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I. Basic Concepts

by John Armstrong



Most of you are undoubtedly aware that color and certain diseases such as progressive retinal atrophy (PRA) are inherited  that is, passed down from one or both the parents. However, you may wonder how a trait that does not appear in the dam's pedigree can suddenly turn up in a litter out of Ch. Jacob Hugelsberg. Is it inherited or just an accident? Surely, Jake has been used so often that someone would have noticed if the problem came from him.

Just how much of a role does genetics play in health, general conformation and temperament? Probably, you would like to know exactly what traits are inherited; but, once someone starts talking about "partial dominance" or "expressivity," you get glassy-eyed. The objective of this guide is to explain some of the basics of inheritance and how to use these concepts to breed healthier dogs — hopefully without losing you in complex technical jargon.

What Traits (or Characteristics) Are Inherited?

The answer is "almost all," from temperament to size and coloring, as well as genetic diseases like progressive retinal atrophy (PRA). Infectious diseases are not inherited, though the susceptibility to them may be, to a greater or lesser extent.

The occurrence of any particular characteristic depends on two factors: genetics and the environment. "Genetics" refers to the encoded information (instructions) controlling all biological processes that are carried within the cells of all living organisms. These encoded instructions are responsible not only for maintaining the continuity of a species (or breed), but also for many of the differences between individuals within a species or breed.

The environment also contributes to the differences between individuals. The relative contribution of genetics and environment is not the same for every trait. Some traits, such as color, are influenced very little by the environment. For others, such as temperament, the effect of the environment is much greater. Geneticists use the term heritability to indicate the proportion of the total possible variability in a trait that is genetic. However, when genetic differences are not the main source of variability, the heritability of a trait may be difficult to establish and may not be the same for different breeds. Therefore, I cannot tell you that the heritability of size, for example, is 70% (or whatever it may be).

Before moving on to a more detailed discussion of genetics, I would like to take a brief look at what is meant by "environment," in the present context. For a puppy, the first environment it encounters is that of the mother's womb. Is the mother well nourished, healthy, and free from stress? How old is she? Is this her first litter? How big is the litter? Once the puppy is born, it experiences a new environment, where it has to compete for food and attention. Litter size is still a factor. How much food does the puppy get? How much attention does it get from the mother, the breeder, and the eventual owner? Does it have a safe and healthy environment? Does it have other dogs to associate with? The answers to these questions define, in part, the puppy's environment.


The gene is often called the basic unit of inheritance. A gene carries the information for a single step in a biological process; but most biological processes — even the ones that may appear to be simple — are made up of more than one step. Thus, one should not get the idea that a trait is determined by a single gene, but rather that the general rule is that many genes control a single trait. A good example is color. In some breeds, such as the Poodle and the Borzoi, there are a great variety of colors, so it should come as no surprise that this is the result of the action of a variety of genes. There are not only genes for making the different colored pigments, but also genes which control the distribution of the pigments, both within the individual hairs and over the entire body. (Other breeds may come in only one color. They have the same genes, but only a single allele of each.)

All animals have thousands of genes, but they do not float around loose in the cells. To make cell division and reproduction more manageable, genes are physically connected to other genes to form chromosomes. Most "higher" animals have two sets of chromosomes: one set from the mother and the other set from the father. So that the number of sets does not keep increasing from one generation to the next, sperm and eggs get only one set each. However, the mechanisms that assure this are not able to tell which chromosomes came from the mother and which from the father. Therefore, the set that is passed on in a particular egg or sperm is a mixed set. The number of possibilities depends on the number of chromosomes. Since dogs have 39 chromosomes in a set, the number of possible combinations is well over one billion! Therefore, the possibility of getting two litter-mates that have exactly the same combination of chromosomes is extremely remote. (Incidentally, wolves also have 39 chromosomes in a set and can breed with domestic dogs. Foxes, however, have only 19 chromosomes and cannot.)

One of the 39 chromosomes carries genes that determine sex. In mammals, the chromosomes carrying the "female" genes is designated X and the one carrying the "male" genes is designated Y. An animal with two X chromosomes will be a female, while one with an X and a Y will be a male. (One with two Ys will be in serious trouble!) Genes other than those determining sex are also located on these chromosomes and are said to be sex-linked.

