By Carol Beuchat PhD
We evaluate the traits of a dog to assess its value as breeding stock. Indeed, this is the stated (historical) purpose of dog shows. But to evaluate a dog as breeding stock, we have to assume that our assessment based on of phenotype (what you and a judge see in the ring) is a reasonable reflection of the "genetic value" of that dog. In fact, many traits are polygenic, and many genes interact with other genes in producing genotype, so in fact your assessment of physical phenotype might not be the best way to assess the genetic value of a dog.
If breeders care about preserving the genetics of the best dogs in a breed, or in preserving the genetics of their own line, they should welcome the opportunity to evaluate not just the main dog of interest, but also as many of that dog's relatives as possible - siblings, parents, offspring, and even more distantly related animals.
Here's why.
Breeding is about producing dogs that have the genes for the traits we want. Selection of mating pairs assumes that the breeder can select for the genes they want by evaluating phenotype. Of course, we know that many traits are polygenic, and for many there is also a strong envionmental influence on phenotype (which you can evaluate by computing heritability - and you should). In fact, phenotype really isn't that good at evaluating phenotype for most traits breeders care about, because genetics often can explain only 15% of 30% of the variation in a trait among dogs (this is the definition of heritability).
So the clever breeder would want to assess not only the potential sire or dam of interest, but also the relatives of those dogs. You will get a better assessment of genetic value of a dog for a particular trait by evaluating not just a single dog, but it's parents, littermates, and (best of all) its offspring. This allows you to determine an "estimated breeding value" (EBV) for the particular traits of interest. Dogs that inherited the traits you want and pass the genes for those traits on to their offspring have genes of high genetic value for those traits. The more information you have for the relatives of a dog about the traits of interest, the better you can assess whether a dog is likely to produce puppies with the traits that you are looking for in your dogs. Indeed, this is the basis of prepotency.
To evaluate the genetic value of a dog for a particular trait, you must evaluate the relatives of a dog you might want to breed to. Even if those dogs are not the best specimens (because they got a less fortuitious assortment of genes than the pick of the litter), or they will never be bred, or even if they have been neutered or spayed, a dog's relatives are collectively a gold mine of information you can use to guide your breeding decisions.
There is currently a ruckus onine about the AKC considering allowing dogs with limited registration in the ring. Breeders should welcome this for two reasons. First, for the information it can provide about the traits of those dogs that can be used to inform the calculation of estimated breeding values.
There is a second consider, which is an argument against limited registration, which prohibits that dog from being bred. If you cross two "good" dogs each puppy only gets half the genes of each parent. Some puppies will inherit a selection of genes that produces a stunning puppy; others will get less appealing features just by the random assortment of parental genes that they inherit. Breeders will often keep the pick of the litter for breeding and send the rest off to pet homes (some with limited registration).
If you want to "protect" your lines, this is not the way to do it. Your lines are a collection of genes that have been selected for over generations. To preserve your lines, you need to preserve those genes. The best way to do that is to breed at least TWO puppies in a litter (which would preserve about 75% of the genes in both parents), or better yet three (which would preserve about 87% of the genes of your carefully selected parents. The dogs you would put on limited registration nonetheless might have the genes to produce spectacular offspring with the right pairing that results in a more fortuitious blend of genes.
Generations of being highly restrictive in mate choice has resulted in a breathtaking loss of genetic diversity in many breeds. In general, only 15-30% of purebred dogs produce a litter. You can't preserve the genes that produce quality animals, or that define your own lines, by discarding part of the gene pool every generation.
Everyone wants healthier dogs. But no amount of selective breeding, or even DNA testing, will improve dog health while we continue to breed in a way that is genetically destructive. We need to distinguish between what is custom and ideology from the basic genetic principles that much be respected if we wish to produce healthy dogs.
Why you need information about every puppy -
https://www.instituteofcaninebiology.org/blog/if-knowledge-is-power-know-every-puppy
If breeders care about preserving the genetics of the best dogs in a breed, or in preserving the genetics of their own line, they should welcome the opportunity to evaluate not just the main dog of interest, but also as many of that dog's relatives as possible - siblings, parents, offspring, and even more distantly related animals.
Here's why.
