Tag Archives: genetics

Pedigree Analysis and How Breeding Decisions Affect Genes

Reprinted by permission, Jerold S Bell DVM

Jerold s Bell DVM, Clinical Associate Professor of Genetics, Tufts Cummings School of Veterinary Medicine

To some breeders, determining which traits will appear in the offspring of a mating is like rolling the dice – a combination of luck and chance. For others, producing certain traits involves more skill than luck – the result of careful study and planning. As breeders, you must understand how matings manipulate genes within your breeding stock to produce the kinds of offspring you desire.

Article
Photo by Dustin Hartje

When evaluating your breeding program, remember that most traits you’re seeking cannot be changed, fixed or created in a single generation. The more information you can obtain on how certain traits have been transmitted by your animal’s ancestors, the better you can prioritize your breeding goals. Tens of thousands of genes interact to produce a single individual. All individuals inherit pairs of chromosomes; one from the mother and one from the father. On the chromosomes are genes; so all genes come in pairs. If both genes in a pair are the same gene (for instance, “aa” or “AA”) the gene pair is called homozygous. If the two genes in a gene pair are unlike (for instance, “Aa”) the gene pair is called heterozygous. Fortunately, the gene pairs that make a cat a cat and not a dog are always homozygous. Similarly, the gene pairs that make a certain breed always breed true are also homozygous. Therefore, a large proportion of homozygous non-variable pairs – those that give a breed its specific standard – exist within each breed. It is the variable gene pairs, like those that control color, size and angulation that produce variations within a breed.

There are ways to measure the genetic diversity of a population. One method is to measure the average inbreeding coefficient (or Wright’s coefficient) for a breed. The inbreeding coefficient is a measurement of the genetic relatedness of the sire and dam. If an ancestor appears on both the sire and dam’s side of the pedigree, it increases the inbreeding coefficient. The inbreeding coefficient gives a measurement of the total percentage of variable gene pairs that are expected to be homozygous due to inheritance from ancestors common to the sire and dam. It also gives the chance that any single gene pair can be homozygous due to inheritance from ancestors common to the sire and dam. It also gives the chance that any single gene pair can be homozygous.

The types of matings that you choose for your breeding animals will manipulate their genes in the offspring, affecting their expression. Linebreeding is breeding individuals more closely related (a higher inbreeding coefficient) than the average of the breed. Outbreeding involves breeding individuals less related than the average of the breed. Linebreeding tends to increase homozygosity. Outbreeding tends to increase heterozygosity. Linebreeding and inbreeding can expose deleterious recessive genes through pairing-up, while outbreeding can hide these recessives, while propagating them in the carrier state.

Most outbreeding tends to produce more variation within a litter. An exception would be if the parents are so dissimilar that they create a uniformity of heterozygosity. This is what usually occurs in a mismating between two breeds, or a hybrid, like a Cockapoo. The resultant litter tends to be uniform, but demonstrates “half-way points” between dissimilar traits of the parents. Such litters may be phenotypically uniform, but will rarely breed true due to a mix of dissimilar genes.

One reason to outbreed would be to bring in new traits that your breeding stock does not possess. While the parents may be genetically dissimilar, you should choose a mate that corrects your breeding animal’s faults but complements its good traits. It is not unusual to produce an excellent quality individual from an outbred litter. The abundance of genetic variability can place all the right pieces in one individual. Many top-winning show animals are outbred. Consequently, however, they may have low inbreeding coefficients and may lack the ability to uniformly pass on their good traits to their offspring. After outbreeding, breeders may want to breed back to individuals related to their original stock, to attempt to solidify newly acquired traits.

Linebreeding attempts to concentrate the genes of specific ancestors through their appearance multiple times in a pedigree. It is better for linebred ancestors to appear on both the sire’s and dam’s sides of the pedigree. That way their genes have a better chance of pairing back up in the resultant offspring. Genes from common ancestors have a greater chance of expression with paired with each other than when paired with genes from other individuals, which may mask or alter their effects.

Linebreeding on an individual may not reproduce a outbred ancestor. If an ancestor is outbred and generally  heterozygous (Aa), increasing homozygosity will produce more AA and aa. The way to reproduce ab outbred ancestor is to mate two individuals that mimic the appearance and pedigree of the ancestor’s parents.

Inbreeding significantly increases homozygosity, and increases the expression of both desirable and deleterious recessive genes through pairing up. If a recessive gene (a) is rare in the population, it will almost always be masked by a dominant gene (A). Through inbreeding, a rare recessive gene (a) can be passed from a heterozygous  (Aa) common ancestor through both the sire and dam, creating a homozygous recessive (aa) offspring.

The total inbreeding coefficient is the sum of the inbreeding from the close relatives (first cousin mating), and the background inbreeding from common ancestors deep in the pedigree. Such founding ancestors established the pedigree base for the breed.
The total inbreeding coefficient is the sum of the inbreeding
from the close relatives (first cousin mating), and the
background inbreeding from common ancestors deep in the
pedigree. Such founding ancestors established the pedigree
base for the breed.

Knowledge of the degree of inbreeding in a pedigree does not necessarily help you unless you know whose genes are being concentrated. The relationship coefficient, which can also be approximated by what is called the percent blood coefficient, represents the probable genetic likeness between the individual whose pedigree is being studied, and a particular ancestor.

We know that a parent passes on an average of 50% of its genes, while a grandparent passes on 25%, a great-grandparent 12.5%, and so on. For every time the ancestor appears in the pedigree, its percentage of passed on genes can be added up and its “percentage of blood” estimated. In many breeds, an influential individual may not appear until later generations, but then will appear so many times that it necessarily contributes a large proportion of genes to the pedigree.

The average inbreeding coefficient of a breed is a measurement of its genetic diversity. When computing inbreeding coefficients, you have to look at a deep pedigree to get accurate numbers. An inbreeding coefficient based on 10 generation pedigrees is standardly used, but requires a computerized pedigree database to compute.

The average inbreeding coefficient for a breed will be based on the age and genetic background of the breed. A mating with an inbreeding coefficient of 14 percent based on a ten generation pedigree, would be considered moderate inbreeding for a Labrador Retriever (a popular breed with a low average inbreeding coefficient), but would be considered outbred for an Irish Water Spaniel (a rare breed with a higher average inbreeding coefficient).

Most breeds start from a small founding population, and consequently have a high average inbreeding coefficient. If a breed is healthy and prolific, the breadth of the gene pool increases, and the average inbreeding coefficient can go down over time. Some dog breeds were established on a working phenotype, and not on appearance. These breeds usually start with low inbreeding coefficients due to the dissimilar backgrounds of the founders. As certain individuals are linebred on to create a uniform physical phenotype, the average inbreeding coefficient can increase.

There is no specific level or percentage of inbreeding that causes impaired health or vigor. If there is no diversity (non-variable gene pairs for a breed) but the homozygote is not detrimental, there is no effect on breed health. The characteristics that make a breed reproduce true to its standard are base on non-variable gene pairs. There are pure-bred populations where smaller litter sizes, shorter life expectancies, increased immune-mediated disease, and breed-related genetic disease are plaguing the population. In these instances, prolific ancestors have passed on detrimental recessive genes that have increased in frequency and homozygosity. With this type of documented inbreeding depression, it is possible that an outbreeding scheme could stabilize the population. However, it is also probable that the breed will not thrive without an influx of new genes; either from a distantly related (imported) population, or crossbreeding.

Fortunately, most breeds do not find themselves in the position of this amount of limited diversity and inbreeding depression. However, the perceived problem of a limited gene pool has caused some breeders to advocate outbreeding of all individuals. Studies in genetic conservation and rear breeds have shown that his practice contributes to the loss of genetic diversity. By uniformly crossing all “lines” in a breed, you eliminate the differences between them, and therefore the diversity between individuals. Eventually, there will not be any “unrelated line” to be found. Everyone will have a mixture of everyone else’s genes. The practice in livestock breeding has significantly reduced diversity, and caused the reduced diversity, loss of unique rare breeds.

A basic tenet of population genetics is that gene frequencies do not change from generation to generation. This will occur regardless of the homozygosity or heterozygosity of the parents, or whether the mating is an outbreeding, linebreeding, or inbreeding. This is the nature of genetic recombination. Selection, and not the types of matings used affect gene frequencies and breed genetic diversity.

If two parents are both heterozygous (both Aa) for a gene pair, on the average, they would produce 25% AA, 50% Aa, and 25% aa. (These are the averages when many litters are combined. In reality, any variety of pairing up can occur in a single litter.) If a prolific male comes out of this litter, and he is homozygous aa, then the frequency of the “a” gene will increase in the population, and the frequency of the “A” gene will decrease. This is known as the popular sire syndrome. Of course, each individual has thousands of genes that vary in the breed, and everyone carries some deleterious recessive genes. The overuse of individual breeding animals contributes the most to decreased diversity (population bottlenecks), and the increased spread of deleterious recessive genes (the founders effect). Again, it is selection (use of this stud to the exception of others), and not the types of matings he is involved in that alters gene frequencies. Breeders should select the best individuals from all lines, so as to not create new genetic bottlenecks.

Decisions to linebreed, inbreed or outbreed should be made based on the knowledge of an individuals traits and those of its ancestors. Inbreeding will quickly identify the good and bad recessive genes the parents share, based on their expression in the offspring. Unless you have prior knowledge of what the offspring of milder linebreedings on the common ancestors were like, you may be exposing your litters (and buyers) to extraordinary risk of genetic defects. In your matings, the inbreeding coefficient should only increase because you are specifically linebreeding (increasing the percentage of blood) to selected ancestors.

Don’t set too many goals in each generation, or your selective pressure for each goal will necessarily become weaker. Genetically complex or dominant traits should be addressed early in a long-range breeding plan, as they may take several generations to fix. Traits with major dominant genes become fixed more slowly, as the heterozygous (Aa) individuals in a breed will not be readily differentiated from the homozygous-dominate (AA) individuals. Desirable recessive traits can be fixed in one generation because individuals that show such characteristics are homozygous for the recessive genes. Individuals that pass on desirable traits for numerous matings and generations should be preferentially selected for breeding stock. This prepotency is due to homozygosity of dominate (AA) and recessive (aa) genes. However, these individuals should not be overused, to avoid the popular sire syndrome.