...and Alleles

Most genes carry out their functions correctly, but some are altered by exposure to radiation (natural or man-made), certain chemicals, or even by accident when a cell divides. A gene may be thought of as a small program. There are many possible places in the program where an error (mutation) might be introduced. Many of these will have the same effect: the program will not function. Others may modify the action of the program. Some may appear not to affect the program at all. Since the latter produce no observable effect, we need not worry about them. All, however, regardless of their effect, change the information carried in the program, so that, strictly speaking, each is a different version of that program. In genetics we call each version an allele. Technically, different versions, even if they produce the same effect, are different alleles; but we generally only worry about the ones that produce different effects, and we simply treat those that produce the same effect as though they were the same.

Though there are potentially a large number of alleles for each gene, by far the most common are those that prevent function entirely. Therefore, for many genes we only find the normal allele, often called the wild-type, and "no-function" (null) alleles. For some genes, we also get alleles that function partially or abnormally. However, no matter how many alleles there are in a population, an individual can carry only two — one from the sire and one from the dam. When the two alleles are the same, the individual is said to be homozygous for that gene. When the alleles are different, it is heterozygous.

Naming Genes

There are rules for naming genes — unfortunately, not all geneticists use the same system. The one I will use here is common, but not universal.

A gene is named for the first mutant allele discovered. For example, in the fruit fly (Drosophila), which normally has dark reddish-brown eyes, a mutant with white eyes was discovered many years ago. Consequently, the particular gene in which this mutation occurred is called "white" and given the symbol w. The mutant allele is designated w (notice that it is italicized), and the wild-type allele is designated w+. Another mutation, discovered later, has light yellowish-brown eyes and is called "eosin." However, it is also an allele of the same gene and is, therefore, not given a different letter designation. Instead, it is designated we. (This system reserves capital letter designations for dominant mutant alleles.)

The alternative system that you will more likely encounter is very similar, except we don't use a + sign to designate the wild-type allele. This can introduce an element of confusion. For example, gray coat color is not considered the normal (wild-type) color in Poodles. However, as it is dominant, it is given the symbol G, while the wild-type allele is g.

The naming of genes can also be eccentric. The dilute gene results in a lightening of the basic color and, appropriately, is designated D. A second gene has a similar effect, and is called C (for color). However, the best known mutant allele of this gene is the one that results in albinos, so the gene really should be called A — but this designation had already been used for agouti.


If, for a particular gene, the two alleles carried by an individual are not the same, will one predominate? Because mutant alleles often result in a loss of function (null alleles), an individual carrying only one such allele will generally also have a normal (wild-type) allele for the same gene, and that single normal copy will often be sufficient to maintain normal function. As an analogy, let us imagine that we are building a brick wall, but that one of our two usual suppliers is on strike. As long as the remaining supplier can supply us with enough bricks, we can still build our wall. Geneticists call this phenomenon, where one gene can still provide the normal function usually met by two, dominance. The normal allele is said to be dominant over the abnormal allele. (The other way of saying this is that the abnormal allele is recessive to the normal one.)

When someone speaks of a genetic abnormality being "carried" by an individual or line, they mean that a mutant gene is there, but it is recessive. Unless we have some sophisticated test for the gene itself, we cannot tell just by looking at the carrier that it is any different from an individual with two normal copies of the gene. Unfortunately, lacking such a test, the carrier will go undetected and inevitably pass the mutant allele to some of its progeny. Every individual, be it man, mouse or dog, carries a few such dark secrets in its genetic closet. However, we all have thousands of different genes for many different functions, and as long as these abnormalities are rare, the probability that two unrelated individuals carrying the same abnormality will meet (and mate) is low.

Sometimes individuals with only a single normal allele will have an "intermediate" phenotype. (For example, in Basenjis carrying one allele for pyruvate kinase deficiency, the average life-span of a red blood cell is 12 days, intermediate between the normal average of 16 days and the average 6.5 days in a dog with two abnormal alleles. Though often termed partial dominance, in this case it would be preferable to say there is no dominance.