Breeding is about producing dogs that have the genes for the traits we want. Selection of mating pairs assumes that the breeder can select for the genes they want by evaluating phenotype. Of course, we know that many traits are polygenic, and for many there is also a strong envionmental influence on phenotype (which you can evaluate by computing heritability - and you should). In fact, phenotype really isn't that good at evaluating phenotype for most traits breeders care about, because genetics often can explain only 15% of 30% of the variation in a trait among dogs (this is the definition of heritability).
So the clever breeder would want to assess not only the potential sire or dam of interest, but also the relatives of those dogs. You will get a better assessment of genetic value of a dog for a particular trait by evaluating not just a single dog, but it's parents, littermates, and (best of all) its offspring. This allows you to determine an "estimated breeding value" (EBV) for the particular traits of interest. Dogs that inherited the traits you want and pass the genes for those traits on to their offspring have genes of high genetic value for those traits. The more information you have for the relatives of a dog about the traits of interest, the better you can assess whether a dog is likely to produce puppies with the traits that you are looking for in your dogs. Indeed, this is the basis of prepotency.
To evaluate the genetic value of a dog for a particular trait, you must evaluate the relatives of a dog you might want to breed to. Even if those dogs are not the best specimens (because they got a less fortuitious assortment of genes than the pick of the litter), or they will never be bred, or even if they have been neutered or spayed, a dog's relatives are collectively a gold mine of information you can use to guide your breeding decisions.
There is currently a ruckus onine about the AKC considering allowing dogs with limited registration in the ring. Breeders should welcome this for two reasons. First, for the information it can provide about the traits of those dogs that can be used to inform the calculation of estimated breeding values.
There is a second consider, which is an argument against limited registration, which prohibits that dog from being bred. If you cross two "good" dogs each puppy only gets half the genes of each parent. Some puppies will inherit a selection of genes that produces a stunning puppy; others will get less appealing features just by the random assortment of parental genes that they inherit. Breeders will often keep the pick of the litter for breeding and send the rest off to pet homes (some with limited registration).
If you want to "protect" your lines, this is not the way to do it. Your lines are a collection of genes that have been selected for over generations. To preserve your lines, you need to preserve those genes. The best way to do that is to breed at least TWO puppies in a litter (which would preserve about 75% of the genes in both parents), or better yet three (which would preserve about 87% of the genes of your carefully selected parents. The dogs you would put on limited registration nonetheless might have the genes to produce spectacular offspring with the right pairing that results in a more fortuitious blend of genes.
Generations of being highly restrictive in mate choice has resulted in a breathtaking loss of genetic diversity in many breeds. In general, only 15-30% of purebred dogs produce a litter. You can't preserve the genes that produce quality animals, or that define your own lines, by discarding part of the gene pool every generation.
Everyone wants healthier dogs. But no amount of selective breeding, or even DNA testing, will improve dog health while we continue to breed in a way that is genetically destructive. We need to distinguish between what is custom and ideology from the basic genetic principles that much be respected if we wish to produce healthy dogs.
Why you need information about every puppy -
https://www.instituteofcaninebiology.org/blog/if-knowledge-is-power-know-every-puppy
Here is a lesson about estimated breeding values from my online course "Managing Genetics for the Future".
Breeding Values
Breeding for the traits you want is very easy if there's only one gene involved and you know which dogs have it. But most things are influenced by many genes and you have no way to know what they are or which your dog has, so it's like trying to paint a landscape when you can't tell the colors of the paints apart until after the painting is done. You can't predict if you'll get what you want when you can't see the colors of the tubes.
You usually don't know the genes your dog has for a particular trait. But it is those genes that determine the "breeding value" of the dog for that particular trait. Dogs with all the right genes for a trait have high breeding value, and dogs that only have some of the right genes have lower breeding value. For traits that are heritable, you want to be able to select for those particular genes. What we need is a way to predict the breeding value of a dog without actually knowing the genes the dog actually has, or even which genes are involved in the trait.
For this, we can use something called "Estimated Breeding Values" (EBVs) which are just that - estimates of the true (but unknown) breeding value of a dog for a particular trait.