Breeders should plan their matings based on selecting toward a breed standard, based on the ideal temperament, performance, and conformation, and should select against the significant breed related health issues. Using progeny and sib-based information to select for desirable traits and against detrimental traits will allow greater control.

This article can be reproduced with the permission of the author. Jerold.Bell@tufts.edu

 

Death by a Thousand Health Tests

Food for thought is always a good thing, at least in my world, it keeps my mind open to new ideas. As I’ve aged I’ve found it’s ever more important not to get stuck in my ways and thinking about what other people have to say on a topic keeps me out of ruts.  So when I read the article I’m sharing with you today about health testing, I found myself thinking. Now, a word of warning, some of my close friends would tell you, “Sally’s thinking takes some rather weird detours now and again, so when she says “I was thinking” you might wanna run for cover!”

We all talk about being a responsible breeder, and of course, we consider a part of that responsibility to be health testing of the parents. Now mind you, I’m getting to that place where I’m almost old as dirt, so I’m one of those breeders who started in the game long before the majority of the health tests of today were available. While I’m all for health testing to gain knowledge of what is in the genes I’m about to mix together, I’m also one of those breeders who will tell you to use a good ole dose of common sense when breeding. While I’d never throw health testing to the side, I am also realizing that as the population of Gordon Setters declines, so follows our number of breeding options. This is a big conundrum we face folks, and it will take dedication, smart decisions and some good old common sense to preserve the best of our breed.

Sally Gift, AZ              Photograph by Susan Roy Nelson, WY

With that said, I don’t know as I agree with everything in this article, but I do know it will give you some food for thought so I’m sharing, for your reading and thinking pleasure.  If you’d like to share your thoughts after reading this feel free to use the comment section!

Breeder On The Edge

Death From a Thousand Health Tests by Amanda Kelly

AUTHOR:  A dedicated hobby breeder in a terminally rare breed, Amanda Kelly perpetually finds herself on the edge of everything from ecstasy to bankruptcy, quitting and insanity.

I had a really interesting conversation with a geneticist the other day that got me thinking: science is offering us more and more great ways to evaluate the health of our dogs…but when does enough turn into too much? When do we cross the threshold from helpful information to complete paralysis? Or outright bankruptcy? How do we avoid both?

Prioritization
The test we were discussing is quite a new one in my breed (Toy Manchester Terriers). It is for a condition called Xanthinuria that causes dogs to form a very rare form of kidney stone. There have only been three clinically affected dogs that I am aware of (full disclosure: we bred one). After encountering the issue, a fellow breeder did a little digging and discovered that a marker associated with the condition in humans worked for our breed as well. Kudos to her for being proactive and finding out more! The American and Canadian breed clubs helped proof the test and voila, it is now available commercially at quite a reasonable cost.

When I looked at dogs in my own breeding program that came up as carriers however, I was surprised as I would have expected more of our puppies to have or be forming stones than was the case.  So, what does that say about the disease? Do all affected puppies form stones? If not, what is the rate?  I found the answers to those Qs simultaneously helpful and troubling.

Apparently, current thinking is that approximately 50% of males with two copies of the mutation form stones or have associated kidney issues, while very few females with the same status have a problem (likely because they do a better job of emptying their bladders). Now, these are just rough estimates because the disease as a whole is rare and hasn’t been extensively studied, but it does raise an important question: what are we as breeders to do with this information and associated results of the genetic test?

The Jigsaw
The simple fact is that the more tests we have, the more pieces of info we have to try and reconcile when planning a breeding. At present, Toy Manchester breeders as a group are variously clearing things like hips, patellas, eyes, thyroid, and hearts plus DNA testing for von Willebrand’s Disease, and, now, potentially xanthinuria. That’s 7 tests, some with questionable value based on anecdotal and surveillance evidence, if we’re being honest. We’re also actively working to identify a test for juvenile cardiomyopathy.

The end result of all of that testing is a ton of information, which is great from the perspective of evaluating the health of individual dogs but also creates a number of very real problems for breeders in areas like liability, reputation and cost.

In the past, these factors were certainly in play but their effects were somewhat muted. Breeders worked for years to learn about their breed and their lines so they could make informed decisions and minimize the risk of producing issues. Health tests initially concentrated on measuring phenotype as an indicator and we worked with what we had. The important thing was that we could confidently tell puppy buyers we had done everything possible to produce healthy, happy puppies and if a problem appeared we were solid in the knowledge we had used all available tools to their best advantage.

Enter the genetic test. In my breed, the first one was for von Willebrand’s Disease (a blood clotting disorder). For years this disease was monitored by assay testing that measured the actual amount of the specific type of clotting factor in the blood and projected genetic status based on corresponding ranges. It was a pain to do but everyone muddled through as it was one of the few standard health tests most breeders did in the 1980s and 90s. When the genetic marker was identified, some breeders lost their ever loving minds. Dozens of valuable dogs were promptly spayed and neutered while breeders across North America began making pronunciations about “never” breeding a carrier even to a clear.

There’s no question, needless damage was done to the gene pool — especially when you consider there had never been a documented case of a Manchester actually bleeding out because it was vWD affected (at least not one I am aware of). Eventually breeders learned how to work with the DNA results and things calmed down. Our new test allowed us to easily avoid producing “affected” puppies (i.e., a dog with two copies of the gene, not necessarily clinically affected) and, regardless of the actual effects of the condition itself, doing so quickly became “right” and “just”.  It was an approach we ourselves endorsed and followed because, after all, “responsible breeders” test.

And thus, the line in the sand was drawn. It’s a line we in the dog community drew ourselves and it’s one most of us dare not cross.

Unlimited Liability
The scientific advancements that brought us more genetic tests took place against an active backdrop that included the rise of animal rights, increasing anthropomorphization of pets, emergence of puppy lemon laws, and the advent of social media. Now, it may seem odd to bring those factors into a discussion of genetic testing, but they each play a very important role in describing the environment within which we are working. An environment that values reputation above all else and that pits breeding decisions against financial liability in a way many breeders don’t consider.

Any breeder with two licks of sense knows that when it comes to breeding dogs, the most important possession you have — more important than any ribbon you may ever win — is your reputation. Your reputation affects everything you do, from access to stud dogs and puppies to demand for same. In a subjective sport like ours, it can even affect your ability to succeed in the show ring.

Protecting, fostering and growing a reputation can become all-consuming. Let’s cut to the chase here: We’re operating in an environment that can make a competition out of anything — which is why sometimes reputation management, and by extension health testing, becomes as much about one upmanship and moral superiority as it is the well-being of the dogs in question. That probably explains why many of the tests done in my breed are done by rote…because they are available, not because we have objectively identified a need for them. Not because we have established that rates of thyroid problems or eye issues, for example, are any higher in our breed than in the general dog population. No, we do them because we can and because we feel (tell one another?) that we should. And why is that? It’s because we have established as fact within our community that good breeders test and bad breeders don’t. So, we all work extra hard to make sure our conduct is above reproach.

That core belief is just as strong outside of the dog community, where we have worked hard to battle animal rights messaging by establishing health testing as a key feature differentiating responsible breeders from backyard breeders. And it’s a great message — easy to understand and easy for the public to actively measure when they are talking to breeders. The trouble is, that message comes pre-loaded with expectations we can never live up to. Expectations that if you buy from a good breeder your dog will never ever have health issues. That health tested parents won’t produce problems. That responsible breeders can be God.

And therein lies the problem. The more health testing we do, the bigger the gap grows between public expectations and the reality of what we can deliver…and with it, our financial liability. Because hey, don’t forget, in addition to health testing, responsible breeders also guarantee their puppies. Whether through provision of a replacement puppy or return of purchase funds, those guarantees do carry financial risk and can’t be dismissed at the best of times and even less so as puppy lemon laws increasingly make puppy health a legal matter. So, tell me…how do you think small claims court would view a breeder that knowingly produces a problem? Or one that unknowingly produces one because they failed to use the tests available? It’s a perfect catch 22 in the making.

Risk Reduction
It’s a simple axiom that the more health testing available, the less we talk about what we’re trying to avoid producing and the more we talk about what we are willing to risk producing. There isn’t a perfect dog out there and every biological organism possesses deleterious genes for something, regardless of whether we can test for it or not.  The more tests available, the more complicated planning breedings becomes because we all naturally want to avoid the chances of producing any problem at all.  But is that a realistic goal?

What did I say we were up to in my breed – seven tests? Eight? Heck, even I lose track sometimes. And all of these tests in an era when the number of puppies being produced continues to drop at an alarming rate. Under 200 Toy and Standard Manchester Terriers “combined” were produced in North America last year, so I’m sure you can image how difficult it might be to match test results for potential breedings (particularly if we’re testing for everything under the sun). Or what the costs of doing those breedings might be as we look further and further afield, let alone the relative cost of doing the health screening to begin with in a breed with relatively small litter sizes and low purchase prices. The financials would rock your world and have you questioning my sanity, so we won’t go there other than to say red is a better quality in a new coat than a ledger (but I digress…).

I asked a few researchers and vets what they felt breeders should do with test results when there are many to consider.  The consistent response was that we need to prioritize — and that’s a completely reasonable thing for a scientist to say…and a very difficult thing for a devoted dog breeder to actually do.

Never mind the costs, appearance or liability — I genuinely don’t want to be responsible through conscious decision for producing a sick puppy. It is one thing to employ testing, tools and techniques to theoretically reduce disease and quite another to look at a plethora of results and say “This one I can live with.”

And what happens once the die is cast?  If we use Xanthinuria as an example, I could choose to breed two carriers together and test all of the puppies…but then what? Sure, knowing a puppy has two copies of the gene and is at higher risk of forming stones will be helpful to an owner who could keep the dog on a low purine diet and perhaps avoid issues altogether…but could I sell a puppy like that? For how much? Would anyone take it if I was giving it away? What level of financial responsibility do I hold if it does develop an issue two, five or 10 years down the road? What if there are multiple puppies with two copies of the gene in the litter?