To carry our brick wall analogy a bit further, what if the single supply of bricks is not sufficient? We will end up with a wall that is lower (or shorter). Will this matter? It depends on what we're trying to do with the "wall" and, possibly, on non-genetic factors. The result may not be the same even for two individuals that have built the same wall. (A low wall may keep out a small flood, but not a deluge!) If there is the possibility that an individual carrying only one copy of an abnormal allele will show an abnormal phenotype, that allele should be regarded as dominant. Its failure to always do so is covered by the term penetrance.

A third possibility is that one of the suppliers sends us substandard bricks. Not realizing this, we go ahead and build the wall anyway, but it falls down. We might say that the defective bricks are dominant. Advances in the understanding of several dominant genetic diseases in man suggest that this is a reasonable analogy. Dominant mutations usually affect proteins that are components of larger macromolecular complexes. These mutations lead to altered proteins that do not interact properly with other components, leading to malfunction of the entire complex. However, some dominant mutations undoubtedly produce their effects in other, poorly-understood ways.

Dominant mutations may persist in populations if the problems they cause are subtle, not always expressed (see below), or occur later in life, after an affected individual has reproduced.

Expressivity and Penetrance

For a breeder, understanding the inheritance of a trait that is controlled by several genes and influenced by the environment can be a nightmare. Suppose, for example, that you are trying to breed apricot Poodles, but instead of getting only a single shade, your litters always have a variety of shades from pale to dark apricot. You might blame it on variable expressivity, which is just a convenient way of saying that you don't know what other genes or environmental factors are also playing a role in determining the color.

One of the classic examples of this in dogs is the variable expression of piebald spotting in beagles shown in Little (1957). The dogs all have the same Sp allele, but the colors range from black-and-tan with white feet to predominantly white with a few black spots.

Penetrance is a similar term-of-convenience (euphemism). If you are 99+ % certain that Fido carries the allele for six toes (because both his parents and all his sibs have six toes), but Fido has the normal five toes, you blame it on incomplete penetrance, try to look authoritative, and hope that no one asks additional questions. [Actually, it would probably be safer just to say that the trait is not always expressed and avoid possible embarrassment.]

The difference between expressivity and penetrance is that with the former, the trait is expressed to a variable extent, while with the latter it may or may not be expressed even though the genetic makeup (genotype) of the animal suggests that it should be.

Sex Linkage

In dogs, as in most animals, sex is determined genetically, but not by a single gene. One of the 39 chromosome pairs is used especially for sex determination. The unusual feature of this system is that the female-determining chromosome, called the X chromosome, doesn't even look like the male-determining Y chromosome — though they are still considered a "pair" and are referred to as the sex chromosomes. (The other 38 are called autosomes.) As everyone likely already knows, females have two X chromosomes and males one X and one Y. The male normally produces an equal number of sperm carrying either the X or the Y chromosome. As his mate will be producing eggs carrying only X chromosomes, an equal number of female (XX) and male (XY) puppies should be produced. Of course, chance plays a major role and litters often don't have a perfect 1:1 ratio.

Mutations undoubtedly occur in genes that control the development and function of the ovaries, testes, and other reproductive organs, but few have been described, probably because disruption of the normal reproductive process results in infertility. However, there are also genes found on the sex chromosomes that have nothing to do with sex determination. Those found on the X chromosome have no equivalents on the Y chromosome. As a result, males have only one copy of these genes. (Since the terms "homozygous" and "heterozygous" apply only when there are two copies, this situation is given a special name: hemizygous.)

When mutations occur in these X-linked genes, the pattern of transmission of the mutant phenotype differs from that seen for an autosomal gene. If a female carries such a trait, she will not express it (as long as it is recessive), but she will pass the trait to half her sons, and as they receive no X chromosome from their father, it doesn't matter what his genotype is — half will be affected. Half the daughters will be carriers, but as these are recessive traits, these carrier daughters will not be affected. If the problem does not affect survival and reproduction, an affected male may pass the gene on to his progeny — but only to his daughters, as his sons will get his Y chromosome, which doesn't have a copy of the gene.

In humans, good examples of sex linkage are red-green color blindness and hemophilia. I have been unable to find an example in the dog. Von Willebrands disease (vWD), a form of hemophilia, is not equivalent to the human X-linked hemophilia and follows a normal autosomal pattern of inheritance.

