Because genes are inherited randomly, not every gene in every parent will be copied into a puppy of the next generation. If an allele is rare in the breed, it can be lost entirely. The change in the composition of the gene pool from generation to generation just due to chance is called “genetic drift”.

Most breeders don’t worry at all about genetic drift. If breed populations were very large, the chance that a rare gene would be lost is low. However, if the population size is small, the loss of rare genes through genetic drift can be high.

For population size, it is not the total number of animals in the breed that matter, but just the ones that are breeding. As we have seen, the breeding population is usually only about 20% of the census population. And if those breeding animals are related, the “genetic size” of the population will be even smaller.

The “genetic size” of a population is called the “effective population size”, Ne.

Ne is the size of a hypothetical population that loses genetic diversity at the same rate as the real one of interest. There are many things that can affect Ne, but two important ones are 1) the number of animals bred and 2) the ratio of females to males, both of which we have discussed for Afghan Hounds.

This graph is very similar to one you’ve seen before. But instead of actual number of animals on the y-axis, this one has the effective population size.

You should know the effective population size of your breed is because it is linked to the rate of inbreeding. As effective population size gets smaller, the rate of inbreeding increases exponentially.

The larger graph (which looks empty) shows how inbreeding (as % per generation) is affected by Ne on linear axes. You can see that for Ne greater than about 100, this line looks nearly flat. Below 100, however, it increases very quickly.

If we log both axes, this curve becomes linear. Now we see in the inset graph that when Ne is small, even a small change will have a large effect on the rate of inbreeding.

What is the message here for Afghan Hounds? As the number of breeding Afghan Hounds continues to decline, we can expect to see inbreeding increase.

For Ne, how small is too small?

This is the graph of effective population size for Afghan Hounds over the years since the breed was founded.

As a general rule of thumb, the effective population size should be about 500. This is considered the size for a sustainably breeding population because the rate of inbreeding will below and there will be low risk of extinction. The effective population size of the Afghan Hound fell below 500 in about 1995 and has declined slowly since.

We are only interested in the most recent decades for Afghan Hounds, so lets change the axes on the graph.

This is just the last few decades from the previous graph, from 1980 to the present.

There is a green line at Ne = 500 is as before. A yellow line has been added at Ne = 100, which is considered a minimum population size.

And there is a red line at Ne = 50, which is considered to be the “emergency” value of Ne, below which a population is at risk of extinction from inbreeding depression and genetic disease.

The effective population size of the breed is currently about 100 and will likely continue to decline. Breeders should act to reduce a further declines in Ne by increasing the fraction of dogs used for breeding. You can do this without increasing the number of puppies produced.

There is a growing list of genetic disorders known to afflict the Afghan Hound.

A few of these might be caused by single mutations for which a test could be developed - e.g., progressive retinal atrophy, von Willebrand’s. But there are no DNA tests available for the Afghan Hound.

Most of these are polygenic, so genetic management must be through breeding strategy.

A last word on GENETIC DISORDERS - We’re doing this all wrong!

Here’s the usual process. A disorder pops up in the breed (popular sire?). We spend money and time to study the disease, look for a gene, and develop a test. For a few problems, we find a gene. For most we do not. And new genetic disorders continue to appear. Dogs are not getting healthier.

We can solve the problem of genetic disorders in dogs faster and better than we are using proper genetic management. Low inbreeding will reduce risk of ALL disorders caused by recessive mutations. Minimize loss of genetic diversity so you don’t lose important genes. (They’re all important!) And avoid popular sires.

Here’s an analogy -

When I was growing up, everybody smoked. Everybody. And much money was raised for lung cancer research.

So we smoked, spent money on cigarettes, doctors, and research, and continued to smoke. This went on for decades, to the delight of the tobacco companies.

Finally, the government launched a war on smoking. There were warnings on cigarette boxes, commercials on TV of people with breathing tubes, and black lungs from autopsies. Smoking was villified. And new methods to help people quit smoking were created - patches, gums, pills, acupuncture, whatever.

People stopped smoking. When was the last time you heard about the scourge of lung cancer? It ceased to be a problem.

The solution was obvious and simple. If smoking causes cancer, don’t smoke.

Here’s my analogy for dog breeders:

We inbreed deliberately, far more than necessary to produce dogs with consistent type.

Inbreeding adversely affects health in dogs. It increases risk of genetic disease, reduces fertility, shortens lifespan, and much more. We spend a fortune for veterinary care, we spend a fortune on tests and veterinary procedures to produce a litter of puppies and there are fewer of them. We spend money for “health tests” to avoid the genetic problems caused by inbreeding, and we invest a huge amount of money supporting research into the many diseases that have become common in dogs.

Just as for smoking and lung cancer, we feed this cycle. Spending money will never solve this problem. DNA tests will not solve this problem. Research will not solve this problem.

The solution is obvious and simple. Don’t inbreed. Restore the gene pool of your breed, and protect that genetic diversity like money in the bank - because literally, it is. Skip the vet bills, the DNA tests, the donations for research, and all the heartache.

The Afghan Hound faces several issues that potentially threaten its future.

1) Falling popularity and therefore declining population size
2) Inbreeding
3) Small gene pool
4) Popular sires
5) Genetic disorders

How can breeders address the issues faced by the Afghan Hound?

Breed smarter. Make the best possible use of the genetic diversity in the gene pool. Avoid multiple breedings, use dogs from underrepresented lines, and breed 2 or 3 pups from a litter instead of just one.
Use information about genetic relatedness (i.e., kinship coefficients) to select less related dogs to breed to. This will reduce inbreeding and the risk of genetic disorders.

NO Popular Sires.

Add fresh genes to the gene pool using dogs from the country of origin. Type can be restored in a generation or two. Health cannot be improved without replacing genes that have been lost. You can’t have type without health.

Instead of just worrying about your next litter, practice breed-wide genetic management.

Keep an up to date pedigree database so you know what animals you have and who they are related to.

Analyze the pedigree data on a regular basis to monitor the genetic status of the breed.
Work with population geneticists to design an efficient strategy for introducing new dogs to the population. Follow the plan so every dog counts.

Use population genetic management instead of mutation tests to reduce genetic disorders.

You are the custodians of a rare breed derived from land race dogs.

With sound genetic management and careful breeding by knowledgable breeders, you can continue to produce healthy, beautiful dogs for many generations.

ADDITIONAL INFORMATION

The analyses presented here are based entirely on a pedigree database that was created by me from a database provided to me by the late Jim Coudriet and Peter van Arkel and records in the Afghan Hound International online pedigree database. I am grateful to both of these sources for the diligence in maintaining these valuable records.

I made use of several subsets of data for analyses: “all dogs”, which included all animals in the database; “with offspring” included only dogs with recorded descendents in the database who were born before 2014, since dogs after this have probably not reproduced; and the “current population” or "reference population", which includes all dogs in the database from 2010 to 2018 and are assumed to be potentially reproductive

We can reduce the risk of hip dysplasia NOW!