The first thing we need is some way to evaluate the phenotype of the trait of interest in each dog. If we wanted estimated breeding values for hip dysplasia, we would need hips scores from each animal. They could be numerical (e.g., 1, 2, 3, 4, for bad to good; or 5.1 or 2.8 for some measurement like the Norberg angle or amount of subluxation), or qualitative (bad, fair, good, excellent). It doesn't matter - just some way of expressing an evaluation of the particular trait you're interested in. These scores or evaluations for hips are clues to the genotype of the animal, but because we know there is an environmental influence as well, we know they won't be perfect, but just an estimate.
How can we estimate an animal's breeding value for a particular trait? If the trait is heritable, knowing the phenotype of the animal's relatives will tell us something about what genes an animal is likely to pass to its offspring.
Pedigree #1
Let's look at the pedigree below of dogs that have been scored for hips - good, bad, and unknown. We're thinking about breeding to one of the puppies in the litter of 7 at the bottom, and as it would happen the dog we really like (third from the right) has a rating of "bad". Should you use this dog?
The parents of that litter both have good hips. The grandsire (top left) has good hips, the granddam is unknown. The scores of the parents of the dam are unknown, but the rest of the maternal granddam's litter are all good. Just eyeballing this information, it seems likely that the sire and dam of the litter have good genes for hips, and that the bad hips on the dog we like could be the result of a fall off the front porch at 6 weeks, or too much kibble as a pup, or some other non-genetic cause. He might have bad genes for hips, but it's not too likely because we have information for a good number of relatives and there is no evidence that there are genes for bad hips hiding anywhere. So you might decide that your pick dog is a good bet to produce your next litter.
Breeding for the traits you want is very easy if there's only one gene involved and you know which dogs have it. But most things are influenced by many genes and you have no way to know what they are or which your dog has, so it's like trying to paint a landscape when you can't tell the colors of the paints apart until after the painting is done. You can't predict if you'll get what you want when you can't see the colors of the tubes.
You usually don't know the genes your dog has for a particular trait. But it is those genes that determine the "breeding value" of the dog for that particular trait. Dogs with all the right genes for a trait have high breeding value, and dogs that only have some of the right genes have lower breeding value. For traits that are heritable, you want to be able to select for those particular genes. What we need is a way to predict the breeding value of a dog without actually knowing the genes the dog actually has, or even which genes are involved in the trait.
For this, we can use something called "Estimated Breeding Values" (EBVs) which are just that - estimates of the true (but unknown) breeding value of a dog for a particular trait.
The first thing we need is some way to evaluate the phenotype of the trait of interest in each dog. If we wanted estimated breeding values for hip dysplasia, we would need hips scores from each animal. They could be numerical (e.g., 1, 2, 3, 4, for bad to good; or 5.1 or 2.8 for some measurement like the Norberg angle or amount of subluxation), or qualitative (bad, fair, good, excellent). It doesn't matter - just some way of expressing an evaluation of the particular trait you're interested in. These scores or evaluations for hips are clues to the genotype of the animal, but because we know there is an environmental influence as well, we know they won't be perfect, but just an estimate.
How can we estimate an animal's breeding value for a particular trait? If the trait is heritable, knowing the phenotype of the animal's relatives will tell us something about what genes an animal is likely to pass to its offspring.
Pedigree #1
Let's look at the pedigree below of dogs that have been scored for hips - good, bad, and unknown. We're thinking about breeding to one of the puppies in the litter of 7 at the bottom, and as it would happen the dog we really like (third from the right) has a rating of "bad". Should you use this dog?
The parents of that litter both have good hips. The grandsire (top left) has good hips, the granddam is unknown. The scores of the parents of the dam are unknown, but the rest of the maternal granddam's litter are all good. Just eyeballing this information, it seems likely that the sire and dam of the litter have good genes for hips, and that the bad hips on the dog we like could be the result of a fall off the front porch at 6 weeks, or too much kibble as a pup, or some other non-genetic cause. He might have bad genes for hips, but it's not too likely because we have information for a good number of relatives and there is no evidence that there are genes for bad hips hiding anywhere. So you might decide that your pick dog is a good bet to produce your next litter.
Pedigree #2
Let's change some of the information about these dogs and evaluate again what you think about your pick out of that litter of seven.
We have two dogs with bad and two with good in the litter, and two with no information. There is no info on the dam or her granddam, but the granddam's littermates had good hips. The sire has good hips as does his sire.
This one is a bit trickier. There are a few worrisome hips in there, and some missing data. What would you do?