There are also traits that are sex-influenced, which means that their expression is influenced by the individual's sex. This does not imply that the gene is sex-linked. A human example is pattern baldness. The gene's expression is influenced by hormonal levels and only one copy of the baldness allele is sufficient to cause baldness in a man, whereas two copies are needed in a woman. In effect, it behaves as a dominant in males and as a recessive in females. Though half the sons of a female carrier will be affected, a heterozygous male will also pass the trait to half his sons.

Thus, any trait that appears more frequently in males than females is suspect as either sex-linked or sex-influenced. If it is passed from the father or the mother to half the sons, it is likely sex-influenced. If it seems to skip a generation and the pattern is grandfather to grandson, it is likely sex-linked.

Determining the Mode of Inheritance

Suppose that you have a litter in which several of the puppies appear to be less healthy than their litter-mates. Suppose that after a few weeks it is readily apparent that they are growing more slowly and appear less energetic. What do you do? Obviously, the first step is take them to your vet for examination.

Without going into details (as this is a hypothetical example), let us suppose that, after appropriate tests, he concludes that they have a hole in the septum between the two sides of the heart that is resulting in a mixing of oxygenated and de-oxygenated blood. Quite aside from any considerations about putting down the affected pups, the question remains: what caused the problem? Was it simply a developmental accident, an environmentally-induced condition, or is it genetic? [I have deliberately picked a condition that may arise for any of these reasons.]

As a rule-of-thumb, if only a single pup is affected, the problem has not turned up before in related litters, and the problem does not occur frequently in the breed, it is likely a developmental accident. Nevertheless, given the usual under-reporting of health problems, especially those that may be genetic, a second litter between the same sire and dam might be warranted.

On the other hand, if all — or even the majority — of the pups were affected, one might be more inclined to look for something in the environment that could have perturbed the normal developmental process. The majority of genetic abnormalities are recessive and, under normal circumstances, the parents are unlikely to be affected (i.e., homozygous). Therefore, if the problem is a genetic one, it is more likely that the parents will be phenotypically normal carriers (i.e., heterozygous), and the expectation is that one-quarter of the progeny will be affected.

While this is important to keep in mind, obtaining a proportion of affected pups in a litter that is substantially lower or higher than one-quarter is no guarantee that the problem is not genetic. Even the larger breeds produce litters of only eight or so, so you would expect only two to be affected. One or three affected would not be considered unusual, and even getting none affected is not considered sufficiently improbable to alarm a geneticist. You might well get no affected pups in one litter and four affected pups in the next!

Dominant mutations having a significant impact on health will, in most cases, result in death before reproductive age is reached. There are exceptions, such as Huntington's Disease in humans. Any late-onset genetic disease, whether dominant or recessive, represents a potential problem. At least with a dominant, you can wait for the progeny to reach an age where the problem would normally have developed, then breed unaffected animals with reasonable assurance that they are not undetected carriers. For example, if the inherited condition develops at six or seven years, you can wait until the dog is three or four years old before breeding it, then not breed any of the progeny until the parents reach seven or eight years of age.

For a dominant mutation that is rare, most crosses will be between a heterozygous affected individual (Aa) and a normal one (aa). The expectation is that one-half the progeny will be Aa. Should both parents be Aa, one-quarter of the progeny will be aa (normal) and three-quarters either Aa or AA. Sometimes, the AA progeny will be affected more severely, or even die before birth.

Doing the necessary crosses to establish the mode of inheritance can be an expensive and time-consuming task, to which is added the thankless prospect of putting down sick puppies and finding pet homes for the remainder. Consequently, test matings are seldom done on a scale sufficient to produce numbers that can be subjected to statistical analysis. [One notable exception is the monumental study by Bourns on day-blindness in Alaskan Malamutes.]

One alternative to test matings is retrospective analysis of the pedigrees of affected animals. As one generally needs a number of related animals occurring over several generations, the problem will likely already have become fairly common. The accuracy of such analyses is directly affected by the number of relatives for which data exists—a strong argument for the open exchange of information between owners, breeders, veterinarians, and researchers.

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Little, C.C. "The Inheritance of Coat Color in Dogs", Howell, New York, 1957.

Willis, M.B. "Genetics of the Dog", Whitherby, London, 1989.

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The term wild-type literally means the most common type found in the wild. In a Samoyed, it would be the color white. In a Poodle, it would be black. Though we usually equate "wild-type" with "normal," and a white Samoyed is certainly normal for the breed, Samoyeds nevertheless have a genetic deficiency in pigmentation.