7/21/2018

By Carol Beuchat PhD

You can't be a dog breeder without worrying about hip dysplasia. It's the single greatest cause of pain and suffering in dogs despite diligent efforts of breeders to reduce risk through selection.

Why have we made so little progress in 50 years? I think there are a number of issues, but one of the most important is that we don't worry as much as we could about environmental (i.e., non-genetic) factors.

For example, these are data for Labrador Retrievers raised from birth under common conditions in a research facility. From each litter of puppies, one puppy of a pair went into the control group and the sibling went into the treatment group. The dogs were raised through adulthood and every year (but one) their hips were evaluated for evidence of dysplasia. The only difference between the control and treatment groups was how much they were fed.

The results of this simple experiment were astonishing. In Labradors that were fed the normal amount of food, more than half had evidence of hip dysplasia by 6 years of age and most by about 12 years. In the treatment group that was fed less, half of the dogs were still free of dysplasia at 12 years old.

The dogs in these two groups were litter mates, so genetics was not responsible for the huge differences in the development of hip dysplasia. The explanation is very simple: dogs that were fed less had a dramatically lower incidence of hip dysplasia.

The food restricted group not only suffered less pain and loss of mobility, they also lived longer. Only about half of the control group lived longer than 11 years and only 30% survived to 12 years. But about 75% of the dogs in the treatment group survived to 11 years and 50% lived to 13.

Think about this. We can make a dramatic difference in the risk of hip dysplasia and quality of life of a dog just by adjusting food intake. If I sold a pill that would make a huge difference like this, I'd be rich and your dog would be much happier.

You have probably heard of many things that are claimed to prevent hip dysplasia. Vitamin C, raw diet, mineral supplements, specific forms of exercise, and on and on. But most of these failed to prove beneficial in careful scientific experiments. Don't waste your time and money on supposed treatments that make no difference. Focus on the things that have been proven to matter and that you can control.

Food just one of the many non-genetic factors that can affect the development of hip dysplasia in dogs. There is much more we can do that will reduce risk and make a real difference in quality of life after the breeding decision is made. You can learn more about the cause and prevention of hip and elbow dysplasia in dog in ICB's online course.

Check out ICB's online course

UNDERSTANDING HIP & ELBOW DYSPLASIA

Learn more about how genes and environment affect the risk of hip and elbow dysplasia, as well as how to use heritability and Estimated Breeding Values (EBVs) to dramatically improve the efficiency of genetic selection.

The 10 week course is online and you can work at your own pace!

Class starts MONDAY, 23 July 2018

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REFERENCES

Smith, GK, ER Paster, MY Powers, DF Lawler, DN Biery, FS Shofer, PJ McKellvie & RD Kealy. 2006. Lifelong diet restriction and radiographic evidence of osteoarthritis of the hip joint in dogs. JAVMA 229: 690-693.

Is BetterBred Better?

7/12/2018

By Carol Beuchat PhD

If you haven't already, please read my recent post, "Assessing genetic diversity and relatedness in dogs using DNA", about methods of assessing relatedness and genetic diversity in dogs. In it I present a brief summary of the comments from a paper just published by Nicholas et al. (2018). I also provide some information from a paper published in 2006 by Oliehoek et al. that evaluated several different ways of estimating relatedness. If you missed that, you should read it now or you won't understand the rest of my comments here.

------->

The method under discussion is used by the genetic diversity test available from UC Davis for dog breeds, breeders should be aware of these potential problems with the accuracy of the test.

You will have noticed that I presented direct quotes from the two papers noted above. I also provided a direct quote from published response by the authors of the first paper. It's important to note that the critical comments were not my opinion, scientific or even personal; they were from two groups of very well known canine population geneticists. I did suggest that the issues might be resolved with data validating the usefulness of the test, and until that is available I would view the test as flawed.

At the end of my blog, I made a big point of the fact that scientists have disagreements all the time, and a lot of the progress made in how we understand the world is the product of critical review and the resulting discussions. The concerns are published and the journal allows the other authors to respond. This is a normal and essential part of the scientific process. These are always civil, respectful debates. If you don't take criticism well, a career as a professional scientists is definitely not for you.

The current debate on the origin of dogs is a great example of various groups of scientists, each with different ideas, duking it out in the scientific literature, one publication at a time. This note in one of the world's most prestigious journals was published in 2013, and the lively debate still continues. I'm sure that sooner or later, we will figure it out and most scientists will come to a consensus. In the meantime, the critical comments of colleagues focus on details, data, assumptions, and methods. There are no personal attacks. Nobody's credentials are questioned. In fact, the scientists that engage in lively debate all know each other, consider themselves colleagues, and are likely to sit down for coffee when run into each other at meetings.

Science is a community of individuals that are committed to figuring out the truth, even if that means there might be winners and losers in the debate. This is the warp and woof of science, and the debate and process of ferreting out the truth is what I love about it.

https://www.nature.com/news/dog-genetics-spur-scientific-spat-1.13227

I brought all this up in my blog - and emphasize it again here - because I expected that there might be some members of the dog community that would see the papers and even my blog post as some sort of personal attack on the Davis test. Clearly it was not. But yes, unfortunately, that is how some took it.

I posted links to my blog in various relevant groups, one of which was the ICB Facebook page. Sure enough, the trolls came.

This person is associated with BetterBred, a company that is using the Davis test as an online breeding tool. She is known to me, because she has been trolling me for years now, as have a number of people associated with the group at BetterBred. She is not a scientist. She has no comments to make about the substance of my blog post.

I did try to make my post understandable to any breeder, from the lawyer and veterinarian to the dog groomer. But Laura Bernier notes (twice) that she didn't understand it, so her comments are not about the substance of that blog but are persona; her intent is apparently to sully my reputation. I've been a professional scientist for nearly 40 years, I have a long list of publications, a record of more than $1.2M in grant support, and the respect of my peers. Her belittling remarks will have not effect at all on my reputation, and they don't even keep me up at night, but I am concerned that she carries around so much anger. Stress isn't good for your health, and I truly hope she gets the help that she needs.

To be fair, I have to say that nobody has been busier with the personal flogging than the person who runs BetterBred, Natalie Tessier Green. I blocked her long ago, but her posts are sent to me by the people that find them offensive or even appalling. This was posted in one of her private groups for users of the BetterBred website and I was gifted several copies.

Natalie Tessier Green has been trolling me for years. She fosters an environment in her company that normalizes this sort of bad behavior, which is not just unprofessional, but antithetical to the process of science. Comments in Natalie's groups often disparage me; it's very reminiscent of the sort of dialog you would hear between two rival clicks at a junior high school.

I'm especially disappointed that Natalie Tessier Green didn't have a single thing to say about the concerns expressed about the Davis diversity test, but she does note that "it is wrong on nearly every point". Note that I don't sell any DNA tests. For a time about 2 years ago I took orders from breeders who didn't have enough dogs to qualify for the volume discount, but the price was Embark's and I made no money from it. As the test became more well known, breeders have been able to find enough other people to send in a bulk order so I no longer do this. I do however recommend Embark's test if I'm asked and in my professional opinion that is the test that would best suit the breeder's needs. The ICB Breeder Tool is built around the test results from Embark. But I have no affiliation with them. None.

