If you are aware of other resources online, please let us know so we can add them.

To get to the stud books, look under the "Resources" tab on the ICB website or link in here -
http://www.instituteofcaninebiology.org/stud-books.html

By Carol Beuchat PhD

Most of the traits you care about in a dog (e.g., hunting ability, temperament, intelligence, athleticism, herding prowess) are determined by many genes - hundreds, and maybe even thousands. The process of breeding and selection basically shuffles the genes from the parents, then distributes a different set to each puppy. If a pair of dogs could produce many thousands of puppies, each will be genetically unique because the many possible combinations of alleles create the possibility of huge variation in the expressed phenotypes of a trait.

If the biology teacher has absolute standards for achievement, the test scores might be A for scores > 90%, B for 80-89%, C for 70-79%, and...well, you know how this goes. Students usually hate this, and for good reason. It is possible that no student scores high enough to get an A grade. Of course, the students will explain this as the test being impossibly hard and an inadequate measure of their understanding. Maybe so, or maybe not. But the preferred method from the perspective of the students is for the grading to be based on the distribution of scores for the students in the class on that particular test. So now, the highest 90% of the scores will get an A, even if those absolute scores were in the 70s. Graded this way, there will always be some students who will get A's, some will get B's, a large group of "average" students whose scores fall in the "bell" of the curve will get C's, and the unfortunate remainder will be in the tail of "less than adequate". (This is how we know that students in the little town of Lake Wobegon are not graded on a curve, because all of them are "above average".)

When you think about it, this is how dogs are evaluated at dog shows. How well you do will depend on who else is in the ring with you. If it's ten excellent dogs, and you are ranked #8 among this elite group, from your point of view you will have been "dumped" by that judge. And we've all seen the best of a bad lot win best of breed, awarding the win of a lifetime to somebody with a mediocre dog. Of course, the problem with this method of evaluating traits (or students) is that it doesn't select for a specific level of quality or performance. You might be the top student in your med school class, but if you went to a mediocre school and weren't competing against top students, your rose will smell just as sweet and your parents be just as proud as for the student at the top of the class at Harvard Med.

Now let's go back to evaluating that large litter of puppies. Each has the same set of parents, so the potential genetic "influence" is exactly the same, but of course every one of them has its own unique mix of paternal and maternal alleles, and every one will be just a bit different from all the others. While you're looking at these puppies trying to make up your mind which are suitable to keep for breeding or show, you're thinking in the back of your mind that you want to breed only "the best to the best". In these puppies, you're looking for the one that got the ideal mix of alleles to produce the dog of your dreams.

As in our classroom of school children, you want to identify the A+ dog, the very best one to keep back. A very experienced breeder will know if none of the pups actually deserves an A+, even the one that is the "pick" of the litter, and decide that none of them are worth breeding. This is the "selection" step of breeding animals, and it is every bit as important as the original decision of sire and dam. This is also the step that can do the most damage to the future quality of the breed's gene pool.

Why is that?

For traits that are determined by a large number of genes, getting an A+ puppy that is out at the tip of the right-hand tail of our bell curve isn't going to happen very often. If there are lots of B-quality puppies but no A+ or even an A-, all of the puppies might go to pet homes. The breeder might have relegated to the dust bin an assortment of alleles that, mixed just a bit differently, could have produced a really exceptional puppy.

It does make sense that you should choose the best stock to breed from, but then we really need to define "best". Should the "best" be only the puppies in the top 99%? Or does it make better sense to consider that the top 10% or even 20% are all nice quality dogs that, with the right mate and a fortuitous toss of the genes, could produce that once in a lifetime dog. After all, it's not a list of "good genes" that makes an animal better, but the mix of genes - some of which might actually be having a negative effect - that collectively determines the quality of an animal. Understanding that the secret to a great dog is getting just the right mix, you can see how reducing the diversity of genes in the gene pool might be robbing you of that possibility in future litters.

In the science of animal breeding, the notion we're talking about here - of the cumulative effect of a mix of genes determining the quality of a trait - is called the "additive genetic effect". Let's see how this might work with a simple example.

We will assume that we have a trait that is determined by the genes at three loci, so there are a total of 6 alleles that can influence the phenotype (A, a, B, b, C, and c). We will also assume that we can assign a value to each of these that reflects the "benefit" or improvement for the trait of interest:

A = 10
B = 20
 C = -11
a = 1
 b = -2
c = 3

So we have six alleles, some that have positive effects and some negative, some with large effects and some with small.