Actually, we should not be saying that the allele functions abnormally. The allele carries the wrong information. The consequence of that information being used results in an abnormal functioning of some process.

Agouti is a sort of mottled brown color not seen in most dog breeds. Geneticists try to be consistent in their naming of genes and don't use different symbols for different species, providing the genes are known to have the same action.

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II. Breeding Schemes

by John Armstrong


Breeders often talk about inbreeding and outcrossing as though they were the only possibilities -- and generally with negative comments about the latter. There are other possibilities, and I have long been a proponent of assortative mating. It is not a theoretical concept that doesn't work in practice; I know several breeders who do it and achieve good results. This essay will attempt to explain why it is a good idea, but first I need to define the alternatives.

Random Mating

Though random mating is not a common breeding practice, understanding what this implies is important. Random mating is exactly what the name implies: mates are chosen with no regard for similarity or relatedness. (If the population is inbred to some extent, randomly-selected mates may be related.)

Random mating is one of the assumptions behind the Hardy-Weinberg formula, which allows one to calculate the frequency of heterozygous carriers from the frequency of individuals expressing some recessive trait in a population. Because inbreeding among purebred dogs and in other small populations decreases the frequency of heterozygotes, these estimates may be higher than the actual incidence.

Inbreeding and Linebreeding

Inbreeding is the practice of breeding two animals that are related (i.e., have one or more common ancestors). The degree of inbreeding may be assigned a value between 0 and 1, called the inbreeding coefficient, where 0 indicates that the animals have no common ancestors. Because the number of ancestors potentially doubles with every generation you go back in a pedigree, you eventually get to a point, even in a very large population, where there are simply not enough ancestors. Thus, all populations are inbred to some degree, and a true outcross (the term generally used when two animals are "unrelated") is not really possible. The term is generally misused to describe a cross between two animals with different phenotypes.

In a population with a limited number of founders, a maximum number of ancestors -- the effective population size -- is reached in some past generation. This number will be governed by various factors, such as the total population size, how far individuals travel during their lifetime, and whether there are inbreeding taboos or other mechanisms that reduce the likelihood of close relatives mating.

Inbreeding, by itself, does not lead to a change in allele frequencies, but does increase the proportion of homozygotes. Thus, in the absence of other practices, inbreeding will lead to a higher proportion of individuals homozygous for deleterious genes, and these are likely to be removed from the breeding pool by natural selection (if they do not survive to reproductive age) or by man.

Linebreeding is merely a term used for a particular type of inbreeding that often focusses on one ancestor who was considered exceptional. Particularly if it is a male, this exceptional ancestor may end up as grandfather and great-grandfather -- sometimes more than once -- in the same pedigree. Father-daughter, mother-son, and some other combinations also result in a disproportionate number of genes coming from a single ancestor. This type of close inbreeding is less common. [In contrast, the mating of full sibs or first cousins doubles up on two ancestors equally.]

As the result of several common practices, most pure-bred domestic animals are more inbred than they really need to be. One is that some breeders own a small number of animals and breed only within their own group. A second is that many breeders have the idea that outstanding animals can be produced by inbreeding -- by doubling up on the good alleles while somehow avoiding the bad. Even if you were to point out that this is a gamble, such breeders might respond that they are simply helping natural selection.

Beyond the conventional close-relative inbreeding, there is another practice that has much the same effect, namely the popular sire phenomenon (generally over-use of a well-promoted champion). In fact, many who breed to such a dog believe they are doing a "good thing," as they will be increasing the frequency of occurrence of the genes that made him a champion. What they may not realize is that they are increasing the frequency of all genes carried by this animal -- whether they are good, bad, or innocuous -- and that champions, like any other animal, carry a number of undesirable recessive alleles that are masked by wild-type alleles. The result of the popular sire phenomenon is that almost all members of the breed will carry a little bit of Jake Hugelberg, and any undesirable trait carried by Jake will no longer be rare. Finding a safe, unrelated mate then becomes an exercise in futility.

If we lived in a world where all the genes followed the simple rule that there may only be good alleles, which are dominant, and bad alleles, which are recessive, then inbreeding could be an effective tool for improving a breed, providing the latter were rare. (See, however, genetic load.)