And that, ladies and gentlemen, is the ethical dilemma of the future.  Perhaps we in smaller, rarer breeds are dealing with it sooner, but it is a dilemma I truly believe every breed and breeder will face at some point.  It has the potential to be absolutely paralyzing as we seek to do the right thing in a world where that is increasingly less black and white than it seemed a few short years ago.

I don’t know exactly how we can or should approach it — perhaps I’m hoping you’ll be able to tell me. I suspect that monitoring of actual breed health through health surveys and breeders sharing information on what they are seeing will be increasingly important if we wish to prioritize according to real information. And I do know that one of the things we absolutely must do is change how we discuss health testing. The way we talk about each other (oh Lordy, put a star next to that one!) and to each other as well as how we portray ourselves to the public. Just as important, we have to think about health tests and results holistically in the context of our breed and gene pool. In our rush to erase problems through testing, we are shown again and again that the devil we don’t know is often worse than the devil we can test for.

What To Do?
This article isn’t intended to form the cornerstone of a campaign against health testing. Far from it. I truly believe we need to use the tools available to us, particularly if they are able to help us avoid devastating issues facing our dogs and puppies. In fact, I and others in my breed have worked hard for more than a decade to see a genetic test developed for juvenile cardiomyopathy because it is a brutal, deadly disease and I want all of us to have a tool that will allow us to make informed choices and stop guessing at how to avoid it.

But I’m also a realist. Health management is a tough nut to crack even for trained geneticists let alone the average breeder doing their best to navigate an increasingly complex and technical landscape. Giving us the test results is the easy part, it seems — figuring out what to do with them is our next great challenge.

The Ins and Outs of Pedigree Analysis

bell-jerold-1520260577

(This article is reprinted with permission of the Jerold M Bell DVM

IT’S ALL IN THE GENES

As dog breeders, we engage in genetic “experiments” each time we plan a mating. The type of mating selected should coincide with your goals. To some breeders, determining which traits will appear in the offspring of a mating is like rolling the dice – a combination of luck and chance. For others, producing certain traits involves more skill than luck – the result of careful study and planning. As breeders, we must understand how we manipulate genes within our breeding stock to produce the kinds of dogs we want. We have to first understand dogs as a species, then dogs as genetic individuals.

The species, Canis familiaris, includes all breeds of the domestic dog. Although we can argue that there is little similarity between a Chihuahua and a Saint Bernard, or that established breeds are separate entities among themselves, they all are genetically the same species. While a mating within a breed may be considered outbred, it still must be viewed as part of the whole genetic picture: a mating within an isolated, closely related, interbred population. Each breed was developed by close breeding and inbreeding among a small group of founding canine ancestors, either through a long period of genetic selection or by intensely inbreeding a smaller number of generations. The process established the breed’s characteristics and made the dogs in it breed true.

When evaluating your breeding program, remember that most traits you’re seeking cannot be changed, fixed or created in a single generation. The more information you can obtain on how certain traits have been transmitted by your dog’s ancestors, the better you can prioritize your breeding goals. Tens of thousands of genes interact to produce a single dog. All genes are inherited in pairs, one pair from the father and one from the mother. If the pair of inherited genes from both parents is identical, the pair is called homozygous. If the genes in the pair are not alike, the pair is called heterozygous. Fortunately, the gene pairs that make a dog a dog and not a cat are always homozygous. Similarly, the gene pairs that make a certain breed always breed true are also homozygous. Therefore, a large proportion of homozygous non-variable pairs – those that give a breed its specific standard – exist within each breed. It is the variable gene pairs, like those that control color, size and angulation, that produce variations within a breed.

BREEDING BY PEDIGREE

Outbreeding brings together two dogs less related than the average for the breed. This promotes more heterozygosity, and gene diversity within each dog by matching pairs of unrelated genes from different ancestors. Outbreeding can also mask the expression of recessive genes, and allow their propagation in the carrier state.

Most outbreeding tends to produce more variation within a litter. An exception would be if the parents are so dissimilar that they create a uniformity of heterozygosity. This is what usually occurs in a mismating between two breeds. The resultant litter tends to be uniform, but demonstrates “half-way points” between the dissimilar traits of the parents. Such litters may be phenotypically uniform, but will rarely breed true due to the mix of dissimilar genes.

A reason to outbreed would be to bring in new traits that your breeding stock does not possess. While the parents may be genetically dissimilar, you should choose a mate that corrects your dog’s faults but phenotypically complements your dog’s good traits.

bell-1.gif (12754 bytes)

It is not unusual to produce an excellent quality dog from an outbred litter. The abundance of genetic variability can place all the right pieces in one individual. Many top-winning show dogs are outbred. Consequently, however, they may have low inbreeding coefficients and may lack the ability to uniformly pass on their good traits to their offspring. After an outbreeding, breeders may want to breed back to dogs related to their original stock, to increase homozygosity and attempt to solidify newly acquired traits.

Linebreeding attempts to concentrate the genes of a specific ancestor or ancestors through their appearance multiple times in a pedigree. The ancestor should appear behind more than one offspring. If an ancestor always appears behind the same offspring, you are only linebreeding on the approximately 50 percent of the genes passed to the offspring and not the ancestor itself.

It is better for linebred ancestors to appear on both the sire’s and the dam’s sides of the pedigree. That way their genes have a better chance of pairing back up in the resultant pups. Genes from common ancestors have a greater chance of expression when paired with each other than when paired with genes from other individuals, which may mask or alter their effects.

bell-2.gif (14375 bytes)

A linebreeding may produce a puppy with magnificent qualities, but if those qualities are not present in any of the ancestors the pup has been linebred on, it may not breed true. Therefore, careful selection of mates is important, but careful selection of puppies from the resultant litter is also important to fulfill your genetic goals. Without this, you are reducing your chances of concentrating the genes of the linebred ancestor.

Increasing an individual’s homozygosity through linebreeding may not, however, reproduce an outbred ancestor. If an ancestor is outbred and generally heterozygous (Aa), increasing homozygosity will produce more AA and aa. The way to reproduce an outbred ancestor is to mate two individuals that mimic the appearance and pedigree of the ancestor’s parents.

Inbreeding significantly increases homozygosity, and therefore uniformity in litters. Inbreeding can increase the expression of both beneficial and detrimental recessive genes through pairing up. If a recessive gene (a) is rare in the population, it will almost always be masked by a dominant gene (A). Through inbreeding, a rare recessive gene (a) can be passed from a heterozygous (Aa) common ancestor through both the sire and dam, creating a homozygous recessive (aa) offspring. Inbreeding does not create undesirable genes, it simply increases the expression of those that are already present in a heterozygous state.

bell-3.gif (5110 bytes)

Inbreeding can exacerbate a tendency toward disorders controlled by multiple genes, such as hip dysplasia and congenital heart anomalies. Unless you have prior knowledge of what milder linebreedings on the common ancestors have produced, inbreeding may expose your puppies (and puppy buyers) to extraordinary risk of genetic defects. Research has shown that inbreeding depression, or diminished health and viability through inbreeding is directly related to the amount of detrimental recessive genes present. Some lines thrive with inbreeding, and some do not.

PEDIGREE ANALYSIS

Geneticists’ and breeders’ definitions of inbreeding vary. A geneticist views inbreeding as a measurable number that goes up whenever there is a common ancestor between the sire’s and dam’s sides of the pedigree; a breeder considers inbreeding to be close inbreeding, such as father-to-daughter or brother-to-sister matings. A common ancestor, even in the eighth generation, will increase the measurable amount of inbreeding in the pedigree.

The Inbreeding Coefficient (or Wright’s coefficient) is an estimate of the percentage of all the variable gene pairs that are homozygous due to inheritance from common ancestors. It is also the average chance that any single gene pair is homozygous due to inheritance from a common ancestor. In order to determine whether a particular mating is an outbreeding or inbreeding relative to your breed, you must determine the breed’s average inbreeding coefficient. The average inbreeding coefficient of a breed will vary depending on the breed’s popularity or the age of its breeding population. A mating with an inbreeding coefficient of 14 percent based on a ten generation pedigree, would be considered moderate inbreeding for a Labrador Retriever (a popular breed with a low average inbreeding coefficient), but would be considered outbred for an Irish Water Spaniel (a rare breed with a higher average inbreeding coefficient).

For the calculated inbreeding coefficient of a pedigree to be accurate, it must be based on several generations. Inbreeding in the fifth and later generations (background inbreeding) often has a profound effect on the genetic makeup of the offspring represented by the pedigree. In studies conducted on dog breeds, the difference in inbreeding coefficients based on four versus eight generation pedigrees varied immensely. A four generation pedigree containing 28 unique ancestors for 30 positions in the pedigree could generate a low inbreeding coefficient, while eight generations of the same pedigree, which contained 212 unique ancestors out of 510 possible positions, had a considerably higher inbreeding coefficient. What seemed like an outbred mix of genes in a couple of generations, appeared as a linebred concentration of genes from influential ancestors in extended generations.

The process of calculating coefficients is too complex to present here. Several books that include how to compute coefficients are indicated at the end of this article; some computerized canine pedigree programs also compute coefficients. The analyses in this article were performed using CompuPed, by RCI Software.

[RCI Note: CompuPed computes Wright’s Inbreeding Coefficient faster and more accurately than any other PC program available. ]

Pedigree of: “Laurel Hill Braxfield Bilye”

( a spayed female Gordon Setter owned by Dr. Jerold and Mrs. Candice Bell, and co-bred by Mary Poos and Laura Bedford.)