I must note here that I am not the only one being trolled. The Dog Diversity Project as well as Embark (which runs their DNA analyses) receive a good volume of hateful Facebook posts from BetterBred. There could be other organizations that find themselves in the crosshairs of BetterBred.

I'm not bothered at all by the attempts of the folks at BetterBred to affect my reputation, although it does upset people who know me, in both the dog fancy and the scientific community. I am, however, tired of the silly attacks. For each one, I get a flood of copies sent to me from people that spot them and find them offensive enough to bring them to my attention. I have to go delete the post, block the author, and add the comments to my "L&S" folder. Yes, it's gotten tiresome.

So, I have now decided to address this problem another way. I will post noxious comments made by anybody affiliated with BetterBred, including their clients, on my website. I will be liberal with links to the BetterBred site, so the curious can see for themselves the vitriol directed by BetterBred and their fans towards members of the canine scientific community. If the posts continue, I'll even set up a separate section on the ICB website where they can be catalogued and searched so that they show up in Google searches for BetterBred.

If anybody at BetterBred has comments about the two papers I blogged about, they should direct them to the authors of those papers, not me; I was not involved with either of them.

Finally -

"Not enough people call you out, because you just block them because you truly don't have the ability to have a decent debate."

No, Laura Bernier, we are not going to have a "debate" this time either. And you now join the others from BetterBred who are blocked and banned for bad behavior.

The Fallout

Oh dear. I didn't even have time to get a cup of coffee after posting this before comments from BetterBred started appearing in my In box.

I actually find this one humorous under the circumstances. Considering.

Then a bit later, a dig about mental illness.
Again, they've been trolling me for years. Yet here I am. Still.

Updated 12 July 1:07 pm to include additional comments.

13 July 2018 - Spammed by BetterBred

Today I get an email from BetterBred, this one some sort of "announcement", for which they have used a DISPOSABLE, TEMPORARY email address. You know, to avoid spam.

Assessing genetic diversity and relatedness in dogs using DNA

7/7/2018

By Carol Beuchat PhD

There are a variety of commercial options available to breeders for assessing the genetic diversity and inbreeding of individual dogs as well as breeds. UC Davis Veterinary Genetics Laboratory offers a test based on microsatellite markers (STRs), and MyDogDNA and Embark Vet offer tests using single nucleotide polymorphisms (SNPs). Microsatellites have been around for decades, while SNP technology has developed rapidly over the last 15 years or so and is increasingly used in genomic studies of animals and plants. Which test is most appropriate for you to use for your own dog will depend on the type of information you need, how you want to use it, and cost effectiveness.

Xoloitzcuintli (Photo: (c) Beuchat)

A paper just published (Nicholas et al. 2018) has expressed some reservations about the microsatellite test being used by Davis. The authors are highly qualified and well known canine geneticists, and their comments are specific and significant. Since they question the validity and appropriateness of the test to estimate relatedness and genetic variation in dogs, it is important for breeders that might use this test to understand the issues.

Below I will summarize the concerns expressed in the paper by Nicholas et al., but first I will also review some information from a paper published in 2006 that also bears on the reliability of the test (Oliehoek et al., 2006). I have excerpted material directly from both papers so you can read the comments from these papers directly.

If you get bored reading about the first issue, don't skip reading about the second one. It is just as important.

Paper by Oliehoek et al, 2006

The effectiveness of methods for estimating relatedness, including the method used by Davis, was examined in a paper by Oliehoek et al (2006). They looked at eight different algorithms, including the one used in the Davis test by Queller & Goodnight (1989), which they refer to as "Q&G". The Q&G estimator was originally designed to estimate relatedness between populations, but with a modification it can be used for pairwise comparisons of individuals.

To do their assessments of the various computation methods, Oliehoek et al. worked with a simulated pedigree so that they could assume that all of the pedigree information was "true" (which wouldn't be the case with real pedigree data). This also allowed them to test the performance of the estimators under various conditions such as random breeding or inbreeding.

After reviewing the information in these two tables, Oliehoek et al. say this:

Oliehoek et al. concluded that two of the algorithms they tested, UCS and Q&G (the one used by Davis), performed so poorly as to not merit further consideration. What is meant by "poorest results"? It means that their estimators of relationship deviated significantly from the true relationships, which were known because they used a simulated pedigree database. They felt that the errors were so consequential that they didn't proceed with further testing of these two algorithms.

Paper by Nicholas et al., 2018

A paper has just been published that is critical of the Davis diversity test (Nicholas et al. 2018) as used in a study of Samoyeds (Pedersen et al. 2017).

Their complaints:

1) "using a small number (33) of microsatellite markers that cover only 66% (25/38) of autosomes is suboptimal for determining genetic variation occurring across the genome"; and

2) "the sample of dogs from which "breed-wide genetic diversity" was estimated contained a substantial but undisclosed number of close relatives (and so was not a random sample nor representative of the wider breed, meaning that the findings pertaining to genetic variation cannot safely be extrapolated without qualification."

The second criticism is specific to the population of Samoyed used in that particular study. The first, however, is about the method itself and would apply to all breeds using the test. Specifically, they are suggesting that it cannot be assumed that the genetic variation determined from a small number of markers on only 25 of 38 autosomes is representative of whole genome diversity.

They go on to say:

"The study used microsatellite markers to estimate the genetic diversity of the Samoyed breed. While microsatellites have previously been used to this, they have largely been superseded by dense SNP chips, where the quantity of bi-allelic marker data provides more precise information on the extent of genetic variation via homozygosity.

The study used 33 short tandem repeats (STRs) on 25 autosomes, which is an average of 1.32 STRs per autosome included. However, since Canis familiaris has 38 autosomes, there was no means in this study to determine genetic variation across 1/3 of the genome. It is highly likely that there is genetic variation present within the Samoyed breed on these 13 autosomes, but this study is simply unable to detect its extent.

Furthermore, genetic variation at genomic regions on the 25 included autosomes not in linkage disequilibrium with the STRs also cannot be detected.

Thus, while this number of STRs may be sufficient for their stated purpose (parentage verification and forensic testing) and an acceptable "broad brush" means of estimating diversity in a population where there is no alternative (such as wild populations), they are unable adequately to describe the extent of genetic variation across the canine genome, including regions of depleted variation due to selection."

This figure represents the 38 autosomal chromosomes of a dog (from Embark). The blue stripes are regions of homozygosity. The small red vertical lines are the positions of the STR markers used in the Davis test. Nicholas et al. are questioning how reliably a test with so few markers - only 25 for 38 autosomes - quantifies the actual genome-wide degree of genetic variability. The critical question here is whether these markers, placed as they are, will accurately assess the true genetic variation across the entire genome of a dog.