Based on these values, the "best" dog would have the combination of alleles that achieves the highest score. The dog with the best genome for this trait would be [AA BB cc], with a total value of

(10+10) + (20+20) + (3+3) = 66.

If we have a trait influenced by more than just a few alleles, there will be many possible genotypes, and it is highly unlikely that we will get the combination of alleles that produces the maximum score in a litter of 5, or even 10, puppies. 

If you choose to keep only the very best puppy from a litter, the average quality of your breeding stock will improve just a bit by saving those copies of the best genes. But you will be eliminating many more copies of those desirable genes simply because they weren't packaged in a way that you thought was worth keeping for your breeding program. 

In fact, some of the puppies in a good quality litter will have received many of the good alleles and only a few of the bad ones, and if you kept some of these better puppies instead of rejecting all but the very best, the average quality of the gene pool of your breeding stock would be higher in the next generation.

Instead of just the top 1% of puppies, you will keep more copies of the good alleles by keeping 10% or even 20% of the top dogs. If you were to select in this way generation after generation, the quality of your animals would progressively improve much faster than if you selected only the few in the top 1%. Every litter would produce a range of quality in the puppies, and on average those puppies would be better than the average in the previous generation because the frequency of the deleterious alleles has been decreased, and the average value of the litter for the trait will be higher.

But for the many traits that are influenced by hundreds or thousands of genes, there is no "best" allele. In fact, it's the variation of alleles in the gene pool that provides the raw material you need in order to select for improvement in a trait. Animal scientists discovered this long ago, and understanding how this sort of selection works has allowed spectacular improvement in traits being selected for.

The beauty of exploiting additive genetic variation is that the end result of selection is the production of animals that can be vastly superior to their ancestors for a particular trait of interest, simply by strategic re-mixing of the genes that have been there since the beginning. Commercial animal breeders have taken advantage of the additive genetic variation in their animals to achieve some spectacular results, such as poultry that grow faster and to a larger size on less food than the original domestic chicken, and cows that produce twice as much milk as they did 40 years ago.

Pushing a trait to such extremes is not necessarily a good idea. Selection for infinite improvement in one trait might reduce the quality of another one. In Holstein cattle, for example, the increase in milk production has resulted in a decline in fertility, which is making it harder to produce more of those terrific milk machines.

But you get the idea - there can be great potential for improvement in a trait if you recognize that achieving it won't come through efforts to narrowly select for a particular "best" gene or genes, but by taking advantage of the additive genetic variation in the gene pool to produce the combinations of alleles that will improve the quality of this generation over the last one.

Are the dogs we have today better than the ones 50 or 100 years ago? They might be. But the one thing that is fairly certain is that the loss of genetic diversity in the gene pool of a breed over the generations has progressively limited the potential additive genetic variation. We have selected strongly for the alleles with large and therefore apparent effects, and not so much for the hundreds of other alleles that could have contributed to improvement, like that little pinch of salt that puts a dish over the top. In whatever ways we have improved dogs, we have at the same time reduced the possibility of producing the truly exceptional dog, the A+ student at Harvard, the one that becomes a legend.

Do the breeders that will come after you a favor. Protect the diversity that is in your gene pool now so it can be remixed to produce better dogs in the future.

By Carol Beuchat PhD

Rummaging through my reprint collection looking for a particular paper, I ran into one published several years ago about the link between inbreeding and genetic disease. It was written by John Woolliams, a very highly regarded animal geneticist, whose research over the decades has done much to improve the science of animal breeding. The paper is for veterinarians, but most of the language is clear enough that it should be accessible to the lay animal breeder.

It's a relatively short paper, but it's rich with information, and I think you'll find it worth more than one reading. It might also be a great starting point for discussions among breeders or in a breed club about basic principles of genetic management and their importance in maximizing vigor and minimizing disease in the animals you breed. I hope you enjoy it.


Woolliams J. 2012. Influence of genetics and inbreeding on disease. In Practice 34: 196-203.

By Carol Beuchat PhD

I couldn't be happier to hear that the good folks at Working Dogs for Conservation have teamed up with the International Fund for Animal Welfare to create "Rescues2theRescue.org", an online platform that will connect shelter dogs needing a home with a REAL JOB in wildlife conservation.

