By Carol Beuchat PhD
You've all heard the breeder's maxim - "Breed the best to the best". Breeders carefully evaluate the good and bad qualities of each puppy in a litter, saving out for breeding only the best quality animals. The rest are spayed and neutered and go off to enjoy their days in a loving pet home, or if not S/N they often go with a contract that restricts breeding or registration. The thought is that this protects the breeder's line and the number and quality of the puppies that are produced.
Let's do a little exercise that explores the genetic consequences of this breeding strategy. For this, you'll need a piece of paper and pencil, and maybe a calculator for some simple math. Go get those now...
Here's the scenario. You go out and find yourself a really nice bitch that you're going to use as the foundation for your line. Then you do months of homework evaluating dogs at shows and scrutinizing pedigrees and health data in the search for the perfect stud dog. When you make that decision you breed these two stunning dogs and produce the litter of your dreams. You watch them carefully as they grow, evaluating structure and temperament, how well they meet perfection in your mind's eye, and how you see each as the possible dog to produce the next generation. Finally, you pick out a really stunning puppy, and send the rest off to their carefully-chosen homes.
When the chosen pup reaches maturity, you repeat the process - evaluate the available mates, scrutinize the pedigrees, review the health test info, and so on until you settle on the perfect match. Again you breed, produce a nice litter, keep the best pup, and repeat, striving for improvement with each generation.
Okay, let's look at the genetics. Get your pencil and paper and make four columns labeled like this:
You've all heard the breeder's maxim - "Breed the best to the best". Breeders carefully evaluate the good and bad qualities of each puppy in a litter, saving out for breeding only the best quality animals. The rest are spayed and neutered and go off to enjoy their days in a loving pet home, or if not S/N they often go with a contract that restricts breeding or registration. The thought is that this protects the breeder's line and the number and quality of the puppies that are produced.
Let's do a little exercise that explores the genetic consequences of this breeding strategy. For this, you'll need a piece of paper and pencil, and maybe a calculator for some simple math. Go get those now...
Here's the scenario. You go out and find yourself a really nice bitch that you're going to use as the foundation for your line. Then you do months of homework evaluating dogs at shows and scrutinizing pedigrees and health data in the search for the perfect stud dog. When you make that decision you breed these two stunning dogs and produce the litter of your dreams. You watch them carefully as they grow, evaluating structure and temperament, how well they meet perfection in your mind's eye, and how you see each as the possible dog to produce the next generation. Finally, you pick out a really stunning puppy, and send the rest off to their carefully-chosen homes.
When the chosen pup reaches maturity, you repeat the process - evaluate the available mates, scrutinize the pedigrees, review the health test info, and so on until you settle on the perfect match. Again you breed, produce a nice litter, keep the best pup, and repeat, striving for improvement with each generation.
Okay, let's look at the genetics. Get your pencil and paper and make four columns labeled like this:
In the first column is the number of puppies in your dream litter (we'll work with 10). Now we're going to estimate how much of a parent's genes will get transferred to the collective genomes of the puppies.
Think about it like this: If you have no puppies (0 in the table above), NONE of the genes in the parent dog get carried to the next generation, right? So under % of parent's genes preserved we have zero.
What if there's only one puppy in the litter? It will get HALF the genes of a parent, so under % of Genes Preserved we put 50%. If half of the parent's genes are preserved in that puppy, then the other half of the parent's genes are NOT preserved. So the second column is for the fraction of the parent's genes that have NOT been carried on in a puppy. If 50% of the genes of the parent are in one puppy, then 50% of the parent's genes are not in a puppy.
Now here it gets a little tricky. Let's say you have two puppies. You know each will get half of each parent's genes, but it's very unlikely that puppy #2 gets the other half of the genes that puppy #1 didn't get. Instead, you would expect puppy #2 to get on average just half of those. This is just probability - and what puppy #2 actually gets could be all the same genes as puppy #1 (unlikely), or none of the genes of puppy #1 (unlikely), or something in between (most likely). So half of the genes that puppy #1 didn't get is 25% of the parent's genome- write that in Column B (half of the remaining genes). So this column is the fraction of a parent's genes that have NOT been copied to the offspring.