Bell 6 Pedigree

To visualize some of these concepts, please refer to the above pedigree. Linebred ancestors in this pedigree are in color, to help visualize their contribution. The paternal grandsire, CH Loch Adair Foxfire, and the maternal grandam, CH Loch Adair Firefly WD, are full siblings, making this a first-cousin mating. The inbreeding coefficient for a first cousin mating is 6.25%, which is considered a mild level of inbreeding. Lists of inbreeding coefficients based on different types of matings are shown in the table below.

bell-4.gif (4971 bytes)

In Bilye’s pedigree, an inbreeding coefficient based on four generations computes to 7.81%. This is not significantly different from the estimate based on the first-cousin mating alone. Inbreeding coefficients based on increasing numbers of generations are as follows: five generations, 13.34%; six generations, 18.19%; seven generations, 22.78%; eight generations, 24.01%; ten generations, 28.63%; and twelve generations, 30.81%. The inbreeding coefficient of 30.81 percent is more than what you would find in a parent-to-offspring mating (25%). As you can see, the background inbreeding has far more influence on the total inbreeding coefficient than the first-cousin mating, which only appears to be its strongest influence.

Knowledge of the degree of inbreeding in a pedigree does not necessarily help you unless you know whose genes are being concentrated. The percent blood coefficient measures the relatedness between an ancestor and the individual represented by the pedigree. It estimates the probable percentage of genes passed down from a common ancestor. We know that a parent passes on an average of 50% of its genes, while a grandparent passes on 25%, a great-grandparent 12.5%, and so on. For every time the ancestor appears in the pedigree, its percentage of passed-on genes can be added up and its “percentage of blood” estimated.

In many breeds, an influential individual may not appear until later generations, but then will appear so many times that it necessarily contributes a large proportion of genes to the pedigree. This can occur in breeds, due to either prolific ancestors (usually stud dogs), or with a small population of dogs originating the breed. Based on a twenty-five generation pedigree of Bilye, there are only 852 unique ancestors who appear a total of over twenty-million times.

Pedigree Analysis of Laurel Hill Braxfield Bilye
(computed to 25 generations)

1st Generation

Linebred Ancesters

Percentage of blood

Appearance in pedigree

# times in pedigree

CH Afternod Drambuie 33.20% 6 33
CH Afternod Sue 27.05% 7 61
CH Afternod Callant 26.56% 5 13
“Grand-Parents” 25.00% 2 1
CH Sutherland Gallant 25.00% 3 2
CH Sutherland MacDuff 25.00% 3 3
CH Sutherland Lass of Shambray 25.00% 3 2
CH Wilson’s Corrie, CD 22.30% 7 200
CH Afternod Buchanon 20.22% 7 48
Loch Adair Diana of Redchic 17.97% 5 12
CH EEG’s Scotia Nodrog Rettes 17.76% 8 181
Afternod Ember of Gordon Hill 17.14% 8 76
CH Afternod Hickory 16.21% 6 27
CH Black Rogue of Serlway 15.72% 9 480
CH Afternod Woodbine 14.45% 6 15
CH Fast’s Falcon of Windy Hill 13.82% 8 66
Afternod Fidemac 13.67% 5 7
CH Page’s MacDonegal II 13.43% 7 56
Afternod Hedera 13.38% 7 56
CH Downside Bonnie of Serlway 12.90% 10 708
Peter of Crombie 12.76% 11 3,887
“Great-Grand-Parents” 12.50% 3 1
CH Afternod Amber 12.50% 5 5
Ben of Crombie 11.83% 11 7,584
Stylish William 11.18% 13 23,764
Stylish Billie 11.08% 14 70,542
Stylish Ranger 10.80% 15 297,331
CH Afternod Kate 10.74% 6 17
Heather Grouse 10.61% 16 1,129,656
Afternod Hedemac 10.45% 7 28

The above analysis shows the ancestral contribution of the linebred ancestors in Bilye’s pedigree. Those dogs in color were present in the five-generation pedigree. CH Afternod Drambuie has the highest genetic contribution of all of the linebred ancestors. He appears 33 times between the sixth and eighth generations. One appearance in the sixth generation contributes 1.56% of the genes to the pedigree. His total contribution is 33.2% of Bilye’s genes, second only to the parents. Therefore, in this pedigree, the most influential ancestor doesn’t even appear in the five-generation pedigree. His dam, CH Afternod Sue, appears 61 times between the seventh and tenth generations, and contributes more genes to the pedigree than a grandparent.

Foundation dogs that formed the Gordon Setter breed also play a great role in the genetic makeup of today’s dogs. Heather Grouse appears over one million times between the sixteenth and twenty-fifth generations, and almost doubles those appearances beyond the twenty-fifth generation. He contributes over ten percent of the genes to Bilye’s pedigree. This example shows that the depth of the pedigree is very important in estimating the genetic makeup of an individual. Any detrimental recessive genes carried by Heather Grouse or other founding dogs, would be expected to be widespread in the breed.

BREEDING BY APPEARANCE

Many breeders plan matings solely on the appearance of a dog and not on its pedigree or the relatedness of the prospective parents. This is called assortative mating. Breeders use positive assortative matings (like-to-like) to solidify traits, and negative assortative matings (like-to-unlike) when they wish to correct traits or bring in traits their breeding stock may lack.

Some individuals may share desirable characteristics, but they inherit them differently. This is especially true of polygenic traits, such as ear set, bite, or length of forearm. Breeding two phenotypically similar but genotypically unrelated dogs together would not necessarily reproduce these traits. Conversely, each individual with the same pedigree will not necessarily look or breed alike.

Breedings should not be planned solely on the basis of the pedigree or appearance alone. Matings should be based on a combination of appearance and ancestry. If you are trying to solidify a certain trait – like topline – and it is one you can observe in the parents and the linebred ancestors of two related dogs, then you can be more confident that you will attain your goal.

GENETIC DIVERSITY

Some breed clubs advocate codes of ethics that discourage linebreeding or inbreeding, as an attempt to increase breed genetic diversity. This position is based on a false premise. Inbreeding or linebreeding does not cause the loss of genes from a breed gene pool. It occurs through selection; the use and non-use of offspring. If some breeders linebreed to certain dogs that they favor, and others linebreed to other dogs that they favor, then breed-wide genetic diversity is maintained.

In a theoretical mating with four offspring, we are dealing with four gene pairs. The sire is homozygous at 50% of his gene pairs (two out of four), while the dam is homozygous at 75% of her gene pairs. It is reasonable to assume that she is more inbred than the sire.

A basic tenet of population genetics is that gene frequencies do not change from the parental generation to the offspring. This will occur regardless of the homozygosity or heterozygosity of the parents, or whether the mating is an outbreeding, linebreeding, or inbreeding. This is the nature of genetic recombination.

bell-5.gif (6068 bytes)

There is a lack of gene diversity at the first (olive) gene pair, so that only one type of gene combination can be produced: homozygous olive. As the sire is homozygous lime at the third gene pair, and the dam is homozygous blue, all offspring will be heterozygous at the third gene pair. Depending on the dominant or recessive nature of the blue or lime genes, all offspring will appear the same for this trait due to a uniformity of heterozygosity.

If offspring D is used as a prolific breeder, and none of the other offspring are bred to a great extent, gene frequencies in the breed will change. As dog D lacks the orange gene in the second pair and the purple gene in the fourth pair, the frequencies of these genes will diminish in the breed. They will be replaced by higher frequencies of the red and pink genes. This shifts the gene pool, and the breed’s genetic diversity. Of course, dogs have more than four gene pairs, and the overuse of dog D to the exception of others can affect the gene frequency of thousands of genes. Again, it is selection (for example of dog D to the exception of others), and not the types of matings he is involved in that alters gene frequencies.

Breeders should select the best individuals from all kennel lines, so as to not create new genetic bottlenecks. There is a tendency for many breeders to breed to a male; who produced no epileptics in matings to several epileptic dams, to an OFA excellent stud, or to the top winning dog in the show ring. Regardless of the popularity of the breed, if everyone is breeding to a single studdog, (the popular sire syndrome) the gene pool will drift in that dog’s direction and there will be a loss of genetic diversity. Too much breeding to one dog will give the gene pool an extraordinary dose of his genes, and also whatever detrimental recessives he may carry, to be uncovered in later generations. This can cause future breed related genetic disease through the founders effect.

Dogs who are poor examples of the breed should not be used simply to maintain diversity. Related dogs with desirable qualities will maintain diversity, and improve the breed. Breeders should concentrate on selecting toward a breed standard, based on the ideal temperament, performance, and conformation, and should select against the significant breed related health issues. Using progeny and sib-based information to select against both polygenic disorders and those without a known mode of inheritance will allow greater control.

Rare breeds with small gene pools have concerns about genetic diversity. What constitutes acceptable diversity versus too restricted diversity? The problems with genetic diversity in purebred populations concern the fixing of deleterious recessive genes, which when homozygous cause impaired health. Lethal recessives place a drain on the gene pool either prenatally, or before reproductive age. They can manifest themselves through smaller litter size, or neonatal death. Other deleterious recessives cause disease, while not affecting reproduction.

Problems with a lack of genetic diversity arise at the gene locus level. There is no specific level or percentage of inbreeding that causes impaired health or vigor. It has been shown that some inbred strains of animals thrive generation after generation, while others fail to thrive. If there is no diversity (non-variable gene pairs for a breed) but the homozygote is not detrimental, there is no effect on breed health. The characteristics that make a breed reproduce true to its standard are based on non-variable gene pairs. A genetic health problem arises for a breed when a detrimental allele increases in frequency and homozygosity.

GENETIC CONSERVATION

The perceived problem of a limited gene pool has caused some breeds to advocate outbreeding of all dogs. Studies in genetic conservation and rare breeds have shown that this practice actually contributes to the loss of genetic diversity. By uniformly crossing all “lines” in a breed, you eliminate the differences between them, and therefore the diversity between individuals. This practice in livestock breeding has significantly reduced diversity, and caused the loss of unique rare breeds. The process of maintaining healthy “lines” or families of dogs, with many breeders crossing between lines and breeding back as they see fit maintains diversity in the gene pool. It is the varied opinion of breeders as to what constitutes the ideal dog, and their selection of breeding stock that maintains breed diversity.