The dogs that make difficult home-bound pets because of their high energy and maybe just a touch of OCD can be just perfect for the sort of work involved in rooting out wildlife traffickers, finding buried sea turtle nests, locating bear poop, sniffing out invasive plant species, and more. They're much better at these things than we mere humans, and for the right dog the job (game) is perfect.

It's a bit ironic that after working so hard with us for thousands of years in the creation of "civilization", they now are the perfect thing to help us round up the bad guys and clean up the mess we made. Those amazing dogs.

Check out the new Rescues2theRescue website.

By Carol Beuchat PhD

You probably see references to the coefficient of inbreeding (COI) often, but do you understand what it means? Here are the answers to some frequently asked questions.

What is the coefficient of inbreeding?
In the early 1900s, animal breeders knew that breeding related animals produced more consistent, predictable traits in the offspring, but they also found that there was some loss in vitality and vigor. Fertility was lower, offspring were smaller, early mortality was higher, lifespan was shorter - things that reduced their profit and the quality of their animals, and the higher the level of inbreeding, the greater the detrimental effects. Both the benefits and the risks of inbreeding are a consequence of homozygosity (see below). So a statistic was devised that estimated the level of inbreeding that would result from a particular cross so breeders had a quantitative way of evaluating both the risks and benefits. 

What does the number tell me?
The coefficient of inbreeding is the probability of inheriting two copies of the same allele from an ancestor that occurs on both sides of the pedigree. These alleles are "identical by descent". The inbreeding coefficient is also the fraction of all of the genes of an animal that are homozygous (two copies of the same allele). So, for a mating that would result in offspring with an inbreeding coefficient of 10%, there is a one in 10 chance that any particular locus would have two copies of the same allele, and 10% of all of the genes in an animal will be homozygous.

What is a "good" value for COI? What COI is "too high"?
The original purpose of the coefficient of inbreeding was to give breeders a number that would indicate both the amount of benefit to be gained from inbreeding as well as the magnitude of the deleterious effects they could expect. The trick for the breeder then is to weight the benefits and risks of a particular breeding and judge what is an acceptable balance. A low COI will have low risk, but it will also only have a modest benefit. A high COI would produce more consistency and prepotency in the offspring, but there will also be a significant loss of vigor and health.

For comparison, mating of first cousins produces a COI of 6.25%; in many societies this is considered incest and is forbidden by law). Mating of half-siblings produces a COI of 12.5%; mating of full siblings produces a COI of 25%

Do I still have to worry about COI if I am doing the health tests for my breed?
YES. For genetic disorders caused by a single recessive mutation, the DNA test will prevent the 1-in-4 risk of producing an affected animal by crossing two carriers. So, that test eliminates a risk of 25% for the disorder caused by that mutation.

But every dog has many mutations, and you have no way to know about them if a dog has only one copy and they are not expressed. If you breed two dogs with some of the same mutations, you can expect that the offspring will be homozygous for 25% of them. Many of these mutations might only have very slight effects that you wouldn't notice as a "disease", but it is the accumulation of these small effects that causes the loss of vigor and vitality in inbred animals that is called "inbreeding depression". DNA tests tell you only about one particular gene, a known risk. But if the COI of a litter is 25%, you can expect that 25% of the deleterious mutations in each puppy will be expressed. 

To breed healthy animals, you need to worry about ALL of the potential risks, and the one thing we can be sure of is that there are many more recessive mutations than the ones we have DNA tests for. Why would you invest in the DNA tests available for your breed, then produce a litter in which 15%, or 25%, or 40% of the other mutations in every animal will be expressed?

You must remember that the coefficient of inbreeding is not a measure of health. It is a measure of RISK, and with or without DNA tests, it is the best way to judge the level of genetic risk you are taking when you breed a litter.

How many generations should I use to calculate the inbreeding coefficient?
If you want to know the risk of inheriting two copies of an allele (good or bad) from an ancestor, that ancestor must be included in your database. If you have a database with just parents and grandparents, the inbreeding coefficient can't tell you anything at all about how likely you are to inherit two copies of an allele from your great great grandfather. A coefficient of inbreeding from a five generation pedigree will be an estimate of the probability of inheriting two copies of the same allele from only the animals in those 5 generations that appear on both sides of the pedigree.