Let's change some of the information about these dogs and evaluate again what you think about your pick out of that litter of seven.
We have two dogs with bad and two with good in the litter, and two with no information. There is no info on the dam or her granddam, but the granddam's littermates had good hips. The sire has good hips as does his sire.
This one is a bit trickier. There are a few worrisome hips in there, and some missing data. What would you do?
Pedigree #3
Here's one more pedigree, and this one is downright complicated. You want to know whether your pick in that litter of 7 has a good breeding values for hips. But looking at this pedigree, it's tough to decide.
Making decisions based on pedigrees can be a real guessing game. But you know that there is a genetic component to hip dysplasia, and you know how these dogs are related, so it seems like there should be some way to come up with a number that would tell us something about the genotype of a particular dog.
This is what EBVs do.
EBVs take into consideration the available hip information for the relatives of a dog as well as their relationships to each other. Littermates and ancestors give us added information that we can build into our estimate of breeding value for the dog we're interested in. And if the dog were to produce a litter, the scores for those puppies could substantially increase our confidence in our estimate of the breeding value of that dog.
In the next section, we'll work through producing EBVs for a very simple pedigree.
Estimated Breed Values Example
BASICS OF EBVs
EBVs use information about the phenotypes of a dog and its relatives to predict genotype of a dog, its "breeding value" for a particular trait. As you looked at the pedigrees above, you were trying to deduce the genetic value of a particular dog for hips based on information about its littermates and other relatives, but as more information is added to the pedigree - which should allow you to make a better guess - it gets harder and harder to mash it all up in your mind to come up with some evaluation of the dog you're interested in. Plus, you might have some biases that interfere with making a completely objective evaluation, like how well you get along with another breeder, or what you know about temperaments of some of these dogs (which would be better to evaluate separately), and even your ability for abstract thinking.
We can eliminate bias and isolate the information about hips from potential environmental effects and anything else that could confound our ability to predict the genetics of a particular dog using EBVs. The EBV of a dog is the RELATIVE genetic value of a member of a breeding population, so if you add data to pedigrees the EBVs of the dogs will change, and hopefully become more accurate predictors of genotype. So EVBs calculated from one group of dogs will not necessarily be comparable to those from another group of dogs unless you have some way of comparing those populations with each other in a standard way (and there are ways to do that). But this is really no different from the evaluations you do in your head, which can only be based on information you have about the dogs.
Determining EBVs for a trait
Let's walk through a very simple pedigree and analysis to see how this works. Here is the pedigree for a group of 9 dogs (there are also a few unknown parents).
BASICS OF EBVs
EBVs use information about the phenotypes of a dog and its relatives to predict genotype of a dog, its "breeding value" for a particular trait. As you looked at the pedigrees above, you were trying to deduce the genetic value of a particular dog for hips based on information about its littermates and other relatives, but as more information is added to the pedigree - which should allow you to make a better guess - it gets harder and harder to mash it all up in your mind to come up with some evaluation of the dog you're interested in. Plus, you might have some biases that interfere with making a completely objective evaluation, like how well you get along with another breeder, or what you know about temperaments of some of these dogs (which would be better to evaluate separately), and even your ability for abstract thinking.
We can eliminate bias and isolate the information about hips from potential environmental effects and anything else that could confound our ability to predict the genetics of a particular dog using EBVs. The EBV of a dog is the RELATIVE genetic value of a member of a breeding population, so if you add data to pedigrees the EBVs of the dogs will change, and hopefully become more accurate predictors of genotype. So EVBs calculated from one group of dogs will not necessarily be comparable to those from another group of dogs unless you have some way of comparing those populations with each other in a standard way (and there are ways to do that). But this is really no different from the evaluations you do in your head, which can only be based on information you have about the dogs.
Determining EBVs for a trait
Let's walk through a very simple pedigree and analysis to see how this works. Here is the pedigree for a group of 9 dogs (there are also a few unknown parents).
We can redraw this as a standard pedigree to make the relationships clearer.
We have information for four dogs about a trait we're interested in that was scored from 1 to 5, with higher scores being better; these numbers are in red.
We want to know which of the dogs, 6, 7, 8, or 9, has the highest breeding value (i.e, the best genotype) for our trait. We don't have trait information about any of the other dogs in the pedigree.