The Doberman Pincher breed is large, and genetically diverse. The breed has a problem with vonWillibrands disease, an autosomal recessive bleeding disorder. Some researchers estimate that up to 60% of the breed may be homozygous recessive for the defective gene, and the majority of the remaining dogs are heterozygous. Therefore, there is diminished genetic diversity in this breed at the vonWillibrands locus. A genetic test and screening program now exists for Doberman Pincher breeders. They can identify carrier and affected dogs, and decrease the defective gene frequency through selection of normal testing offspring for breeding. By not just eliminating carriers, but replacing them with normal testing offspring, genetic diversity will be conserved.

Dalmatians have a high frequency defective autosomal recessive gene controlling purine metabolism. Homozygous recessive individuals can have urinary problems due to urate bladder stones and crystals, and an associated skin condition (Dalmatian Bronzing Syndrome). At one time, the breed and the AKC approved a crossbreeding program to a few Pointers, to bring normal purine metabolism genes into the gene pool. The program was abandoned for several reasons, but it was accepted that the number of individual Dalmatians with two normal purine metabolism genes far exceeded the few Pointers that were being used in the program. The impact of other Pointer genes foreign to the Dalmatian gene pool could have had a greater detrimental effect than the few normal purine metabolism genes being imported through the program.

PUTTING IT ALL TOGETHER

Decisions to linebreed, inbreed or outbreed should be made based on the knowledge of an individual dog’s traits and those of its ancestors. Inbreeding will quickly identify the good and bad recessive genes the parents share in the offspring. Unless you have prior knowledge of what the pups of milder linebreedings on the common ancestors were like, you may be exposing your puppies (and puppy buyers) to extraordinary risk of genetic defects. In your matings, the inbreeding coefficient should only increase because you are specifically linebreeding (increasing the percentage of blood) to selected ancestors.

Don’t set too many goals in each generation, or your selective pressure for each goal will necessarily become weaker. Genetically complex or dominant traits should be addressed early in a long-range breeding plan, as they may take several generations to fix. Traits with major dominant genes become fixed more slowly, as the heterozygous (Aa) individuals in a breed will not be readily differentiated from the homozygous-dominant (AA) individuals. Desirable recessive traits can be fixed in one generation because individuals that show such characteristics are homozygous for the recessive genes. Dogs that breed true for numerous matings and generations should be preferentially selected for breeding stock. This prepotency is due to homozygosity of dominant (AA) and recessive (aa) genes.

If you linebreed and are not happy with what you have produced, breeding to a less related line immediately creates an outbred line and brings in new traits. Repeated outbreeding to attempt to dilute detrimental recessive genes is not a desirable method of genetic disease control. Recessive genes cannot be diluted; they are either present or not. Outbreeding carriers multiplies and further spreads the defective gene(s) in the gene pool. If a dog is a known carrier or has high carrier risk through pedigree analysis, it can be retired from breeding, and replaced with one or two quality offspring. Those offspring should be bred, and replaced with quality offspring of their own, with the hope of losing the defective gene.

Trying to develop your breeding program scientifically can be an arduous, but rewarding, endeavor. By taking the time to understand the types of breeding schemes available, you can concentrate on your goals towards producing a better dog.

Further Reading:

If you are interested in learning more about these subjects, consult the following books:

  • Abnormalities of Companion Animals: Analysis of Heritability
    C.W. Foley, J.F. Lasley, and G.D. Osweiler, Iowa State University Press, Ames, Iowa. 1979.
  • Genetics for Dog Breeders
    F.B. Hutt, W.H. Freeman Co, San Francisco, California. 1979.
  • Veterinary Genetics
    F. W. Nicholas, Clarendon Press, Oxford England. 1987.
  • Genetics for Dog Breeders
    R. Robinson, Pergamon Press, Oxford England. 1990.
  • Genetics of the Dog (equally applicable to cats & other animals)
    M.B. Willis, Howell Book House, New York, New York. 1989.

Dr. Bell is director of the Clinical Veterinary Genetics Course for the Tufts University School of Veterinary Medicine and national project administrator for numerous genetic disease control programs of pure-bred dogs. He performs genetic counseling through Veterinary Genetic Counseling and practices small animal medicine in Connecticut. He and his wife breed Gordon Setters. This article can be reprinted with the permission of Dr Bell (Jerold.Bell@tufts.edu)

Small Population Breeds and Issues of Genetic Diversity

bell-jerold-1520260577 By Jerold s Bell DVM, Clinical Associate Professor of Genetics, Tufts Cummings School of Veterinary Medicine.  Reprinted by permission of the author.

(This article was originally published in the March 2007 AKC Perspectives Delegates Newsletter.)

Issues of genetic diversity are a concern to dog breeders, and this can be especially so for breeds with small populations. The concern is whether there is enough genetic variation within a breed’s gene pool to maintain health and vitality. Breeders should be concerned about genetic diversity, because there are examples where damage has been done to a breed due to breeding practices. Restriction of genetic diversity can also occur in large population breeds.

All genes come in pairs: one from the sire and one from the dam. Each gene in the pair is called an allele. If both alleles in a pair are of the same type, the gene pair is homozygous. If the two alleles are different, the gene pair is heterozygous. While each dog can have a maximum of two different alleles at a gene pair, many different alleles are potentially available to be part of the gene pair. The greater the number of alleles that are available at each gene pair (called genetic polymorphism), the greater the genetic diversity of the breed.

If there is no breed diversity in a gene pair, but the particular homozygous gene that is present is not detrimental, there is no negative effect on breed health. The characteristics that make a breed reproduce true to its standard are, in fact, based on non-variable (that is, homozygous) gene pairs.

The origins of the breeds have a lot to do with genetic diversity. A breed established with a working phenotype tends to have diverse founder origins, and significant diversity. Even with substantial population bottlenecks, the breed can maintain considerable amounts of genetic diversity. This was shown in a molecular genetic study of the Chinook breed, which was reduced to 11 modern founders in 1981. Breeds established by inbreeding on a limited number of related founder individuals could have a reduced diversity. Many breeds have also gone through diversity reducing bottlenecks; such as occurred during World War II. For most of these breeds, their gene pools have expanded through breeding for many generations, resulting in a stable population of healthy dogs.

There are two factors that must be considered when evaluating genetic diversity and health issues in a breed; the average level of inbreeding, and detrimental recessive genes. With a small population, there is a tendency to find higher average inbreeding coefficients due to the relatedness between dogs from common ancestors. There is, however, no specific level or percentage of inbreeding that causes impaired health or vigor. The problems that inbreeding depression cause in purebred populations stem from the effects of deleterious recessive genes. If the founding population of a breed produces a high frequency of a deleterious recessive gene, then the breed will have issues with that disorder. This can be seen as smaller litter size, increased neonatal death, high frequency genetic disease, or impaired immunity. If these issues are present then the breed needs to seriously consider limited genetic diversity.

The issue of high average inbreeding coefficients is one that all breeds go through during their foundation. As the population increases and the average relatedness of dogs goes down (based on a fixed number of generations), the average inbreeding coefficient for the breed will go down. The effect of initially higher inbreeding coefficients in small population breeds will depend on the presence of deleterious recessive genes that will be expressed when homozygous.

Some breeders discourage linebreeding and promote outbreeding in an attempt to protect genetic diversity in their breed. It is not the type of matings utilized (linebreeding or outbreeding) that causes the loss of genes from a breed gene pool. Rather, loss of genes occurs through selection: the use and non-use of offspring. If a breed starts limiting their focus to breeding stock from a limited number of lines, then a loss of genetic diversity will occur.

The process of maintaining healthy lines, with many breeders crossing between lines and breeding back as they see fit, maintains diversity in the gene pool. If some breeders outbreed, and some linebreed to certain dogs that they favor while others linebreed to other dogs that they favor, then breedwide genetic diversity is maintained. It is the varied opinion of breeders as to what constitutes the ideal dog, and their selection of breeeding stock based on their opinions, that maintains breed diversity.

The most important factor for diminished genetic diversity in dog breeds is the popular sire syndrome. The overuse of a popular sire beyond a reasonable contribution through frequent breedings significantly skews the gene pool in this direction, and reduces the diversity of the gene pool. Any genes that he possesses – whether positive or negative – will increase in frequency. Through this founder’s effect, breed related genetic disease can occur. Another insidious effect of the popular sire syndrome is the loss of genetic contribution from quality, unrelated males who are not used for breeding. There is a finite number of quality bitches bred each year. If one male is used in an inordinate amount of matings, there will be fewer females left for these quality males that should be contributing to the gene pool. The popular sire syndrome is a significant factor in both populous breeds and breeds with small populations.

The best methods for ensuring the health and diversity of a breed’s gene pool are to:

  1. Avoid the popular sire syndrome.
  2. Utilize quality dogs from the breadth of your population to expand the gene pool.
  3. Monitor genetic health issues through regular health surveys.
  4. Do genetic testing for breed-related disorders.
  5. Participate in open health registries, such as CHIC (www.caninehealthinfo.org) to manage genetic disorders.

 

(This article can be reprinted with the written permission from the author: jerold.bell@tufts.edu)

Related article – Outcrossing Does Not Equal Gene Pool Diversity

Photograph courtesy of Susan Roy Nelson is not intended to illustrate any point in the article, it is presented for your viewing pleasure only.

 

Save

Outcrossing Does Not Equal Gene Pool Diversity

In previous articles we’ve talked about the shrinking population of the purebred dog and specifically about how much smaller the Gordon Setter population is today – over 70% fewer Gordons than twenty years ago. The current bottleneck in the number of Gordon Setters available for breeding calls for us, as responsible breeders, to evaluate each mating more carefully to determine if it will accomplish our own goals while also considering the impact our mating will have on the breed gene pool. As breeders in today’s world we are not only charged with improving the breed, we are also called upon to ensure that our breeding activity has a positive impact on the preservation of the breed gene pool.  The good news my friends, is that all of this can be less painful to accomplish than you might have thought.

For topics like this I call on experts for advice, and I am grateful to Jerold S. Bell DVM, Clinical Associate Professor of Genetics, Tufts Cummings School of Veterinary Medicine for the guidance he’s offering. Jerry’s article Small Population Breeds & Issues of Genetic Diversity is the resource used for this article and is quoted here, and reprinted entirely elsewhere on the blog with his permission. (Click the title above to link to that article.)