Unfortunately, geneticists discovered, fairly early in the game, that there are also alleles that could be described as fair or poor. (They are generally ones that retain a portion of their normal function.) Suppose we have a "mutant" allele that has lost only one-fourth of its normal function. In many cases, this would not even have a noticeable effect. If you made an individual homozygous for this allele, you would not even be aware that you had done so. Now consider that the same fate may befall a number of genes during an inbreeding program. Eventually, you will have an individual that is considerably less fit than one carrying the normal alleles for all (or even most of) these genes. There is no magic formula for regaining what you have lost. You must start again.

[Sometimes mutant alleles result in an even more dramatic loss of function, but remain undiscovered under normal conditions. A good example is vWD in Dobermans.]

About the only animals that are routinely inbred to a high level are laboratory mice and rats. There, the breeders start breeding many lines simultaneously in the expectation that the majority will die out or will suffer significant inbreeding depression, which generally means that they are smaller, produce fewer offspring, are more susceptible to disease, and have a shorter average lifespan. Dogs are no different. If you can start with enough lines, a few may make it through the genetic bottleneck with acceptable fitness. However, dog breeders generally don't have the resources to start several dozen or more lines simultaneously.

If that is not sufficient to discourage you, then consider the following. During the past 25 years, geneticists have been going out and measuring genetic diversity in natural populations directly by looking at the DNA or proteins, rather than at the phenotype. They have found that many individuals that cannot easily be distinguished by their phenotypic appearance nevertheless have considerable differences in their genotype. This came as a considerable surprise, as the expectation was that those alleles that reduce function even only marginally should, over time, be selected against in the real world.

This discovery led to the theory of neutral isoalleles and the concept that heterozygosity might actually be a good thing -- of itself. Neutral isoalleles produce proteins that are different but that function equally well under normal conditions. In combination, they may function even better. Consider the analogy of a soccer match in which each team is allowed two goalies. One team has identical twins who are good at covering the center, the other fraternal twins, one of whom is better at covering the right and the other the left. All else being equal, which team is going to win?

This is not a universally accepted theory, but today one is hard pressed to find a conservation or zoo biologist concerned with preserving an endangered species who would not list maintaining maximum genetic diversity as one of his/her primary goals. They equate inbreeding depression with loss of heterozygosity.

Assortative Mating

Assortative mating is the mating of individuals that are phenotypically similar. It is a normal practice, to some degree, for humans and various other species. Though phenotype is a product of both genotype and environment, such individuals are more likely to carry the same alleles for genes determining morphology. If we are talking about a conformation that is basically sound from the structural point of view, the genes involved will have been subjected to natural selection for thousands of years and will most likely be dominant. The major characteristics that set one breed apart from another will likely have been fixed early in the breed's history. ("Fixed" means that there is only one allele of present in the population. If there is only one allele, the question of dominance does not apply unless you mix breeds.)

Consequently, when you look at a dog, you are looking at his genes. If the conformation (or, for that matter, the temperament, intelligence, or whatever) is not good, then you are very likely looking at a dog or a breed that is homozygous for one or more recessive alleles that you would probably like to get rid of. If it is the dog and not the breed, you may elect not to breed him, or you may look for a mate that covers the problem. If it is the breed, the only solution would be to introduce some genes from another breed. (That would be an outcross!)

Breeding together animals that share dominant good alleles for most of their genes will produce mainly puppies that also carry these genes. Even if the parents are not homozygous for all these good alleles, you should still get many that are suitable. More important, if animals heterozygous for certain genes are more fit, assortative mating will preserve more heterozygosity than inbreeding. However, unlike inbreeding, assortative mating should not result in an increased risk of the parents sharing hidden recessive mutations. Though we might like to eliminate deleterious recessives, everyone carries a few. Trying to find the "perfect dog" without either visible or hidden flaws is like betting on the lottery. There may conceivably be a big winner out there, but they are certainly not common.

The more you try to cover the deficiencies in one dog with good qualities in another, the less the dogs will have in common. If, then, the results are unsatisfactory, they should not be blamed on assortative mating, as that is no longer what you are doing.