You might look at this and that the only information you have to work with are the scores for those 4 dogs. But there is more than that. Those dogs are all related to each other - some are full sibs and all share a grandsire, dog 1. So you know they share genes from dog 1 that affect their status for the trait we're interested in. We just need to figure out a way to to use the relationship information to make a prediction about genotype for each of our 4 dogs.
We're about to do some simple math. Don't let your eyes glaze over. These calculations are VERY simple and you'll never have to do them yourself. But it's useful to know where numbers come from, so don't sweat it; just follow along. Remember, these are actually the steps you might try to go through in your head when you evaluate a pedigree, but instead of making a wild guestimate we're going to see how we can do a tiny bit of simple math that will let us hang numbers on a tree that will allow you to compare dogs in a quantitative way.
Determining relatedness
The first thing we need to figure out is the level of relatedness of each of these related dogs to each other. We know that progeny share half the genes of each parent. So the genetic relatedness of 6 and 7 to their parents 2 and 3 is 0.5. We are going to continue to figure out the pairwise relationships for all of the dogs and collect that information in a table with 9 columns and 9 rows. We can color in these first comparisons in orange. Notice that we have to do this for both places where those pairs of animals appear in this matrix.
The other set of numbers we can fill in is the relationship of a dog to itself, so comparing 1 to 1 the relationship is 1.0, and 2 to 2 is 1.0, and 3 to 3 is 1.0, so you can fill in all those numbers, which will fall on the diagonal in the table.
Next, what is the genetic relatedness of 6 to his grandsire 1? Because a dog gets half the genes of its parent, with each generation the influence of an ancestor goes down by half. So 6 has half (o.5) the genes of 3, and 3 has half (0.5) the genes of 1. Therefore, 3 should have [(0.5)(0.5)], or one quarter, 25% of the genes of its grandsire 1. So in our table, we can put this number in for the relationship of 6 to 1, and it's the same for the sibling 7 (in yellow).
Next, what is the genetic relatedness of 6 to his grandsire 1? Because a dog gets half the genes of its parent, with each generation the influence of an ancestor goes down by half. So 6 has half (o.5) the genes of 3, and 3 has half (0.5) the genes of 1. Therefore, 3 should have [(0.5)(0.5)], or one quarter, 25% of the genes of its grandsire 1. So in our table, we can put this number in for the relationship of 6 to 1, and it's the same for the sibling 7 (in yellow).
Before we go further, we need to remind ourselves that although we know that a dog has exactly 50% of the genes of a parent, it doesn't necessarily have 25% of the genes of a grandparent. That's because the sample of genes it gets from a parent is random and might include more genes that came from one grandparent than the other. In fact, it is highly unlikely that a dog will get exactly 25% of its genes from a grandparent. So when we calculate relatedness of dogs related more distantly than parent and offspring, the number we get is just an estimate. Just like flipping a coin 20 times and getting 13 heads instead of 10, the sample of genes a dog gets from its parent won't necessarily be exactly half of the genes from a grandparent.
We see in this pedigree that we have two sets of siblings that share a common grandsire. We can figure out the relatedness of dog 8 with dog 3 by accounting for each step between them. If you've taken the (free!) ICB course about coefficient of inbreeding (COI Bootcamp), you will remember this is exactly what we did when we traced paths to come up with a prediction of shared alleles. If you haven't taken the COI course, what we're going to do next might not immediately make sense to you, but we're not going to do a separate lesson on this step. It's enough if you understand the general principles, which are that each step in a pedigree represents a sampling of 50% of the alleles of the immediately related dog, and by counting up how many steps there are connecting one dog with another we can estimate their genetic relatedness.
We're going to trace a path like this:
8 ---> 4 --> 1 --> 3
We see in this pedigree that we have two sets of siblings that share a common grandsire. We can figure out the relatedness of dog 8 with dog 3 by accounting for each step between them. If you've taken the (free!) ICB course about coefficient of inbreeding (COI Bootcamp), you will remember this is exactly what we did when we traced paths to come up with a prediction of shared alleles. If you haven't taken the COI course, what we're going to do next might not immediately make sense to you, but we're not going to do a separate lesson on this step. It's enough if you understand the general principles, which are that each step in a pedigree represents a sampling of 50% of the alleles of the immediately related dog, and by counting up how many steps there are connecting one dog with another we can estimate their genetic relatedness.