Has the Gordon Setter population reached a level where we should consider it a “small population breed”? Perhaps not, yet..who’s to say? The point here is that the population of the Gordon Setter has shrunk dramatically (Honey, I Shrunk the Kids!) and as it is now substantially smaller, breeders must be aware of how important our breeding choices become when viewed in terms of the health of our breed gene pool. Just as there are fewer Gordon Setters, so too are there far fewer breeders bearing the responsibility for their preservation. With fewer breeders we find that many of the older lines are harder if not impossible to find today.

Jerold S. Bell DVM –  *Issues of genetic diversity are a concern to dog breeders, and this can be especially so for breeds with small populations. The concern is whether there is enough genetic variation within a breed’s gene pool to maintain health and vitality. Breeders should be concerned about genetic diversity, because there are examples where damage has been done to a breed due to breeding practices. Restriction of genetic diversity can also occur in large population breeds.

Putting a lesson in genetics aside for another time, let’s talk today about genetic diversity in our breed gene pool.  Quoting Jerold S. Bell DVM  * There are two factors that must be considered when evaluating genetic diversity and health issues in a breed; the average level of inbreeding, and detrimental recessive genes. With a small population, there is a tendency to find higher average inbreeding coefficients due to the relatedness between dogs from common ancestors. There is, however, no specific level or percentage of inbreeding that causes impaired health or vigor. The problems that inbreeding depression cause in purebred populations stem from the effects of deleterious recessive genes. If the founding population of a breed produces a high frequency of a deleterious recessive gene, then the breed will have issues with that disorder. This can be seen as smaller litter size, increased neonatal death, high frequency genetic disease, or impaired immunity. If these issues are present then the breed needs to seriously consider limited genetic diversity. 

In this statement then, as a group of dedicated breeders, we find a key to issues or symptoms, whose frequency of expression within the breed need monitoring. An increase or spike in these symptoms throughout the breed population, that goes beyond normal expectations, should be a cue that breeders need to seriously consider if we are experiencing limited genetic diversity in our breed gene pool. As a group we must be willing to share our breeding experiences with a wide audience of our peers. Additionally, we must understand that GSCA Health and Genetics committee surveys are also a vital indicator of the breed health, especially as it pertains to breed gene pool diversity.

As we talk about gene pool diversity, we may find some breeders who discourage linebreeding and promote outcrossing (outbreeding) as the way to protect genetic diversity in the breed. While this does sound like an easy, and maybe even an obvious answer, outbreeding would not provide the complete solution.

Jerold S. Bell DVM – *It is not the type of matings utilized (linebreeding or outbreeding) that causes the loss of genes from a breed gene pool. Rather, loss of genes occurs through selection: the use and non-use of offspring. If a breed starts limiting their focus to breeding stock from a limited number of lines, then a loss of genetic diversity will occur.

The process of maintaining healthy lines, with many breeders crossing between lines and breeding back as they see fit, maintains diversity in the gene pool. If some breeders outbreed, and some linebreed to certain dogs that they favor while others linebreed to other dogs that they favor, then breedwide genetic diversity is maintained. It is the varied opinion of breeders as to what constitutes the ideal dog, and their selection of breeeding stock based on their opinions, that maintains breed diversity.

The most important factor for diminished genetic diversity in dog breeds is the popular sire syndrome. The overuse of a popular sire beyond a reasonable contribution through frequent breedings significantly skews the gene pool in this direction, and reduces the diversity of the gene pool. Any genes that he possesses – whether positive or negative – will increase in frequency. Through this founder’s effect, breed related genetic disease can occur. Another insidious effect of the popular sire syndrome is the loss of genetic contribution from quality, unrelated males who are not used for breeding. There is a finite number of quality bitches bred each year. If one male is used in an inordinate amount of matings, there will be fewer females left for these quality males that should be contributing to the gene pool. The popular sire syndrome is a significant factor in both populous breeds and breeds with small populations.

I believe as a whole, that Gordon Setter stud dog owners have worked hard to manage stud dogs properly to avoid the “popular sire syndrome”. This is not an easy task to manage as so many variables, including emotions come into play. Hats off to all who have kept a diligent and watchful eye on our breed through proper stud dog management.

As I look back at what Dr. Bell has written, I realize that our breed is fortunate to have had many breeders, both past and present, who have contributed much to preserve the Gordon Setter; sometimes they contributed matings that improved specific aspects of the breed and sometimes they contributed by using breeding practices that preserved genetic diversity. Moving forward, our breed needs us to continue to attract and mentor a diverse group of breeders who also possess an understanding of the principles of gene pool diversity. As we have seen, there is simply not one step or one action to preserve diversity, instead there is a collection of various actions, that when understood and followed by the individual breeder, with each breeder working alongside the many other breeders – it is when we work as a collective group that we accomplish that one common goal – preservation of the purebred Gordon Setter…oh, and don’t forget there is still improvement of the breed to consider!

Jerold S. Bell DVM writes:  *The best methods for ensuring the health and diversity of a breed’s gene pool are to:

  1. Avoid the popular sire syndrome.
  2. Utilize quality dogs from the breadth of your population to expand the gene pool. (as new genes cannot be added to a closed registry this refers to preserving genes that might otherwise be lost by selection of only a few sires out of the many available)
  3. Monitor genetic health issues through regular health surveys.
  4. Do genetic testing for breed-related disorders.
  5. Participate in open health registries, such as CHIC (www.caninehealthinfo.org) to manage genetic disorders.

Small Population Breeds & Issues of Genetic Diversity by Jerold S. Bell DVM

Photograph by Susan Roy Nelson shared for your viewing pleasure, is not intended to illustrate any point in the article.

 

 

 

 

Ruff-ly Speaking – Then and Now

If I were to tell you that by my ruff estimate

in 1955 there were approximately 1,407

AKC registered Gordon Setters of breeding age in the U.S.,  and by comparison

in 2015 that same population is only 796,

would you begin to understand why I believe that the time to take steps as a group to improve the odds of breed preservation is right now?

Here is how I arrived at the numbers:

The number of AKC Gordon Setter registrations for 1945 showed 265 new dogs registered, and ten years later in 1955 there were 375 new registrations. To obtain an estimated number of breeding age Gordons starting the year 1955, I assumed an average increase of eleven dogs each year from 1945 through 1954 for a total of 2,815 new Gordon Setters between the age of zero to ten years old who would have been in the breeding pool on January 1, 1955. For ease of calculation, I assumed all of the new dogs that were registered lived to be age ten, so more dogs are allowed in these estimates than were actually available as mortality isn’t factored. Going on, using the assumption that dogs under age two and over age eight would not be bred,  we would lose about half of the total ten year population which left us with 1,407 total dogs for use in our breeding pool at the start of 1955.

Fast forward to the last ten years, 2005 through 2015, and rounding the numbers there were approximately 825 new Gordon Setters registered in 2005 and 380 registered in 2015 for an average decrease of 44.5 dogs per year giving an estimated population of 6,248 dogs at the start of 2015 who are between the age of zero and ten years old. Again, as in the 1955 estimate, in this calculation we are going to exclude the dogs in that pool who are under two and over age eight, so 50% of the population is deleted bringing us down to 3,124 breeding age Gordon Setters. But here in the future, statistics published by the ASPCA* tell us that 83% of all household dogs are spayed or neutered so in 2015, unlike 1955, we must now subtract another percentage of our Gordon Setter population from the breeding pool as they are no longer fertile. I was generous with our Gordon Setter breeding population and only took 70% of the total away from our breeding pool because of spay/neuter which left us with 937 Gordon Setters to breed from. But wait, we aren’t done here in 2015, we also need to subtract dogs we delete from the pool due to the Health Screenings we apply, so another chunk of our breeding pool goes away, and for this calculation I said that 15% of the 937 remaining dogs would fail one test or another and thus be subtracted from the pool by their breeder/owners, leaving us with an estimated 796 Gordon Setters in the U.S. today who are fertile and available in a breeding pool. In case you missed it, let me just point out again, that number is 600 dogs fewer than our predecessors started with in 1955 after importing Gordon Setters in the post war era to improve and increase the U.S. breeding stock.

12417772_10209182845590502_5748115236916692300_n
Photograph by Susan Roy Nelson

Yes, this is a “ruff” estimate on my part, it takes the number of new registrations and uses certain assumptions to propose an estimated population. But I’ve not exaggerated any numbers or needlessly subtracted from the population. I believe this is a realistic estimate of the Gordon Setter breeding pool as it may have existed then and could exist today .

What does all this mean to breeders?

What does this mean to you? A few things need to come to the forefront to be managed, taught, and promoted by us. Now more than ever before we need breeders who are familiar with inbreeding as it pertains to genetics, and the meaning of maintaining diversity as best we can in an already heavily inbred population. Now more than ever before we need breeders who are open about the issues that arise in their litters that could be a result of genetic mutation. Now more than ever before we need to promote and market the purebred dog through social media and other free and open avenues that are affordable. Now more than ever we need to replace the concept of finding every pet at the local shelter with information about the value of finding a pet with the purebred’s predictability of size and temperament to start the list. It’s our job to take the purebred dog, for us the Gordon Setter, global with each of us taking responsibility for telling some part of the story, each of us taking responsibility for mentoring the new, each of us taking responsibility for the breeding pool and each of us understanding that the restrictions we’ve applied to ourselves as breeders, pertaining to pets and our concept of backyard breeders may need change with revisions in order so that we welcome newcomers into the fold to mentor and teach them about the joys of purebreds, the joys of breeding, and the meaning of health clearances. We need to learn how to tell the value in every dog as it pertains to our breeding pool, perhaps no longer limiting ourselves strictly to champions or top winners for example. I could go on, but I’ll stop here and let you all chime in with more “we need to” ideas.