These are the relevant parts of the response to Nicholas et al. from Pedersen et a. (2018):

"Professors Nicholas and Mellersh and Dr Lewis were concerned about the methodology that led us to conclude that Samoyed lack genetic diversity...

Their first criticism involved the use of 33 microsatellites markers across only 25/38 autosomes. This was linked to another question pertaining to why microsatellites were even being used at all, given modern SNP technology. The microsatellites chosen for this study were vigorously selected for their ability to discern genetic differences by the International Society for Animal Genetics, with addition of several new markers from our Veterinary Genetics Laboratory. The microsatellites are known to be highly polymorphic and have been used successfully for many studies concerning parentage and genetic diversity.

Some of the added markers were for the DLA class I and II regions, which contains genes concerned with immune responses. This region is in strong linkage disequilibrium, with one copy inherited by descent from each parent. It is extremely difficult to define the DLA region using SNPs due to the numerous polymorphisms, but it is very efficient and accurate to track this region using microsatellites. DLA haplotypes are powerful identifiers of breed founders.

We were also concerned about the fact that our markers did not cover every chromosome and added 25 more microsatellites to cover missing chromosomes. We found that the additional microsatellites, although carefully selected, did not add anything to the power of the current 33 markers to study breed-wide genetic diversity and relatedness. We also compared genetic diversity in Standard Poodles by both microsatellites and 170K SNPs and found no major differences...

We are confident, therefore, that the genetic diversity we were measuring in Samoyed was accurate as described and that employing large panels of SNPs would not significantly alter the conclusions."

The problem I suspect Nicholas et al. will have with this is that there is no information provided that directly addresses their concerns about the measurement of genetic variation. Much of the response was about the markers for DLA and was not relevant to the estimation of autosomal genetic variation. Assurances were offered that, in unpublished experiments they did, the addition of 25 microsatellites "did not add anything to the power of the current 33 markers". Further, a comparison of diversity measured with the microsatellite panel and 170K SNPs "found no major differences". However, no data are provided to support either of these statements. It would have been appropriate and useful for them to provide the data and analyses behind these statements, but unfortunately they do not.

The reason the methods and results of research are provided in such detail when published is to support the claims made about the data to the satisfaction of other scientists. Here, we're supposed to just "take their word for it". I think many scientists would be concerned about doing this.

Now what?

Where does that leave us? Breeders have to assume that information provided to them by science professionals is "true". Davis is arguably the best vet school in the country, and they have a stellar group of veterinary and population geneticists with much expertise and sound reputations. I would go to them for advice or information and I have. But on this one thing, I have to agree with my scientific colleagues: the information provided by the Davis test is likely flawed and should not be used by breeders unless it can be proven otherwise.

The fix for the problems with the method used to calculate internal relatedness could be simple. Redo the calculations using the equation that performed best in the simulations by Oliehoek et al. Davis could do this, or the dog owners could provide their data to somebody carefully chosen to have the appropriate expertise for reanalysis, preferably one of the authors (e.g., Pieter Oliehoek).

The issue with the reliability of the test because it uses too few markers is more difficult to remedy and just as serious. This test is the basis for several published studies, and there is a growing list of breeds that are using it for assessment of genetic variation and relatedness in making breeding decisions.

Breeders need to be aware of these issues. There is no more serious concern about a method than that the data produced are not reliable. There are other test options available that use SNPs, and for breeders that must also do trait or mutation testing those are probably more cost effective. SNPs are rapidly replacing STRs in many applications, and there is considerable value in having data from today's dogs that will be compatible with data for future generations. Breeders should carefully assess what information they need, now and in the future, and select the test option that best suits these requirements.

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POSTSCRIPT

The layperson might be horrified to read the critical comments about a scientific study from other scientists. Be assured that this is the normal process of science. A scientist can expect every word that comes out of their mouth for their entire career to be scrutinized, assessed, and criticized by their colleagues. The criticism will be direct but never personal. In fact, it could be said that scientists sit around picking away at the work of their colleagues for mental sport. It is interesting, stimulating, even fun, and it often results in useful insights that advance a project or field. It is not "bashing", "slamming", or any of the other many terms I have heard used by dog breeders in these contexts. Indeed, I have never heard these terms used by scientists about each other; they simply are not appropriate because they imply that the comments are unfair, inappropriate, and personal, when they are not. Scientists disagree with each other all the time. It's the normal warp and woof of science.

By way of an example, my own favorite criticism was directed to me by the editor of a journal to which I had sent a manuscript for review very early in my career. Although the reviews were favorable, the editor (whom I knew) told me that he didn't like the statistics I had used and suggested that were he to publish the paper, I would "come to find it an embarrassment" later in my career. I sent the paper to another (better!) journal, which published it. It was well-received, and I have never been embarrassed about it. The editor and I remained friends and colleagues.

REFERENCES

Nicholas FW, C Mellersh, & T Lewis 2018. Letter to the editor regarding an autosomal recessive mutation in SCL24A4 causing enamel hypoplasia in Samoyed and its relationship to breed-wide genetic diversity. Canine Genetics and Epidemiology 5: 4. DOI 10.1186/s40575-018-0059-7

Oliehoek PA, JJ Windig, JAM van Arendonk, & P Bijma. 2006. Estimating relatedness between individuals in general populations wiht a focus on their use in conservation programs. Genetics 173: 483-496.

Pedersen NC, B Shope, and H Liu. 2017. An autosomal recessive mutation in SCL24A4 causing enamel hypoplasia in Samoyed and its relationship to breed-wide genetic diversity. Canine Genetics and Epidemiology 4:11. DOI 10.1186/s40575-017-0049-1

Pedersen NC, B Shope, and H Liu. 2018. Letter to the editor regarding an autosomal recessive mutation in SCL24A5 causing enamel hypoplasia in Samoyed and its relationship to breed-wide genetic diversity. Authors' response. Canine Genetics and Epidemiology 5: 4. DOI 10.1186/s40575-018-0059-7

Using genomics to manage genetic disease. You don't need to find the gene

6/30/2018

By Carol Beuchat PhD

Genetics has been revolutionized in the last decade by the development of amazing new technology. For decades, geneticists relied on markers called microsatellites, which are stretches of DNA with repeated element that can differ from individual to individual. In closely related animals, the repeated pattern would be similar, whereas the pattern would be more and more dissimilar in animals that are less related.

How SNP technology is revolutionizing genetics

Our ability to resolve genetic relationships among individuals has been revolutionized by technology that can identify hundreds of thousands, or even millions, of DNA markers. Distributed densely over all of the chromosomes, these markers, called SNPs (pronounced "snips"), can reveal present genetic relationships in fine detail. Even more amazing, SNPs can tell us about genetic history - what carnivores are the dog's closest relatives, where the world's dog populations originated, what breeds were used in the creation of new breeds by crossbreeding, and even how long in the past a cross-breeding occurred. The amount and quality of information is breathtaking, and the study of canine genomics has been changed forever. This SNP technology is referred to as "Next Generation Sequencing" (NGS), because it truly did propel genomics into the "next generation".