But the whole point of the coefficient of inbreeding was to give breeders a way to weigh the potential benefits and risks that would result from genes that are homozygous. So you need ALL of the ancestors of a dog to be in the pedigree database you use, and for purebred dogs this means a pedigree database that goes back to the first registered dogs in the breed - the founders. 

What if there are missing pedigree data?
A dog with one or two missing parents is disconnected from its ancestors, so "on paper" it can't inherit two copies of the same allele and its coefficient of inbreeding will be incorrectly calculated to be zero. Of course, that will underestimate the inbreeding estimates for all of that animal's descendants as well. One way to get around this is to create a "virtual" dog for the missing animal and assign to it the average level of inbreeding of dogs in the same generation. 

Can I use the coefficient of inbreeding to reduce the risk of genetic disorders in my puppies?
Absolutely! This exactly what it was designed to do. Just remember that the COI is an estimate of the predicted loss of vigor and general health to expect as a consequence of the expression of recessive mutations. Except during the development of a new breed when you want to use inbreeding to fix type, you should strive to keep inbreeding below 10% to achieve modest benefit with modest risk.

Uh-oh. What if the level of inbreeding in my breed is already too high?
The closed gene pools mandated by kennel clubs for purebred dogs necessarily result in inbreeding, and in many breeds the average level of inbreeding is already high. This is the reason the occurrence of genetic disorders in purebred dogs is steadily increasing (you can watch the "genetic disorder counter" here) at the same time as lower fertility, smaller litters, and higher puppy mortality are making breeding ever more difficult.

Your first option is to make the best possible use of the genetic diversity that still exists in your breed. Identify lines that are not closely related to yours, and even if those animals wouldn't be your first pick in terms of type, a cross producing a lower COI will be beneficial in the next generation in terms of health. A genetic analysis of your breed's pedigree database can help you find these less related animals using something called cluster analysis. Don't assume that animals from different lines or even in different countries are less related. Calculate the inbreeding coefficient of a potential mating from a good pedigree database that goes back to founders. An "outcross" to a dog that is more related than you realize is likely to produce a litter with lots of nasty surprises.

What if your breed is so inbred that there is nowhere for you to go to find less related animals? Unfortunately, many breeds are facing with this problem. Genetic diversity is unavoidably lost from a breed every generation, and to restore diversity and reduce inbreeding you need a way to put the genes back by breeding to an unrelated dog, probably of a different breed. If your breed is already highly inbred and struggling with significant health issues, this is not a trivial thing to do. The animals to outcross to must be selected very carefully. For example, breeding to another highly inbred dog, even of a different breed, will produce offspring that all have the same alleles for the genes that were homozygous in the parent. The key to managing recessive mutations in any population is keeping them rare, so adding animals to the population that share many of the same mutations is asking for trouble down the road. Also, incorporating new genetic material into the breed will require a well-designed strategy worked out for at least the next 4 or 5 generations. A single crossbreeding followed by sequential backcrossing into the breed will remove most of the genetic diversity you were hoping to introduce. You definitely need to start with a carefully designed plan designed by geneticists with the tools to do it properly.

Avoiding high levels of inbreeding in the first place is much easier than trying to fix things after inbreeding becomes a problem. Breeders should work together to monitor the inbreeding of their breed so they can all benefit from healthier puppies that meet their goals as breeders now and in the future.

What do scientists have to say about inbreeding and health in purebred dogs?

If you breed purebred dogs, and if you care both about the health of the puppies you produce as well as the future of the breed, you need to understand why the list of genetic disorders in dogs continues to get longer and longer.

• It's not because of environmental toxins.
• It's not because of vaccines.
• It's not because of commercial dog foods.
• It's not because of backyard breeders and puppy mills.
• It's not because of better diagnostics and veterinary care.

What's the problem?
Among biologists, veterinarians, and genetic researchers, there is no controversy over the cause of the growing list of genetic disorders in dogs. The genome of every animal harbors many mutations that are passed from generation to generation with no harmful effects because they are recessive. Most genetic disorders in dogs are not caused by a new mutation, but by mutations that are ancient, originating in some animal hundreds or even thousands of generations ago, or perhaps even a legacy of the progenitor wolf. These mutations result in a genetic disorder when a dog inherits two copies. The increasing burden of genetic disease in purebred dogs is a direct and predictable consequence of breeding practices that increase the expression of deleterious alleles.