The risks involved

Some trait that breeders consider desirable could be the result of homozygosity for a recessive allele for gene A or gene B. Obviously, crossing an AAbb with an aaBB will produce AaBb progeny that will not express this trait. (However, aside from some of the genes affecting coat color, I can think of no examples.)

If care is not taken to go back far enough in the pedigrees, you may have two animals with similar phenotypes resulting from common ancestry. Whether you are inbreeding unintentionally or intentionally, the consequences are the same. The solution is simple: check the heritage.

Because assortative mating involves selection (you are hopefully mating the best together, and not the worst), you are denying some dogs the opportunity to pass their genes on to the next generation. This is, perhaps, the subtlest of risks, as it does not seem to involve doing anything "wrong." Most would argue that it is merely doing what nature does -- eliminating the least fit. But what if some of these "less-than-best" happen to be the only ones to carry the best allele for some gene? Out goes the good with the bad!

This is primarily a "low-numbers" risk. The larger the population, the less likely we are to find that important alleles are carried by only a few individuals. However, it pays to know where the diversity lies. Do any of you know which, among the current dogs, are most likely to carry the genes of any given founder?

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Inbreeding calculations do not account for the possibility that an allele will become homozygous by "chance," though this, too, can be calculated if the frequency at which an allele occurs in the whole population is known. Most basic Genetics texts explain how. (See, for example, Willis, pp. 293-295, "The Hardy-Weinberg Law.")

I have seen figures of 2500 genetic diseases in man and there are likely to be as many in Canis familiaris, taken as a whole. In man. the vast majority are rare (allele frequencies of < 0.01, which means < 1 in 1000 affected). However, everyone carries three to five "lethal equivalents." This is their "genetic load." Canine breeds are often established with a handful of founders, so we end up with a subset of one or two dozen problems, at frequencies at least 10-fold higher. [If we had five founders, each with a unique set of problems carried as single recessive alleles, the allele frequency of each will initially be ~ 0.1 and ~ 1% will be affected.

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III. The Nature of Genetic Disease

by John Armstrong


Many people label any problem that appears to be inherited a "genetic disease." However, though there are legitimate genetic diseases, there are also a variety of problems that have an inherited component but are of a fundamentally different nature. Dealing effectively with any genetic problem requires an understanding of the relationship between the genes (genotype) and the phenotype. In many cases this is lacking. In this article, I would like to describe some of the differences, in order to give breeders and owners a better understanding of what they are dealing with.

Inborn Errors of Metabolism: The true "genetic diseases"

The first clearly-described relationship between genotype and metabolic deficiencies is credited to Sir Archibald Garrod, an English physician. In 1901, he showed that the inherited disease alkaptonuria results from an inability to metabolize certain amino acids, leading to the accumulation of homogentisic acid. Some of this compound accumulates in skin and cartilage (the latter leading to arthritis). The rest is excreted in the urine, turning it black. Garrod suggested that the metabolic block was caused by an enzyme deficiency, though this was not confirmed until the enzyme (homogentisic acid oxidase) was characterized in 1958.

Since Garrod's time, many other inherited metabolic diseases have been discovered. Some can be managed by careful attention to diet; others cannot. A particularly nasty example is Tay-Sachs disease, which involves an enzyme important in lipid metabolism. Individuals homozygous for a deficiency in this enzyme accumulate a compound called a ganglioside in the nervous system. They appear normal at birth, but progressively lose motor function and die around three years of age. There is no treatment.

Most of these conditions involve mutations that lead to the production of a nonfunctional enzyme, or one that is totally absent. In heterozygotes, the single good copy of the gene is generally able to produce sufficient enzyme to handle the normal workload. However, in a few cases, carriers as well as affected individuals have to be careful about their diet or may exhibit less severe phenotypic effects.

Example of inherited metabolic diseases in dogs include phosphofructokinase deficiency in Cocker and Springer Spaniels, and pyruvate kinase deficiency in Basenjis.

Not all mutations involve metabolic pathways. Some involve proteins that have structural roles in cells and tissues. Others involve regulatory genes that control the correct sequence of events during development. These may lead to such problems as septal defects in the heart or the failure of the embryonic kidney to develop into the adult form. Nevertheless, all can legitimately be considered genetic diseases, as there is a direct one-to-one relationship between a single mutated gene and a particular problem.