We're going to trace a path like this:
8 ---> 4 --> 1 --> 3
At each of 3 steps, we have a factor of 0.5 to account for, so we estimate the relatedness of dog 8 to dog 3 as
(0.5)(0.5)(0.5) = 0.125
This will be the same for all of the pairs of dogs that are 3 steps from each other, so we can fill in those values in our table (green).
(0.5)(0.5)(0.5) = 0.125
This will be the same for all of the pairs of dogs that are 3 steps from each other, so we can fill in those values in our table (green).
We have one more set of relationships to figure out, this time between dogs 6 and 7 with dogs 8 and 9. This is just like the one we just did but with an additional step, as here:
8 ---> 4 --> 1 --> 3 --> 7
Just like before, we count the steps between the first dog and the last dog in the path (4), and multiply 0.5 by itself that many times. So
(0.5)(0.5)(0.5)(0.5) = 0.0625
We can fill in those values in our matrix (pink).
8 ---> 4 --> 1 --> 3 --> 7
Just like before, we count the steps between the first dog and the last dog in the path (4), and multiply 0.5 by itself that many times. So
(0.5)(0.5)(0.5)(0.5) = 0.0625
We can fill in those values in our matrix (pink).
So now we have a matrix with estimates of the degree of relatedness of each of the related dogs in our pedigree. And remember, you'll NEVER have to do these calculations yourself (!!!). You input your pedigree into the computer and it spits this matrix out in an instant.
Heritability
There's one more thing we have to consider when we evaluate the breeding value of a dog for a particular trait, and that's its heritability. If the heritability of the trait is zero, then we're done here; if it's 1, then we know that any dog that got the gene(s) will have the trait. But the heritability of most traits is somewhere between 0 and 1, and we need to take that into consideration when we try to estimate the breeding value for that trait.
You learned how heritability is calculated from your BugsVille simulation. Let's say that the heritability of the trait we're interested in here is 0.2, or 20%.
Computing the EBVs
Okay, here is where we give all of this information to the computer, the black box does some mystery math (called "matrix algebra") that is no fun to do by hand, and something else called BLUP (Best Linear Unbiased Prediction, also no fun to do yourself), and it spits out some numbers that tell us something about the breeding values of our 4 dogs. Remember, these are estimates - we can never know the true breeding value unless we know the actual genes involved, but this is a quantitative prediction, which will be far more accurate than what you would come up with by squinting at the pedigree, testing the wind, and making your best guess.
So, the computer grinds away on these data and comes out with some numbers (males in blue, females in red).
Heritability
There's one more thing we have to consider when we evaluate the breeding value of a dog for a particular trait, and that's its heritability. If the heritability of the trait is zero, then we're done here; if it's 1, then we know that any dog that got the gene(s) will have the trait. But the heritability of most traits is somewhere between 0 and 1, and we need to take that into consideration when we try to estimate the breeding value for that trait.
You learned how heritability is calculated from your BugsVille simulation. Let's say that the heritability of the trait we're interested in here is 0.2, or 20%.
Computing the EBVs
Okay, here is where we give all of this information to the computer, the black box does some mystery math (called "matrix algebra") that is no fun to do by hand, and something else called BLUP (Best Linear Unbiased Prediction, also no fun to do yourself), and it spits out some numbers that tell us something about the breeding values of our 4 dogs. Remember, these are estimates - we can never know the true breeding value unless we know the actual genes involved, but this is a quantitative prediction, which will be far more accurate than what you would come up with by squinting at the pedigree, testing the wind, and making your best guess.
So, the computer grinds away on these data and comes out with some numbers (males in blue, females in red).
The first thing you'll notice is that we got estimates of the genetic value of every animal in the pedigree except for the unknowns and dog #1, because he has no known ancestors. Then, notice that some of these numbers are positive and some are negative. This is because the EBV for a dog is relative to the population average. Our rating scale was positive numbers from 1 to 5, so a dog with a positive value is better than the average (numbers in green) and if negative is worse than average (numbers in red).