For many years, SNP technology was very expensive and beyond the reach of the layperson. But the cost has come down dramatically in the last few years, and you can now send off a sample of spit to any of a number of companies that will tell you where your ancestors lived, which of your genes are links to particular traits or diseases, and even the nationalities in your background. What started as "recreational" genomics is now driving advances in diagnosis and treatment of diseases.

SNP technology offers some amazing opportunities to learn about the genes in dogs. Companies are popping up that offer to identify the breeds in a mix (some with better success than others). For breeders, high resolution SNP genotyping is providing data that can be used with powerful analysis tools in molecular biology and population genetics to improve our ability to select for the traits we want and against the ones we don't more efficiently than ever before. In fact, livestock breeders can now take a DNA sample from an animal at birth and know the traits the animal will have as an adult. Could we be using these techniques to breed better dogs?

How we can use SNP genotyping to manage genetic disease

We can use the power of high resolution SNP analysis to reveal the details of genetic relationships among animals. A potential sire that might look like an outcross to your bitch on paper can instead be very similar genetically because of relationships among ancestors many generations back in the pedigree. When you are choosing a sire to improve a trait, reduce the risk of genetic disease, or increase the genetic diversity in your line, reliable information about the DNA in the dogs can be the difference between success and failure. Let's look at an example of how we can use information about genetic relationships to manage a genetic disorder in dogs.

An organization breeding Labradors for guide dogs was having a problem with elbow dysplasia (ED) (Ubbink et al 1998). They had good pedigree records and used these to map the genetic relationships among the dogs in their breeding stock using kinship to determine relatedness and a technique called cluster analysis to form clusters of related dogs.

This is a "dendrogram", a diagram similar to the branches of a tree that displays the genetic relationships among animals. On the right side of the chart is a numeric scale of relatedness. The shortest branches indicate the highest similarity between individuals; so the very short branches at the level of 0.125 (red arrow), reflect relatedness comparable to a half-sib mating. The next number, 0.0625, corresponds to the relatedness (inbreeding) produced by mating first cousins, and the numbers above that correspond to successively lower degrees of relatedness.

After creating this map of the relatedness of the dogs in their breeding colony, the number of dogs with ED was indicated by shading the bar of that group. This clearly revealed that the dogs with ED were closely related and clustered together in one region of the map. Using this information based on genetic relatedness, ED could be reduced by identifying the unaffected dogs that were at high risk because they belonged to genetic clusters containing affected dogs - and without knowing anything at all about the genes involved or mode of inheritance.

This analysis was done in 1998, not using a fancy modern DNA test, but a carefully-tended pedigree database. The limitation of using pedigrees for the general population of purebred dogs is that they are often incomplete, they can (and surely do) contain errors, and often are not even available.

But now using genomic data, we can reconstruct the genetic relationships among the individuals in a population of dogs with no information at all about pedigree history. While this technique is not conceptually new, it has not been used by breeders. This could truly revolutionize the way we manage genetic diseases in dogs.

Using SNP genotyping to map genetic relationships

Many breeds are highly inbred and have low genetic diversity. Will this technique using DNA to establish genetic relatedness work for purebred dogs?

I have gathered some DNA data in public archives from published studies that were analyzed using high density SNP genotyping, then used cluster analysis (as was done above) to produce the map of genetic relatedness for a number of breeds. These are displayed below, and many show that there are genetically distinct subpopulations within a breed that could be exploited to look for patterns in the expression of genetic disorders. We know nothing about who these dogs are, but the charts show that there is sufficient genetic differentiation in a breed to use for this type of analysis. On each one I have indicated with a red square the first major division to make it easier for you to visualize the groups. For some of these we clearly need more data, and for all of them we need data for known dogs. But this should give you a good idea of what some of these look like.

Irish Wolfhound

Golden Retriever

German Shepherd

Miniature Schnauzer

Boxer

Vizsla

Rottweiler

Havanese

Bernese Mountain Dog

Newfoundland

French Bulldog

Cairn Terrier

Can we do this for your breed?

Here we describe a very powerful technique to sort out genetic relationships among individuals that can be used to improve genetic management of disorders without knowing the genes involved. There is a long list of inherited disorders that breeders are struggling to manage in the absence of genetic information for guidance. Epilepsy, cancer, heart disorders, kidney disease, neurological problems, degenerative myelopathy, and the list goes on and on. We're not making much progress.

We can do this now. We need DNA genotype data for current dogs, including those in the breeding population, to establish the genetic subgroupings within the breed. We need the incidence data for the disorders of interest.

It might not take a lot of data to reveal the information we need. In the example of Laboradors above, data from just a few dogs would indicate the location of the cluster containing the affected dogs. You could take action using this information far sooner than if you needed 20 affected and 20 clear dogs to search for genes.

If you're interested in using this powerful technique for your breed, please contact us. We can set up a Genetic Management Workshop for your breed where breeders and PhD population geneticists with expertise in canine genomics and breeding can discuss goals and resources, and work together to develop a breeding plan to address problems.

We now have amazing tools to help breeders manage the growing list of genetic disorders in dogs. Let's use them!

How much does outcrossing improve genetic diversity?

6/28/2018

By Carol Beuchat PhD

Even 100 years ago, breeders of domestic animals realized that continuous inbreeding resulted in deterioration in the quality of their stock. To remedy this, every few generations a relatively unrelated animal would be crossed in to the population to freshen up the gene pool and reduce the level of inbreeding. In fact, the coefficient of inbreeding was devised in the 1920s as a way to estimate the level of inbreeding so breeders would know when it was time to do an outcross.

Many modern dog breeders follow a similar regime, breeding close for a few generations then out to a relatively unrelated dog. But is this as effective as we think it is?

For one thing, our dogs are much more inbred than they were a century ago. Many breeds have average levels of inbreeding above 20%, and too many are even higher. With such high levels of inbreeding and low genetic diversity, the dogs in a breed can all be more similar genetically than half- or even full siblings - or even more. How much can you expect to gain from an "outcross" that really amounts to close inbreeding?

One way we can get an idea of the potential benefits of an outcross is by using simple mathematical models of population genetics (Windig & Doekes 2018).

Researchers have simulated various outcrossing strategies for the Saarloos Wolfhond (a cross between a wolf and German Shepherd created in about 1935) and an unrelated "donor" breed. The Saarloos Wolfhond has been a relatively small breed since it was founded, with about 25 litters produced per year and high rates of inbreeding. In the last decade or so, genetic disorders have become a problem and signs of inbreeding depression (smaller litters) have appeared. Because of this, an outcross project was started in 2016.

The researchers assessed the consequences of four types of crossbreeding schemes on inbreeding.

1) A single outcross with no backcross;
2) A single outcross with backcross;
3) Repeated outcrosses with backcrossing;
4) Continuous outcrossing.