If there is anyone who wants to debate my estimates, who can show me that I’m way off in some far, far fetched land, please do chime in to show where I’ve gone astray. I’d love to learn I’m wrong this particular time! (grin)

From the Institute of Canine Biology this link and these words of wisdom:

HOW POPULATION SIZE AFFECTS INBREEDING

While inbreeding has the beneficial effects of reducing variation in litters and increasing apparent prepotency of sires and dams, it also has the very undesirable effect of increasing the expression of genetic disorders caused by autosomal recessive genes.  So managing inbreeding in populations of animals is necessary for the control of genetic disease.

It’s not enough just to carefully choose the sire and dam of the next breeding.  For sustainable breeding over the longer term, inbreeding must be managed in the entire population, and often breeders don’t have a good understanding of the factors that affect rates of inbreeding.  One of the most important is the size of the population of animals.  Large populations change more slowly and are more predictable over time; small populations are genetically unstable because they are more sensitive to effects of chance and because change can occur very quickly.

Sally Gift, Mesa AZ

Photography by Susan Roy Nelson

*statistics on spay/neuter

 

Did Our Gene Pool Shrink (Again) in 2015?

In 2015 the number of AKC registered Gordon Setters continued it’s 20 year drop, down by another sixty dogs. Is there any end in sight to this trend, and are we seeing the first signs of extinction for some purebreds, including our own breed? In the last 20 years the Gordon Setter population has dropped by 71%. What is the impact to a breed like ours when 71% of their population is no longer available for breeding?

In the U.K., The Kennel Club considers the Gordon Setter as a “vulnerable” breed at only 234 registrations in 2015. I’m wondering how we should label the Gordon here in the states, considering that the population of the U.S.,  319 million, is nearly five times that of the U.K. at 64 million, but the U.S. Gordon Setter at 381 new registrations is only about one and a half times the 234 registrations in the U.K., a significantly smaller per capita number.

Could this mean that the breed is in an even more precarious and vulnerable position in the U.S.?

With this alarming decline in the breed’s population, if you’re breeding Gordon Setters there are a few things to consider as you go about planning new litters, and one of those considerations includes the need to develop a good understanding the of the gene pool and how your choices will impact preservation of the breed.

Your next litter is like a big fish in a small pond. As there fewer and fewer Gordon Setters whelped each year, the overall number of Gordon Setters available for breeding is dropping to an all time low, so litters that are born now will have a bigger impact on the future and preservation of the breed than the many litters that were born 20 years ago. Is it possible that we are losing genetic diversity in our breed population due to the decline in the overall number of new litters produced, and that our gene pool might also be shrinking? Unfortunately that answer may be Yes.

As breeders then, we need to ensure we have a basic understanding of genetic concepts and what it means to maintain genetic diversity. As our pool of fertile dogs continues to decline in number, the chance of finding unrelated genetically diverse dogs has fallen dramatically, which becomes especially relevant if we later find we need those dogs to help resolve a health issue from a newly recognized gene mutation.

Just as we pay attention to the need for health clearances when preparing for a litter, so too must we pay similar attention to understanding and analyzing the pedigrees of the resulting litter. Now is the time when we need to embrace the concept of preserving  offspring from the bloodlines of many various kennels and engage in preserving semen from healthy dogs of good quality, preserving many dogs of good quality from both show and field, not only those who are our top winners. Should we be doing more and more blending of the typical show and the field lines, or importing semen or dogs from other countries? These tactics and many more, now more than ever before need our attention, as breeders work to preserve the best qualities of our gorgeous breed, along with the diversity in our gene pool needed to safely continue the Gordon Setter in a healthy state.

With all that said, the following is an excellent article to get you started from The Institute of Canine Biology. It is a basic discussion about the gene pool. Today’s “Required Reading” for every Gordon Setter breeder I do believe!

What’s in the Gene Pool?

The founding of the breed – the Gene Pool

pool.jpgLet’s pretend these 11 dogs are the “founders” of your breed – they are the first dogs entered into the studbook.  All subsequent members of the breed are descended from these dogs only.  The breed has a closed gene pool.

All of the genetic variability that will ever exist in your new breed is present in these dogs.  Mutations probably won’t add new, useful genetic variation because most mutations are detrimental.  If the mutated gene is dominant and detrimental, it will likely be weeded out very quickly.  If the mutation is recessive, it is not expressed unless an animal is homozygous for the allele by inheriting a copy from each of its parents.  In the heterozygote condition, a mutated recessive allele can lurk in the genome for generations without ever causing a problem.  So, unless additional “founders” are added to the population at a later date, all of the genes you will ever have to work with in your breeding program are present in these dogs.

In each of these dogs there are at least a few (and perhaps many) recessive genes that could cause genetic disorders.  But these disorders will only expressed if a dog is homozygous for the disease allele – it must have TWO copies, one from each parent.  As long as the disease genes are rare in the population, very few animals will ever display the illness.

Can the gene pool get bigger? (No!)

Okay, starting with your 11 founder dogs, let’s let them reproduce.  To keep it simple, we will let them produce only identical copies of themselves – clones.

Now we have 27 dogs, all of which are exact copies of one of the founders.  What has happened to the size of the gene pool?

Nothing.pool1

You now have more dogs, and you now have more copies of the genes found in the dogs that had more offspring, like that busy gray dog with the red tongue.  So, the frequency of particular alleles is different in this population than in the founders, but the number of different alleles in the population is exactly the same.  (We’re ignoring the possibility of a mutation for now.)

What if the dogs reproduce normally instead of producing clones?  In sexual reproduction, each puppy receives one set of genes from each parent.  And, each puppy receives a different mix of parental genes, so each one is a bit different.  Also, each parent dog has a different number of offspring and might mate multiple times with different dogs.  So the frequency of the various alleles in the population could be very different in this new population than in the founders.

But again, even though there are now more dogs in the population, the gene pool does not get bigger.

In fact, it doesn’t matter how large this breed gets – it might someday grow to thousands of dogs – but as long as the stud book is closed, the gene pool will never be larger than it was when the breed is founded.

Can the gene pool get smaller?  (Yes!)

poo12The gene pool of a closed breed can never get bigger.  But it can get smaller.

What if dogs with black ears were less fertile, or had higher puppy mortality, or had some other biological problem?  The frequency in the population of the genes causing the black ears would be reduced by natural selection – black-eared dogs would contribute fewer copies of their genes to the next generation. Eventually, by genetic drift (chance) or natural selection, the genes in black-eared dogs would become rarer and rarer, and might eventually be eliminated from the population entirely.

What if breeders didn’t like black ears, so all the puppies with black ears were spayed or neutered and sent to pet homes?  Those alleles will become less frequent in the population, and they might be eliminated completely because of artificial selection courtesy of the breeder.

The gene pool gets smaller when genes are completely eliminated from the population.  It is unlikely that a gene will be restored by chance mutation, and the only other way it can be restored is if an animal is introduced into the breeding population that carries that gene and who reproduces successfully.

In purebred dogs, when the stud book is closed, no new alleles can be introduced into the breed.  The loss of an allele is permanent and reduces the heterozygosity in the genome for that gene.

http://www.instituteofcaninebiology.org/whats-in-the-gene-pool.html

Sally Gift, Mesa AZ

 

 

 

Save

Genetic Testing While Preserving the Best Breed Qualities – Let’s Start the Conversation

One of the most controversial topics, and the most difficult to teach about breeding, is the use of genetic testing and the application of those test results when choosing a mating pair to “improve and preserve the breed”. This is an area where it can often appear, especially to the less experienced breeder, that some prominent and successful breeders are talking out of both sides of our mouths. From one side we say genetic testing is a must if you intend to breed, and then from the other side we say “oh, but don’t throw the baby out with the bathwater” just because the dog is a carrier or affected doesn’t mean they shouldn’t be bred. Improving and preserving the Gordon Setter breed, is nowhere near as simple as choosing to mate only those dogs who pass every genetic clearance. Making the right breeding decision, finding the right sire for a dam… well it’s just not a black or white, right or wrong decision process. So, we’re going to say here, that the first and the most important thing a potential breeder needs to learn, before making breeding decisions, before assuming that the right choice is to breed only those dogs who clear every genetic test, the first thing that potential breeder needs to learn and completely understand is what constitutes a mediocre dog, a good dog and a great dog. With this understanding, one can then come prepared to recognize why, and when it is imperative to include great dogs in the gene pool – and yes, even those good and great dogs who did not clear every genetic hurdle may be needed in that gene pool. Remember, these dogs have many other qualities that are vital to preserving and improving the breed.

Photo by Bob Segal
Photo by Bob Segal

I read an article by Brian Lynn published by Paw Print Genetics that spoke about this topic. I’m sharing Brian’s article here as it fits with what I wanted us to be thinking, learning and talking about…how to use genetic testing appropriately, especially at a time when we must always consider the shrinking size of our breed population and thus our gene pool. We do need to encourage and promote genetic testing. We do NOT need to eliminate every dog who is affected or a carrier, but we do need to aptly apply the judicious choice of the appropriate breed qualities in the dogs we chose to breed. Breeders also need to be able to share every genetic test result on every dog, and they should be able to do so without fear of censor by their peers. The behaviors that cause our breed harm…breeders who cover or omit negative test results…and breeder/exhibitors who gossip about or denounce their peers who have shared information honestly and freely. Compete in the ring with each other folks, we don’t need to compete with each other over breeding choices, stud services and the like, there simply aren’t enough of us left to be that cut throat toward each other.

“When we breed to better a line of purebred dogs, many intangible or subjective variables come into play – conformation, athleticism, intelligence, trainability and more. Mentoring and experience, even the gut instinct borne from these teachings, can make assessing those variables easier. As we learn more and develop an eye for evaluating and reading dogs, the standards for what constitutes a ‘better’ dog, one worthy of breeding, usually rise. The comparative knowledge experience brings allows us to differentiate a ‘great dog’ from a ‘good’ one; what might have been an acceptable to us a decade ago, might not make the cut today. And therein creates the economic correlation of supply and demand among top breeders.