Now, in the third column where we're keeping track of the amount of a parent's genome we have captured in puppies, we can add 25% to 50% (what we already had in puppy #1), for 75%. This means that a litter of two puppies will have about 75% of all the genes found in a parent, and that 25% of the parent's genes are not present in the puppies.
Okay, so we can continue this for litters of 3 pups, 4 pups, and so on, with each additional puppy adding to the fraction of parental genes that get passed to the litter. You're going to repeat the calculations we just did for each additional puppy. Don't get a brain knot over this. Take the number in "half of genes", divide by two, and write that in the blank cell below it. Now add that number to the last number in the % of parent's genes column, and write that number in the blank. Do this for each of the 10 puppies in the litter.
Now, let's see what we have here. (If you didn't bother to do the math and write out your table, I'm not going to do it for you and you wan't have a clue what we're talking about below. So go get your pencil and just do it.)
I want you to draw a little graph like this one. I've already added the two data points we figured out above, and you can add the additional points up to 10 puppies.
Think about it like this: If you have no puppies (0 in the table above), NONE of the genes in the parent dog get carried to the next generation, right? So under % of parent's genes preserved we have zero.
What if there's only one puppy in the litter? It will get HALF the genes of a parent, so under % of Genes Preserved we put 50%. If half of the parent's genes are preserved in that puppy, then the other half of the parent's genes are NOT preserved. So the second column is for the fraction of the parent's genes that have NOT been carried on in a puppy. If 50% of the genes of the parent are in one puppy, then 50% of the parent's genes are not in a puppy.
Now here it gets a little tricky. Let's say you have two puppies. You know each will get half of each parent's genes, but it's very unlikely that puppy #2 gets the other half of the genes that puppy #1 didn't get. Instead, you would expect puppy #2 to get on average just half of those. This is just probability - and what puppy #2 actually gets could be all the same genes as puppy #1 (unlikely), or none of the genes of puppy #1 (unlikely), or something in between (most likely). So half of the genes that puppy #1 didn't get is 25% of the parent's genome- write that in Column B (half of the remaining genes). So this column is the fraction of a parent's genes that have NOT been copied to the offspring.
Now, in the third column where we're keeping track of the amount of a parent's genome we have captured in puppies, we can add 25% to 50% (what we already had in puppy #1), for 75%. This means that a litter of two puppies will have about 75% of all the genes found in a parent, and that 25% of the parent's genes are not present in the puppies.
Okay, so we can continue this for litters of 3 pups, 4 pups, and so on, with each additional puppy adding to the fraction of parental genes that get passed to the litter. You're going to repeat the calculations we just did for each additional puppy. Don't get a brain knot over this. Take the number in "half of genes", divide by two, and write that in the blank cell below it. Now add that number to the last number in the % of parent's genes column, and write that number in the blank. Do this for each of the 10 puppies in the litter.
Now, let's see what we have here. (If you didn't bother to do the math and write out your table, I'm not going to do it for you and you wan't have a clue what we're talking about below. So go get your pencil and just do it.)
I want you to draw a little graph like this one. I've already added the two data points we figured out above, and you can add the additional points up to 10 puppies.
Is this what you expected to see? What does this plot say to you?
---------------
After you've thought about that a bit (go back and think about it if you skipped that question), let's also express this another way. In the 4th column of your table, calculate 100 minus the value in column 3. So for the 0 puppy, that's 100%; for puppy #1, it's 50%; for puppy #2 it's 25%, and so on.
Now draw another graph, with the same x axis but this time the y axis will be "% of genes lost".
These two graphs tell a very important story. From your first litter, with your special bitch and the spectacular sire, you saved one puppy. What fraction of your foundation bitch's genes will get passed to the next generation? What fraction of her genes are not saved and are lost to your future breeding efforts forever?