For each of these scenarios, they ran multiple simulations to produce information on the degree of variation that might be produced in a real, randomly breeding population.

The F1 from a cross of the recipient (Saarloos) and the unrelated donor breeds will have an inbreeding coefficient of 0%.

They found that a single outcross followed by one or more generations of backcrossing reduced the beneficial effect of the outcross and sometimes even increased the rate of inbreeding. In the cross breeding, the first generation receives 50% of alleles from each of the donor and recipient parents. But in subsequent backcrosses, half of the donor genes are lost on average, so that after a few backcrosses the remaining donor contribution was inconsequential.

This result is not unexpectded, but it should give pause to those that undertake a crossing program that consists of a single donor cross followed by serial backcrosses. Kennel clubs typically prefer 3 backcrosses before admitting the descendants of a crossbreeding program to the studbook. But the simulations show that the required backcrosses essentially flush the donor genes from the recipient gene pool and there is no net benefit. Indeed, there are multiple examples of crossbreeding programs that failed or produced little benefit because the introduced genetic variation was subsequently lost.

Regular outcrossing was the most effective strategy for reducing the rate of inbreeding in the Saarloos Wolfhond, but still the outcomes of the simulations were highly variable. The scenario of regular outcrossing generally reduced the rate of inbreeding, but the inbreeding rates were highly variable, and in some simulations all of the donor genetic contribution was lost.

What this study clearly showed is that using outcrossing to reduce the rate of inbreeding requires careful management in order to ensure success, and the benefit achieved will be small unless crossing is done on a regular basis. One key to success is to follow outcrossing with strategies to increase the effective population size. Otherwise, inbreeding will quickly return to previous levels.

This outcross simulation used a completely unrelated (fictitious) breed as a donor. For breeders that are crossing to what they hope are relatively unrelated dogs in their own breed, the benefit will be much less if the level of relatedness among individuals is high.

The authors of the study also addressed an issue often raised by breeders in discussions of outcrossing.

"The unwanted introgression of (unknown) deleterious alleles from a donor breed is often used as an argument against outcrossing. Since probably all animals carry recessive deleterious alleles, this may indeed be the case. However, the opposite, introgression of beneficial alleles is possible as well. The chance that different alleles are present in the donor breed depends on how closely related the breed is." (Windig & Doekes 2018)

This study highlights the difficulty in reversing the effects of inbreeding and loss of genetic diversity in closed populations of dogs. While simple in concept, genetic rescue is complex and challenging, and undertaking a program without an effective plan for maintaining the added diversity will likely achieve little. Fortunately, the authors point out, the efficiency and chance of success can be improved using "genomic-assisted selection". For this, microsatellites (STRs) have largely been replaced by next-generation sequencing using high-density (> 100,000) SNP genotyping, which now produces vastly more detailed information at a reasonable cost.

This cutting-edige technology as well as the necessary expertise to design an effective outcrossing program is now available to dog breeders, offering them the possibility of reducing the burden of genetic disorders in dogs in future generations.

Ironically, the modern solution to the problem of genetic disorders in dogs goes back to the time-tested method used a century ago- the regular introduction of new genes into the gene pool. These days, the rehabilitation is more difficult because the levels of inbreeding are very high, but we can improve the chances of success using population genetics and genomics.

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You can now enroll your breed in the new ICB Genomic Management Workshops, in which breeders and expert scientists will work together to assess the genetic status of your breed and design effective breeding strategies to reduce inbreeding, increase genetic diversity, and improve the health of the dogs.

We are accepting breeds now, so don't miss this opportunity to be one of the first we work with in the flagship program. You can read more about the new ICB Genomic Management Workshops HERE.

Don't miss out on our "Incentive" offer of a free course for each participant for the first three breeds enrolled!

REFERENCES

Windig JJ & HP Doekes. 2018. Limits to genetic rescue by outcross in pedigree dogs. Journal of Animal Breeding and Genetics 135:238-248.

Are you improving genetic diversity, or just pushing the peas around?

6/26/2018

By Carol Beuchat PhD

It's the classic scene. The family sits down at the dinner table and Billy grimaces at the food on his plate. He hates peas. HATES peas. So while acting non-chalant and seeming to really dig into his meal, Billy was actually deftly using his fork to push one pea to the other side of the plate, and another up under the thigh bone from his drumstick. A few disappeared under the pile of mashed potatoes, one leaped from the plate and fell to the floor, and soon it looked like he had done a decent job of getting down most of the despised peas.

But Mom is no fool. "Billy", she says sternly, "eat your peas instead of just pushing them around on the plate!" Busted.

We risk doing a similar thing when making decisions about the ideal sire and dam for the next litter of puppies. Let's say you have a bitch you want to breed and you're considering four or five potential sires. You also have some DNA test information that allows you to compare the genetic similarity of the bitch with each of the sire candidates. Selecting the sire that is least similar to the dam should produce puppies with the lowest average inbreeding.

But does this tell you everything you need to know? Are you really improving genetic diversity? Or are you just pushing the peas around on the plate?

Let's consider 2 things. First, let's look at genetic relatedness.

By "relatedness", we refer to the genetic similarity of a dog to the other dogs in the population. Closely related dogs will be more similar; distant relatives will be less similar.

There will always be genetic differences between two dogs, no matter how closely related they are, because no two puppies will inherit exactly the same alleles out of all the zillions of possible combinations. So even among closely related dogs, you should always be able to identify a dog that is "least" related, and if you're shopping for sires this one might look like the best bet.

The problem here is that you can identify a dog that is less related compared to the others, but it might still be very closely related - much more closely related than you would risk breeding to if you knew the actual genetic level of relatedness (First cousins? Half-siblings? Full siblings???).

Let's consider an example. We have a population of about 80 dogs in a particular breed, and you are sorting through them to identify which of the sires you are considering is least similar to your bitch. You make your choice and since they don't share any common ancestors for several generations, you're happy.

But the kinship coefficients of the dogs would tell a different story. The kinship coefficient for a pair of dogs is the fraction of their genes that are identical by descent. This sounds like it's related to inbreeding, and it is. In fact, the inbreeding coefficient of a dog (the fraction of the genes in an individual that are identical by descent) is equal to the kinship coefficient of its parents. Since we know that most genetic disorders in dogs are caused by recessive mutations, the kinship coefficient also tells us the risk of producing a genetic disorder caused by a recessive mutation in the puppies.

If you determine the kinship coefficients between the bitch and each of the potential sires, you choose the one with the lowest kinship coefficient. However, the kinship coefficient reveals that this "least related" dog is actually more similar to the bitch genetically than you would expect of a full sibling. The data for the kinship coefficients with these potential sires are:

1) 0.388
2) 0.693
3) 0.340
4) 0.398
5) 0.288

Sire number 5 has the lowest kinship coefficient so is least related. But that kinship coefficient indicates that he and the bitch are more similar genetically than you would expect for full siblings, which would have a kinship coefficient of 0.25.