Here are some examples of what the experts say:

Why aren't we solving the problem?
Adding to the problem of management of genetic disorders in dogs is the fact that in many cases breeders don't know what to do about them. The research and veterinary communities realize this:

What should we do?
Clearly, if the best, most diligent efforts of responsible breeders are not solving the problem, then doing more of the same isn't going to improve things.

Among the "solutions" that will NOT solve the problem are:

• stricter selection of which dogs are allowed to bred
• reliance on knowing what's in your lines
• more studies of the diseases, especially ones like cancer and epilepsy
• elimination of the deleterious alleles from the gene pool
• research to identify the "bad" genes
• development of more genetic tests
• ignore the problems
• hope

You probably see some of your strategies on this list. But none of these address the roots of the problem as indicated by the scientists and veterinary professionals above, and as they point out, many of these things actually make the problem worse. They also point out, though, that while breeders are being offered new tools like DNA tests, they are given insufficient instruction in how to use them properly. 

Even worse, many times breeders don't have the basic information and expertise they need to understand the current genetic status of their own breed.  For example, "care must be taken [not to reduce] effective population size". Do you know the effective population size of your breed? (Do you know what "effective population size" means?) Are you using EBVs to improve the efficiency of selection against genetically complex diseases? (Do you know what "EBV" means?) Do you know the distribution of founder alleles in your current breeding population? (Do you know your breed's founders?) Do you know that most genetic disorders in dogs are caused by recessive mutations and that they are completely avoidable? (Do you understand why?)

No amount of money - and by now it must be millions per year - invested in more research and more testing is going to stem the tide of genetic disorders in purebred dogs. That seems clear. So how are we going to solve this problem?

The solution will come - and can only come - from the breeders. Not by doing more of the same, but by recognizing that traditional breeding practices have created the problem, and that breeders will need to learn about breeding strategies that will allow them to produce puppies that meet their goals as a breeder and will also live long, healthy lives.

If you breed dogs, and if you consider yourself a responsible breeder, you will need to learn more about genetics. You will need to understand not just classical Mendelian genetics, but also population genetics and some basic molecular genetics. Appropriate courses should be available at any university, or you might find them at your local community college. As far as I am aware, ICB is the first (and only) to offer courses in population genetics expressly designed for dog breeders, but you might find comparable course material in courses for hobby breeders of horses, cats, alpacas, or other domestic animals. If you have some background already in biology, you can learn from many books that aren't specifically about dog breeding but cover the relevant material. (I can recommend some that are appropriate for your particular background).

It won't be enough for you to learn all of this new stuff while your fellow breeders do nothing. You are all family through your shared gene pool, and improving the health of dogs will necessarily be a cooperative, community effort. A single hugely popular sire can devastate the gene pool of a breed in a generation, and breeders need to recognize that they will all share in the genetic tragedy that is likely to become apparent a few generations down the line. Find some fellow breeders that share your concern for the future of your breed and sign up for a class together. Join ICB's Breeding for the Future group, or a comparable forum moderated by scientists, not a bunch of fellow breeders who have lots of opinions but little knowledge. Pay attention to the research progress in canine genetics, so you will be aware of new developments and opportunities for you to further your knowledge.

Of the many stake-holders in the health of purebred dogs, the ones that will - and must - ultimately solve the problem are the breeders. For this you will need education. There's a lot for you to learn, so make a pledge to start now.

Farrell LL, JJ Schoenbeck, P Wiener, DN Clements, and KM Summers. The challenges of pedigree dog health: approaches to combating inherited disease. Canine Genetics and Epidemiology 2:3.

Leroy G and M Abitbol. 2010. Breeding strategies against genetic disorders in dog breeds.

Mellersh C. 2012. DNA testing and domestic dogs. Mammalian Genome 23:109-123.

Ostrander EA. 2012. Both ends of the leash - the human links to good dogs with bad genes. New England Journal of Medicine 367: 636-646.

Padgett GA. 1998. Control of canine genetic diseases. Howell Book House, NY.

Rooney, N and D Sargan. 2009. Pedigree dog breeding in the UK: a major welfare concern? A report commissioned by the the Royal Society for the Prevention of Cruelty to Animals.