Each time you pick only the best puppy from a litter to breed, you only capture half of the genes of each parent. The other half get tossed out. But you originally picked that sire and dam because they had qualities you really liked. You can't expect to get the exact same qualities in the offspring because each gets only half the genes in each parent. So what you're hoping for is a lucky blend of the genes from sire and dam that get passed to each puppy. It's that particular mix of genes, including the regulatory genes, the epistatic interactions, the epigenetic factors, and (don't forget) the environment that produced those parents, and likewise these things will determine the traits of the offspring. The number of different ways you could sample the genes of each parent and mix them together is what gives you the variation in each litter that you evaluate when choosing the best puppy. Without that genetic variation, there is less phenotypic variation, and you don't have much variety - good or bad - to choose from.
Do you really want to discard half the genes of each parent because they didn't end up in just the right mix to produce the dog of your dreams in that litter? Once tossed, you can't get those genes back except by crossing into your line a dog that has some of them, but no dog will have the full complement of the genes you want to add back. You're much better off keeping more than one puppy from your litter, and you can look at your graph now and figure out how much you're likely to gain with each additional puppy so you can balance that with how many additional puppies you want to stay in the gene pool
In the last graph we drew (from the data in the fourth column), what you see is the relentless attrition of the gene pool of your line based on how many puppies are kept in the breeding pool. You think you're saving the "best" genes in the "best" puppy, but you are only saving the best COMBINATIONS you got in that particular pup. If you had 100 puppies from that pair of parents, each one would be different and some might be even better than the best pup in that first litter. Just by chance.
I can hear you all grumbling that I'm completely clueless, because you can't breed a bunch of dogs from each litter; it would be a glut of puppies that you would need to find homes for, and who could afford it with all the DNA test costs, vaccinations, food, not to mention time and space. Of course, these are very real limitations. But if you think about this a bit, I think you might see that it might be prudent to consider the longer-term consequences to your line when deciding which and how many dogs to breed. You can't breed everybody, but breeding three or even two substantially increases the fraction of the genes you preserve. After 5 or 6 pups there are diminishing returns, so you can weigh cost and benefit. But breeding only one pup per litter is throwing out a lot of genetic raw material that would be better to keep in the gene pool.
What about an entire breed?
We've been thinking about this in terms of your personal breeding program and the line you're hoping to develop (or preserve). But exactly the same math applies to the gene pool of the breed as to individual breeding programs. Study after study has found that after a breed enters the "purebred" studbook, genetic diversity is lost very rapidly as a consequence of selective breeding.
For example, analysis of the pedigree data for 10 breeds of dogs in the UK KC registry found that 7 of those lost more than 90% (!!!) of unique genetic variability in only 6 generations (Calboli et al 2008). This is because only a fraction of the dogs in the population are bred, and the genes in the rest are lost to the breed. And if there is a popular sire among that small breeding population, the damage done is even greater.
If we go back to our genetic pantry analogy, you can understand how losing genetic variation will impact your breeding program in the future. You can't make dessert if you tossed out the last of the sugar. If spices represent the various alleles that occur for a particular gene, tossing out a random handful of those may wipe curry, chili, and cinnamon toast off the menu.
The way we have been breeding dogs for the last 100 years has been throwing out potentially useful (even essential) genes each and every generation. We might be getting better and better at making our favorite dish, but the menu has been getting shorter and shorter. It IS possible to lose enough genes that we can no longer make a dog that works, and if you consider that dogs that don't live past their prime are "broken", then we have a lot of breeds that are on the genetic precipice. We need to fix this or we'll lose them completely. And we need to stop breeding in a way that tosses out the genetic ingredients that we need to build healthy, beautiful, and functional dogs.
---------------
After you've thought about that a bit (go back and think about it if you skipped that question), let's also express this another way. In the 4th column of your table, calculate 100 minus the value in column 3. So for the 0 puppy, that's 100%; for puppy #1, it's 50%; for puppy #2 it's 25%, and so on.
Now draw another graph, with the same x axis but this time the y axis will be "% of genes lost".