Wow. You wouldn't do a full sibling mating, and this mating would be a similarly close inbreeding. From the data for the other sires, it looks like there is very high relatedness among many of the dogs in the population, whose kinship coefficients go as high as 0.693!

When you compared the dogs relative to each other, one dog looked like a good choice. But after looking at the actual kinship coefficients of the potential parents, you decide that the marriage is much too close for comfort.

Above, I noted that there were two things we needed to consider when making mate selections based on information about relatedness from DNA data. The first was the absolute, and not just the relative, genetic relatedness.

The second issue comes from the first. Genetically similar dogs will have similar mutations. The least related pair based on kinship coefficients will nevertheless share many mutations if they are as similar as full siblings. They might be from different lines and not share any kin for many generations, but genetic similarity brings with it high risk of producing a genetic disorder. Mating of full siblings, with a kinship coefficient of 0.25, has a 25% risk of pairing up two recessive mutations.

Let's look at another example using this same breed. Below is a "dendrogram", a family tree that is based on kinship coefficients determined using a high-density (> 200,000 markers) SNP panel that has considerable power for resolving relatedness among closely related individuals.

On the panel on the left, I have indicated the results of genetic testing for the mutation (VWF) responsible for von Willebrand's disease in this particular breed. Individuals that tested clear have a little "c" at the left end of the branch. Individuals that are carriers of the mutation have two asterisks (**), and dogs that are homozygous (and therefore affected by the disorder) are indicated with four asterisks (****).

You should be able to scan from the top of the chart to the bottom and easily pick out the clear, carrier, and affected dogs. What you will probably notice is that the VWF mutation is widespread in this breed. If there wasn't a test for this disorder, you might think you're avoiding it by choosing dogs that are not closely related to each other. But, as we saw above, all of these dogs are very similar genetically, regardless of how unrelated they might appear on paper.

Status of VWF test

Status of 4 DNA tests
(as 1/2/3/4)

So, simply choosing to breed to a dog that is the least related "relatively", and is from a different branch of the family tree, will get you no points for improving genetic diversity. Furthermore, a serious mutation is so widespread in the breed, unbeknownst to you, that you stand about a 1 in 4 chance of producing a puppy with a problem. In the case of this particular breed, there are test data for 4 known mutations. When all those data are considered together in the panel on the right, you see that in the population of about 80 dogs, only 7 tested clear for everything. If you're trying to avoid producing a genetic disorder in the next litter, you don't have many ways to avoid it.

Considering the more complete information for genetic similarity provided by the kinship coefficients, together with the DNA test results, you can see that you aren't really going to improve the genetic diversity in your litter, no matter what you do. You can make all the comparisons and choose what looks like the best one option, but it's really just pushing the peas around on the plate.

NEW: ICB Genetic Management Workshops

6/25/2018

By Carol Beuchat PhD

ICB is proud to announce a new program for breeders, the ICB Genetic Management Workshops. Now for the first time, breeders can get a scientific assessment of the genetic status of their breed as well as professional guidance in setting up a breeding program aimed at improving the health of their dogs.

The Workshops will partner breeders with veterinary and population geneticists to do a detailed assessment of the genetic health their breed using both DNA and pedigree information. Then the scientists will work with the breeders to design a breeding program that will address the genetic issues and provide a foundation for sustainably breeding healthy dogs into the future.

The mission of ICB since it was founded in 2012 is to provide purebred dog breeders with the tools and information they need to make breeding decisions that will improve the health of dogs. Breeders will have unparalleled access to guidance from world experts in canine genetics, as well as the tools and expertise of conservation geneticists.

About the Workshops
The ICB Genetic Management Workshops will be ICB's flagship program and the first of its kind. In these Workshops, breeders and scientists will sit down together, evaluate the genetic status of the breed, diagnose the problems, and come up with breeding strategies and recommendations that will improve health. The goal will be to provide a plan that is feasible for breeders to follow and which will have short- and long-term outcomes for health improvement. Genetic assessment of a breed and development of breeding strategies will use the the new ICB Breeder Tool. It will provide breeders with a detailed assessment of the genetic health and issues of their breed and the information they need for making the best possible breeding decisions going forward.

Genetic Assessment from DNA
The genetic assessment of the breed will use DNA genotyping and mutation testing information. The current commercial provider of suitable data is Embark Vet, which uses a state-of-the-art, high-density Illumina SNP analysis with more than 200,000 markers distributed over the entire genome, including all 38 autosomes, the sex chromosomes, and mitochondrial DNA. This is the same platform used by canine genetics research laboratories worldwide and provides the most comprehensive and detailed analysis available. Because this platform is so widely used, marker data produced by research laboratories can be added to our databases to increase our sample size and the breadth of the gene pool represented.

Genetic and Demographic Assessment From Pedigree Data
Assessment of the genetic status of the breed should ideally include a pedigree database, which provides information about the genetic history of the breed, founder dogs, bottlenecks, changes in population size. Information from the DNA analyses can be used to verify pedigree relationships. In the absence of a useable pedigree database (e.g., because of errors, missing data), the DNA can be used to establish the genetic relationships of the current dogs, which will provide the information needed by breeders for genetic management going forward.

A good pedigree database, or genealogy reconstructed from DNA data, can be used to locate the genes causing a genetic issue without needing to identify the specific genes responsible. This is especially valuable for complex and polygenic disorders for which it would be difficult and expensive to identify the causative alleles (e.g., cancer, epilepsy). A pedigree database also provides the foundation for estimated breeding values (EBVs), which substantially improve the efficiency of selection.

Professional Expertise
The problems faced by breeders struggling to manage genetic disorders are complex. If they could be solved using simple solutions, breeders would have solved them long ago. In fact, the best efforts of dedicated breeders have not been enough to make progress against the especially difficult problems like cancer and epilepsy.

We now have tools that can provide the detailed genetic information about a breed that is necessary to design a strategy for genetic management and improved health. We are coupling these tools with PhD professionals from around the world that have expertise in the disciplines relevant to addressing the problems at hand: veterinary genetics, population genetics, canine husbandry, physiology, and behavior.

Our Goals
The Breed Workshops are not courses, although the participants will surely learn a lot. Our overriding goal is to solve problems and provide breeders with the guidance necessary to work towards healthier dogs when planning their very next litter.

Commitment
The Breeder Workshops involve a partnership with a shared commitment from both the ICB team that is working with the breeders, as well as from the breeders, who need to be willing to commit to implementing the plan produced by the workshop. If breeders cannot make a commitment to implement the strategies they have developed with the assistance of the scientific team, we will not accept them for a workshop. We want to see RESULTS that make a significant difference in the health and welfare of dogs.

For this reason, we have some basic requirements before we will agree to run a workshop for a breed. Any plan will require the breeding of dogs, so we must have sufficient breeders involved to support this. We will also need to know that the puppies produced can be placed in homes that will properly care for them and retain them until they can be bred if they are suitable. This will probably require many non-breeder participants. People that have left breeds because of their health issues might be ideal for raising puppies produced in the program.