These numbers tell us some interesting things. From the traits scores we recorded, we would have thought that dog 9 (score = 5) and dog 7 (score = 4) had the best potential to produce offspring with good scores. In fact, dogs 8 and 9 have the same breeding values (0.13), and dog 7 in fact has a negative score, as does her littermate dog 6. The actual test scores for these dogs would have led you astray in evaluating these dogs - you probably would have decided that dog 7 was more valuable to you genetically than dog 8, but in fact the genotype for 7 is worse than the population average for the trait you scored.
Remember - these EBV scores were based on three kinds of information: your scores for each of 4 dogs, how all of the dogs are related to each other, and the heritability of the trait in this population. The estimated breeding values you get might not be at all what you thought they were, but this technique has been used for decades in the breeding of domestic animals and plants and has been shown to be superior to any other method of improving the selection for particular traits.
Managing multiple traits
You can also use EBVs for multiple traits at a time. Say you are interested in selecting for 3 traits at the same time. One trait is of foremost importance (e.g., a potentially lethal disease), and the other two less so (e.g., litter size and temperament). You can weight the evaluations for each trait and compute an EBV that takes into consideration those weights. You want good litter sizes and great temperaments, but your foremost concern is minimizing the risk of producing puppies with a potentially lethal disease. Guide dog breeding programs might use 7 different traits in their calculations, including ones for health, size, temperament, coat, or whatever else that is important to them.
How can EBVs be used?
EBVs can be used for ANY trait that is heritable. They have been widely used for decades in the breeding of livestock for production, and although they are not widely used by the show dog breeder, they are starting to be used in dogs.
- Health, conformation, and behavior traits in guide dogs
- Hip dysplasia in dogs (e.g., in the UK, Finland, and US)
- Syringomyelia and Chiari Formation in Cavalier King Charles Spaniels
- Breeding programs to improve behavior
- Improvement of working abilty
EBVs in horses
You can get a better idea of their potential from the types of traits they are being used for in horses. Notice also that EBVs can be based on DNA information if the association between a trait and DNA is known.
You can get a better idea of their potential from the types of traits they are being used for in horses. Notice also that EBVs can be based on DNA information if the association between a trait and DNA is known.
Do estimated breed values work?
You will remember that phenotype (P) depends upon both genetics (G) and environment (E):
P = G + E
When you're looking at hip scores, or at one descended testicle, or an x-ray of dysplastic elbows, or the MRI of a Cavalier King Charles Spaniel suspected to have syringomyelia, you are assessing phenotype only. You have no idea how much of the variation you see from animal to animal for your trait of interest is attributable to genetics and how much to environment. Because selection can only operate on genetics, knowing the true genetic value for a trait in a particular dog is extremely EBVs they have been proven to be of great value in the artificial selection of particular traits in livestock and other domestic animals.
"But", you say, "dogs aren't livestock". Can EBVs be used successfully in dogs?
Here are a couple of examples. You will see that in both, the efforts of breeders to control a genetic problem had little success before the adoption of EBVs.
Historically, Boxers have had a high incidence of cryptorchidism (one or both testicles fail to descend). If neither testicle descends the dog will be sterile (the heat of the body interferes with sperm production), but a dog with one testicle is fertile although prone to testicular tumors. Apparently, most living Boxers can trace their pedigrees to four German stud dogs - Sigurd von Dom and his three grandsons, Utz von Dom, Dorian von Marienhof, and Lustig von Dom. All four of these dogs produced cryptorchid offspring.
First efforts to reduce the frequency of cryptorchidism in Boxer began in 1942, with a total ban on breeding cryptorchids. Nevertheless, the incidence of cryptorchidism increased over the next 40 years from about 6% in 1941 to 10% in 1981in East German dogs. In West Germany, it increased from 7% in 1959 to 14% in 1985. In 1985, concerns about genetic diversity in the breed prompted encouragement to breeders to breed to lesser known males, but this did not improve the incidence of cryptorchidism. The unification of Germany in 1984 improved access to a broader gene pool, but cryptorchidism increases unabated for the next 10 years. In 1996, once again strict regulations on breeding were imposed, excluding a bitch from breeding if she produced cryptorchid offspring in 2 litters, and eliminating sires with more than 15% cryptorchids in at least 20 offspring. These measures reduced the frequency of cryptorchids, but it also removed 84% of the reproductive dogs from the breeding pool and improvement tailed off after a few years.