These two graphs tell a very important story. From your first litter, with your special bitch and the spectacular sire, you saved one puppy. What fraction of your foundation bitch's genes will get passed to the next generation? What fraction of her genes are not saved and are lost to your future breeding efforts forever?
Each time you pick only the best puppy from a litter to breed, you only capture half of the genes of each parent. The other half get tossed out. But you originally picked that sire and dam because they had qualities you really liked. You can't expect to get the exact same qualities in the offspring because each gets only half the genes in each parent. So what you're hoping for is a lucky blend of the genes from sire and dam that get passed to each puppy. It's that particular mix of genes, including the regulatory genes, the epistatic interactions, the epigenetic factors, and (don't forget) the environment that produced those parents, and likewise these things will determine the traits of the offspring. The number of different ways you could sample the genes of each parent and mix them together is what gives you the variation in each litter that you evaluate when choosing the best puppy. Without that genetic variation, there is less phenotypic variation, and you don't have much variety - good or bad - to choose from.
Do you really want to discard half the genes of each parent because they didn't end up in just the right mix to produce the dog of your dreams in that litter? Once tossed, you can't get those genes back except by crossing into your line a dog that has some of them, but no dog will have the full complement of the genes you want to add back. You're much better off keeping more than one puppy from your litter, and you can look at your graph now and figure out how much you're likely to gain with each additional puppy so you can balance that with how many additional puppies you want to stay in the gene pool
In the last graph we drew (from the data in the fourth column), what you see is the relentless attrition of the gene pool of your line based on how many puppies are kept in the breeding pool. You think you're saving the "best" genes in the "best" puppy, but you are only saving the best COMBINATIONS you got in that particular pup. If you had 100 puppies from that pair of parents, each one would be different and some might be even better than the best pup in that first litter. Just by chance.
I can hear you all grumbling that I'm completely clueless, because you can't breed a bunch of dogs from each litter; it would be a glut of puppies that you would need to find homes for, and who could afford it with all the DNA test costs, vaccinations, food, not to mention time and space. Of course, these are very real limitations. But if you think about this a bit, I think you might see that it might be prudent to consider the longer-term consequences to your line when deciding which and how many dogs to breed. You can't breed everybody, but breeding three or even two substantially increases the fraction of the genes you preserve. After 5 or 6 pups there are diminishing returns, so you can weigh cost and benefit. But breeding only one pup per litter is throwing out a lot of genetic raw material that would be better to keep in the gene pool.
What about an entire breed?
We've been thinking about this in terms of your personal breeding program and the line you're hoping to develop (or preserve). But exactly the same math applies to the gene pool of the breed as to individual breeding programs. Study after study has found that after a breed enters the "purebred" studbook, genetic diversity is lost very rapidly as a consequence of selective breeding.
For example, analysis of the pedigree data for 10 breeds of dogs in the UK KC registry found that 7 of those lost more than 90% (!!!) of unique genetic variability in only 6 generations (Calboli et al 2008). This is because only a fraction of the dogs in the population are bred, and the genes in the rest are lost to the breed. And if there is a popular sire among that small breeding population, the damage done is even greater.
If we go back to our genetic pantry analogy, you can understand how losing genetic variation will impact your breeding program in the future. You can't make dessert if you tossed out the last of the sugar. If spices represent the various alleles that occur for a particular gene, tossing out a random handful of those may wipe curry, chili, and cinnamon toast off the menu.
The way we have been breeding dogs for the last 100 years has been throwing out potentially useful (even essential) genes each and every generation. We might be getting better and better at making our favorite dish, but the menu has been getting shorter and shorter. It IS possible to lose enough genes that we can no longer make a dog that works, and if you consider that dogs that don't live past their prime are "broken", then we have a lot of breeds that are on the genetic precipice. We need to fix this or we'll lose them completely. And we need to stop breeding in a way that tosses out the genetic ingredients that we need to build healthy, beautiful, and functional dogs.
- Calboli FCF, Jeff Sampson, N Fretwell, & DJ Balding. 2008. Population structure and inbreeding from pedigree analysis of purebred dogs. Genetics 179:593-601.
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