The minimum involvement for a workshop is 50 participants with a fee of $200 ea. These can be breeders as well as non-breeders who wish to support the effort. For large breeds, it will take a substantial commitment by breeders to make a meaningful improvement in the genetics of the breed. A few enthusiastic breeders cannot make a significant difference. This will need to be a substantial, collaborative effort with a long-term commitment. With proper planning and scientific support, the breeding program has the greatest chance of success.

Arranging a Breed Workshop
Any group of breeders can request a workshop for their breed. It would be ideal to have club support, but if that is not forthcoming we will work with a group of independent breeders that can meet the requirements for participation and commitment.

We will need the DNA genotyping results from Embark (or other sources using the Illumina canine SNP chip) for a sufficient number of dogs to be able to do meaningful analyses. For some breeds, there are data already available for anonymous dogs from research studies to provide baseline information about the breed. Participants will add to this the genotyping and mutation/trait testing information for current dogs as necessary to fill any gaps and to provide the information needed about the current breeding population of dogs. There is a table below with a current inventory of data, to which data will be added on an ongoing basis from research studies as well as dogs in the breeding population.

How Long Will It Last?
If we have the necessary information organized properly ahead of time, we anticipate that analysis and design of a breeding program should take 8 to 10 weeks. But we'll keep working until we're done. The final product is a breeding strategy to be implemented by workshop participants.

What You Will Need
This will be work, for both the participants and the scientists involved. It will be a commitment of time as well as learning so that participants understand the rationale for the breeding plan and its goals. You will need enthusiasm and dedication to the project for the long term if you are truly going to make a difference.

We will need the genetic data files from analysis using the Illumina SNP chip, either from Embark or research projects using the Illumina chip. DNA analyses from the Davis genetic diversity program use microsatellites (STRs); the data are not compatible with data from other sources and lack the resolution of the SNP data. Mutation testing from MyDogDNA/Mars can be used, but their DNA genotyping data is not compatible because they use a proprietary chip. So, stick with Embark if you do any commercial DNA analyses.

We will be accepting breeds for workshops on a first-come, first-served basis. We need a commitment with payment for at least the minimum 50 participants at $200 ea to get a reserved spot on the calendar. If small breeds are unable to meet the requirement of 50 participants, please contact us to discuss whether we can design a program for the breed with fewer breeders.

Data Already Available
DNA data already available for some breeds that can be used in analyses. We have data for most AKC breeds and at least 50 dogs of these breeds (# in parentheses):

American Cocker Spaniel (70)
Border Collie (50)
Boxer (160)
Cairn Terrier (60)
Cavalier King Charles Spaniel (50)
English Setter (80)
English Springer Spaniel (50)
German Shepherd (130)
Golden Retriever (250)
Irish Wolfhound (210)
Labrador Retriever (630)
Maltese (80)
Miniature Schnauzer (60)
Rottweiler (80)
Vizsla (90)
Yorkshire Terrier (180)

Enroll for a Genetic Management Workshop
We are scheduling workshops on a first-come, first-served basis. You will need a minimum commitment of 50 participants.

Please contact us to discuss setting up a Genetic Management Workshop for your breed.

Contact:

Carol Beuchat PhD
Scientific Director
Institute of Canine Biology
carol@instituteofcaninebiology.org

A DNA Primer for Dog Breeders: Quick Start Guide

6/21/2018

A DNA PRIMER FOR DOG BREEDERS
ICB Breeder Tool Quick Start Guide

POPULATION LEVEL ANALYSES

1) Measures of Genetic Diversity

Observed Heterozygosity (Ho)

Inbreeding (breeding of related animals) results in homozygosity, in which an individual inherits two copies of the same allele from an ancestor (e.g., AA or aa).

The opposite of homozygosity is heterozygosity, in which an animal inherits two different alleles (version of a gene).

Observed Heterozygosity: higher numbers are better

Genomic Inbreeding (F)

An estimate of inbreeding can be computed from a pedigree database. Inbreeding can also be estimated directly from DNA data as genomic inbreeding. It can be determined as the fraction of the genome that is homozygous (the "realized" inbreeding) from "runs of homozygosity" (ROH).

F of 0.2 corresponds to an inbreeding coefficient of 20%.

Genomic Inbreeding (F): lower numbers are better

Genomic Inbreeding (Fis)

With information about allele frequencies in a population from SNP data, inbreeding can be assessed relative to what would be expected in a randomly breeding population. If zero is the expected inbreeding under random mating, positive values of Fis indicates preferential inbreeding ("excess" homozygosity) and negative values of Fis indicate preferential outbreeding.

Genomic Inbreeding (Fis): lower, negative numbers are better

2) Measures of Relatedness

Kinship Coefficient (K)

The degree of genetic similarity between two individuals due to common ancestry is the kinship coefficient (K). The kinship coefficient of a sire and dam is also the predicted coefficient of inbreeding of their offspring. For full siblings from unrelated parents K would be 0.25, and their offspring would have an inbreeding coefficient of 25%.

A kinship matrix displays the Kinship Coefficient of each individual with all others in the population. This matrix is a color coded "heat map" in which red indicates K > 0.25, yellow is K = 0.125, and green is K = 0.625. These correspond to full siblings, half siblings, and first cousins, respectively. (See "How to read a heat map".)

Kinship coefficient (K): lower numbers are better

Kinship Matrix

Mean Kinship (mK)

The degree of relatedness of animals in a population can be assessed as the average of the kinship of an individual with every other member of the population (mean kinship, mK).

Individuals that are least related to the rest of the population will have the lowest mK. Individuals that have many relatives in the population will have a high mK.

Mean kinship (K): lower numbers are better

Genetic Relationships

The genetic relationships among the animals in a population can be determined using the kinship coefficient, K, which reflects the alleles that are identical by descent (i.e., from common ancestors).

Genetic relationships are displayed as a dendrogram, the "family tree". Animals that are more closely related are connected by shorter branches. Relatedness is also indicated by the colors in the "heat map", in which blue is least related and red is most closely related. (See "How to read a heat map" and "How to read a dendrogram".)

Dendrogram: shorter branches indicate closer relationship

3) Population Structure

Principal Components Analysis (PCA)

PCA is a statistical technique for revealing similarity of individuals, which doesn't necessarily correspond to relatedness. The genetic difference between two individuals is the length of a line that connects them on the graph ("genetic distance").

This can be used to visualize subpopulations of animals; e.g., field vs show dogs, European vs Canadian dogs.

Principal Components Analysis (PCA): similar individuals are closer together

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​A DNA PRIMER FOR DOG BREEDERSICB Breeder Tool Quick Start Guide

1) Measures of Genetic Diversity

2) Measures of Relatedness

3) Population Structure

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The Genetics of Behavior & Performance
Online course starts 4 March 2019
10 weeks, $125

A DNA PRIMER FOR DOG BREEDERS
ICB Breeder Tool Quick Start Guide