Finally in 2000, Germany removed all restrictions related to cryptorchidism and instituted the use of estimated breeding values (EBVs) to improve selection against cryptorchidism. Within only 3 years they saw marked improvement. This information is from a report published in 2003; more recent information is not available, but it would be very interesting to see if there was continued improvement or if cryptorchidism was at least reduced to a tolerable level.
EBVs have been use for some time to reduce the frequency of canine hip dysplasia (CHD) in many breeds. These are data from a breeding program against CHD in the Hovawart. Again, because selection against phenotype failed to produce consistent improvement for several decades, severe breeding restrictions were instituted in 1984 that banned all affected dogs from breeding. This actually made things worse, reducing the number of unaffected dogs and increasing the number of dogs classed as borderline.
In 1989, selection based on EBVs was instituted, and this produced immediate, significant improvement in hip scores, and in only 5 years more than 80% of all dogs had normal hips and severely afflicted animals were nearly eliminated.
These are dramatic examples of the improvements that can be achieved in just a few years by using EBVs to guide selection instead of phenotype. EBVs also breeders to distinguish between, for example, dogs with bad hips and dogs with the genes for bad hips - essentially separating the potential influence of environment from the underlying genotype that the breeder is really interested in. This means that fewer animals will get removed from the gene pool, because dogs with a bad phenotype but good genotype for the trait of interest can be kept in the breeding stock for potential use.
Using EBVs for selection can produce one problem that is common to phenotypic selection as well. If everybody rushes to the dog with the best EBV score, this will increase inbreeding if care is not taken to balance the reproduction of animals across the breadth of the gene pool. This should be a basic part of sound genetic management of a breeding population of animals anyway, regardless of the scheme breeders are using to make breeding decisions.
EBVs will be new to many dog breeders, but in fact they have been used for decades to guide breeding decisions of service dogs. Using EBVs, a well-run organization can manage genetic disorders, limit inbreeding, and produce dogs with the traits that are important in a service dog, even in a closed gene pool. This improves the efficiency the breeding program because more of the dogs produced are suitable for service.
Dog breeders can used EBVs to dramatically improve their ability to improve the traits they want and reduce or even eliminate the ones they don't. EBVs can be used on any trait that can be evaluated by the breeder - temperament, size, herding ability, coat quality, heart disease, "showiness", hip dysplasia - anything you can judge to be better or worse, desirable or not desirable. EBVs are becoming available in more and more countries, and they are the most powerful tool now available for improving the health and well being of dogs.
Using EBVs for selection can produce one problem that is common to phenotypic selection as well. If everybody rushes to the dog with the best EBV score, this will increase inbreeding if care is not taken to balance the reproduction of animals across the breadth of the gene pool. This should be a basic part of sound genetic management of a breeding population of animals anyway, regardless of the scheme breeders are using to make breeding decisions.
EBVs will be new to many dog breeders, but in fact they have been used for decades to guide breeding decisions of service dogs. Using EBVs, a well-run organization can manage genetic disorders, limit inbreeding, and produce dogs with the traits that are important in a service dog, even in a closed gene pool. This improves the efficiency the breeding program because more of the dogs produced are suitable for service.
Dog breeders can used EBVs to dramatically improve their ability to improve the traits they want and reduce or even eliminate the ones they don't. EBVs can be used on any trait that can be evaluated by the breeder - temperament, size, herding ability, coat quality, heart disease, "showiness", hip dysplasia - anything you can judge to be better or worse, desirable or not desirable. EBVs are becoming available in more and more countries, and they are the most powerful tool now available for improving the health and well being of dogs.
Did you learn anything useful about estimated breeding values? Consider taking the online course from which these units were shared, "Managing Genetics for the Future". Learn more here -
https://www.instituteofcaninebiology.org/openreg-managinggenetics.html
https://www.instituteofcaninebiology.org/openreg-managinggenetics.html
You can learn more about the genetics of dogs in ICB's Online Courses.
*** Population Genetics for Dog Breeders ***
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*** Population Genetics for Dog Breeders ***
Next class starts 30 March
Visit our Facebook Groups
ICB Institute of Canine Biology
...the latest canine news and research
ICB Breeding for the Future
...the science of animal breeding