As we eliminate potential breeding partners in favor of ‘better’ dogs, those that will truly improve a line and therefore breed, fewer and fewer potential partners exist. That makes the remaining pool of dogs more desirable and valuable.

When the qualities that elevated a dog to the top of the gene pool are combined with the objective results of canine genetic screening, a breeder is truly ‘bettering the breed’ by passing along the best physical and mental qualities the dog possesses while reducing or eliminating detrimental genes.

However, some people believe genetic testing poses the risk of reducing the gene pool of quality dogs too much. Certainly, if you were to remove every dog that was determined to be an affected or a carrier of an inherited disease, that upper echelon of dogs within a breed could theoretically bottleneck (especially if it’s a small gene pool to begin with); and/or leave dogs that don’t complement and strengthen each other consistently enough to better the breed across necessary qualities, regardless of genetic diversity. True, the knowledge of genetic mutations in two dogs could prevent a top-notch breeding from taking place, but in the big picture of bettering a line and breed, that’s a small concession.

But that’s not how genetic screening works. Genetic screening of canines for inherited diseases provides the knowledge to breed responsibly and with scientific evidence. Breeding to a carrier, or especially affected, dog is a personal decision each of us must weigh, but it can be done safely. Using genetic science, we can determine the mode of inheritance, as well as the variability and expressivity of a gene. With the knowledge of today’s science, we can breed smarter and safer than ever before.

Genetic screening makes a dog a known quantity. Combined with its physical, mental and psychological qualities, genetic screening allows for healthier decision-making choices that truly ‘better the breed.’ The fact that a dog is a known quantity in a gene pool makes it more valuable; a dog’s accomplishments set it apart from the general population, and genetic screening, regardless of results, put it in an even more elite pool of dogs.” read more here

So, this is where the conversation turns to you. I’ve said my small piece and offered food for thought through Brian’s article. Time for you all to join in here and share your thoughts, opinions and questions.

Photographs by Bob Segal

Sally Gift, Mesa AZ

Save

Population Analysis of the Gordon Setter – Genetic status of purebred dogs in the UK

Many thanks to Jerry Nelson for sharing these links with us on our Facebook group Gordon Setters Students and Mentors. They are directly related to the genetic consequences that can arise from the decline in the Gordon Setter population here in the U.S., and though we do not have a similar study/review underway in the U.S. (that I am aware of – remember how  I said we are behind the eight ball on this issue?) we can certainly use these publications to gain an understanding of what’s at stake and the importance of the issue and our response to it..  My hat is off to the UK for this valuable information. Thank You!

To read the very important “The Kennel Club” report ” Population analysis of the Gordon Setter Breed published September 2015 click the bold title.

Photo of Mista by Susan Roy Nelson

Sally Gift, Mesa AZ

Genetic status of purebred dogs in the UK – The Institute of Canine Biology.

By Carol Beuchat PhD

Just published today in Canine Genetics and Epidemiology is a study of the population statistics and genetic diversity of all 215 breeds registered by the Kennel Club, using data from the pedigree database from 1980-2014. The paper is a welcome addition to the literature, updating and eclipsing the earlier (and epic at the time) study by Calboli et al in 2008.

If you’ve been wondering if you should take a course in population genetics, this paper will convince you. (Check out the courses that ICB offers here.) The health of the dogs we breed depends fundamentally on the quality of the gene pool, and assessments of the genetic health of the gene pool are necessarily based on population-wide analyses. So there is much here about effective population size (Ne), which is determined by the rate of change in the average level of inbreeding in the population.

At the core of the paper are data for inbreeding over the years since 1980. Unfortunately, the data for individual breeds are not in the paper, or even in the supplementary documents available from the publisher (where they would be available in perpetuity), but instead are available as individual pdf documents on the Kennel Club website. If the address to that web page should ever change (and surely it will), the link published in the manuscript will be useless. So, download your favorite breed now, just to be safe.

Summarizing their findings about inbreeding, they say:

“The trend over all breeds was for the rate of inbreeding to be highest in the 1980s and 1990s, tending to decline after 2000…to sustainable levels, with some modest restoration of genetic diversity in some cases.”

While there are breeds in which inbreeding does stabilize (e.g., the Labrador Retriever; figure on the right), it is certainly not the case that this is a general pattern across all breeds.

Picture

LABRADOR RETRIEVER
Below are some examples of breeds in which inbreeding doesn’t stabilize after 2000, but increases continuously over the period of the study. Perhaps these are breeds that didn’t benefit from a surge in imports after 2000 (wish we could see the data for imports), but there is no evidence that breeders have been adjusting breeding strategies to reduce the level of inbreeding. If that was happening, it would be evident in the distance between the observed and expected inbreeding lines in these graphs. The expected level of inbreeding assumes that breeding is random; the higher observed level indicates that the animals being bred together that are more closely related than the population average. This also indicates the potential magnitude of the reduction in inbreeding that could be achieved by a change in breeding strategy.

Average inbreeding coefficient over 1980-2014
Upper: English Cocker (left), English Springer (right)
Lower: Akita (left) , Bull Terrier (right)

Picture

English Cocker

Picture

English Springer

Picture

Akita

Picture

Bull Terrier

As I noted above, the effective population size (Ne) is determined by the rate of inbreeding in the population. The rule of thumb used by conservation biologists as the minimum Ne necessary to maintain a sustainably breeding population has risen over the last few years from 50 unrelated, randomly breeding animals to 100, and even more recently 500, as biologists reassess the realities of both in situ and captive animal management (you can read about the latest argument over revision here). That aside, it is useful to look at some of the data on Ne from the present study.

Below I have graphed the data for Ne (from the Supplementary documents) for those breeds in which there were more than 50 registrations per year; that is, the more populous breeds. I have superimposed lines at Ne = 50 (red), Ne = 100 (yellow), and Ne = 500 (green), to correspond with the various rules of thumb under debate.

Download a larger version of this figure:

Ne by breed.png

Download File



If we wanted to conservatively go with the minimum Ne of 500, only 2 breeds would make the grade, and only about half of the breeds with registrations higher than 50/year would make the Ne = 100 cutoff. There are a good number of breeds for which Ne is <50 on this graph, and I haven’t looked at it yet but I would wager that the majority of breeds with fewer than 50 registrations per year will be below the red line as well. (If there were 50 dogs in the population, half male and half female, and all animals bred, the Ne would be 50. Breeds with fewer than 50 registrations per year would be cutting it mighty close.)
There is much more that could have been done with the data available to the authors than they presented in the paper and supplements. Just for fun, I have pulled the data for Labrador Retrievers from the paper and supplements and (quickly) put together some graphs that might be useful for breeders. (Similar analyses can be done for the other breeds on request.)
For instance, below is a graph of the fraction of puppies produced each year by top-ranking sires. You can see that about 30% of the pups born yearly were produced by only the top 5% of sires.
The impact of top-ranked popular sires is even more obvious in this figure of the maximum number of pups produced by a single sire in a year compared to the population average. Note that the y axis is logged, otherwise the data for the averages would all be to low to see.

(You can see more of the analyses of the Labrador data here.)

I would have to say that, after a few hours of fiddling with the available data, the paper’s summary is rosier than the actual picture. The statement that levels of inbreeding are looking much better since 2000 is quite misleading – it could simply be an artifact of the importation of unrelated dogs, and there are plenty of breeds in which the rate of inbreeding has stayed on the same trajectory for decades and could very well continue. The number of breeds with effective population sizes well into the danger zone should be a heads up for breeders, especially in those breeds that could increase Ne with the simple strategy of breeding a larger fraction of available dogs and balancing the ratio of males to females (as I discuss here).

The caveat here is that these data are for an artificial population – the dogs registered with The Kennel Club. Before 2000, it was effectively a closed population, and since then has the addition of imports with only 3 generations of pedigree information, which makes them appear in analyses like this to be new, unrelated founders. At least The Kennel Club should be congratulated for including geneticists on their staff who have access to the pedigree data and the expertise necessary for these analyses. What a pity that the AKC does not do the same.

You can read The Kennel Club’s press release about the study here.

The Power of the Breeding is in the Dam

17914667639_a238b6ba9c_k
Photo by Bob Segal from 2015 GSCA National Specialty

I’m picturing a long time friend of mine who is sitting at home reading this, nodding her head while silently cheering me on as we’ve always shared a common thought about dog breeding…”the power of the breeding is in the quality of the dam“. Oh, we’re not the first to say or believe this, and we won’t be the last, but if there is one thing that has been of the most value to me, it has been this guiding principle.

Does the bitch carry a sort of magical sauce that causes her contribution to a litter to be greater than that of the dog? If so, what is that sauce, how does it work? I don’t have a black and white answer for you, but I do have some reading to share, it is interesting, enlightening, and who knows, maybe it’s the start to proving what our gut instinct has been telling us, that the bitch genes carry more influence, that she contributes more to the litter than her half of the genes and what she gives through her nurturing.

Here is the first of the links for you, an article titled GENETIC X FACTOR SHARED written by Master Breeder, Barbara “BJ” Andrews. It’s a fast, easy read that shares great points. All you have to do is point your little cursor at the colored title, click, and a new page will open for you! Oh, you will have to do your own reading, sorry it’s not an audio book!

18096800602_c259fb6832_k
Photo by Bob Segal from the 2015 GSCA National Specialty

Barbara Andrews refers to information that is coming from the Thoroughbred industry and I have an article or two from them to share with you as well. The first is this (just point and click, you know the routine) Maternal Influences Make a Difference | BloodHorse.com.

The next link is to the actual abstract that founded the article Potential role of maternal lineage in thoroughbred breeding strategy

If I were here to simply offer advice it would be that, to be successful breeding dogs you must always maintain focus on the quality of the bitch you put in your whelping box. But, this is not new advice, it is ages old and comes from the experience of many wise men practicing long before me. Yes, the stud dog you choose is important, very important, but I believe that as the study of genetics moves ever deeper there may some day be scientific evidence to prove that the power of the breeding is in truly the dam.

18575025092_b26c6c09cb_k
Photo by Bob Segal from the 2015 GSCA National Specialty

Sally Gift, Mesa AZ