Conformational Diseases: The result of unnatural selection

Problems such as bloat (gastric dilatation-volvulus, or GDV) and hip dysplasia clearly have a genetic component, but also an environmental component and, perhaps, a behavioral one, as well (which also may be determined partially by the genes).

Bloat is not a "genetic disease" in the same sense as the metabolic and other disorders described above, and it seems unlikely that a single gene is responsible for bloat. One might better compare a bloat attack to a bad case of indigestion in a human. Some people are more prone to such attacks than others, and there may well be an inherited component, but other factors also come into play. Research into bloat suggests that diet, behavior, and conformation may all play a role.

Leaving aside the question of the role of genetics in behavior, the results suggest that the incidence of bloat increases with the size of the dog and the depth-to-width ratio of the chest cavity. This is a conformational problem, not a genetic disease. Certainly, the overall conformation is, ultimately, determined by the genes, but not by a single gene. There are probably dozens or hundreds of genes that go into determining the shape and size of the head, trunk, and limbs. Wherever there is genetic variability, one can select for larger, smaller, narrower, wider, etc. If the fancy as a whole decides that a taller, narrower dog looks more "refined," more of that description will be kept for breeding purposes, and the population will be shifted toward a more bloat-prone conformation.

When it comes to the question of correcting this problem, the solution, in theory, is simple. We stop breeding for a bloat-prone conformation and select for a slightly smaller dog with a chest cavity that is not so deep or narrow. Some may regard this as a retrogressive step, but we have to decide which we want to sacrifice.

I do not rule out the possibility that two dogs of identical conformation may have one or more genes that lead to one being more bloat-prone than the other. If we could identify these genes, we might be able to reduce the incidence of GDV somewhat while retaining some of the desired "refinement."

While it may be argued that there is nothing wrong with a tall, narrow dog aside from the greater risk for bloat, selecting for a conformation that is not functionally sound is a recipe for disaster. Wild canids do not move awkwardly. Any that did would be eliminated by natural selection. After thousands of years of evolution, the musculoskeletal system of the average wolf has found a combination that works efficiently. Because there is diversity in the gene pool, there is always the possibility of a chance combination of genes that produces an individual that can move more quickly and efficiently. There is also the possibility that a less efficient combination may arise, but it is not likely to be favored.

In the artificial world of the show dog, one can insulate an individual from natural selection and favor a conformational extreme, because the breeder or the public thinks it looks more attractive or just different. Two such extreme dogs, bred together, may lead to something even more extreme and more popular. However, the changes in one component must be accompanied by changes in others, or the result, from a structural standpoint, may impose stresses that the components are not designed for. The result will be components easily damaged or deformed while the puppy is still growing.

In such a case, one may not be dealing with genes that are "bad" and make a nonfunctional or defective product, just with a bad combination of genes. But if, during this "unnatural selection," the genes necessary to make a good combination have been discarded, where does this leave the breed?

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All in the Family (Part 4)


Reprinted from "Bloat Notes", Jan. 1998
Published by the Canine Gastric Dilatation-Volvulus Research Program
School of Veterinary Medicine, Purdue University
W. Lafayette IN 47907-1243


We continue to follow a family of Irish Setters in which several dogs have already bloated. This family study is another attempt to better understand genetic influences on bloat, which can cluster within certain families (familial bloat) or occur in unrelated animals (sporadic bloat). Geneticist Dr. Robert Schaible and Irish Setter breeder Jan Ziech collaborated with the Purdue Bloat Research Team in this study.

Measurement data and bloat histories were collected for all but 1 of 15 surviving pups in 2 litters, whelped in 1988 and 1991, respectively, that had the same dam but different sires. The parents' measurements and bloat histories were obtained. The pedigree was plotted on a scale of chest depth/width ratios. The ratios in this family are spread across a wide range of values for Irish Setters enrolled in the ongoing prospective study.

The pattern suggested that incomplete dominance of a major gene is the mode of inheritance of chest depth/width ratio. The data support the hypothesis that dogs with a deeper chest relative to width are at greater risk of developing bloat than dogs of the same breed with smaller chest depth/width ratios. The pattern for this family will not be complete, however, until all dogs have been followed throughout their lifetime. Breeders who want to do a similar family study can call Dr. Schaible at 812-876-9884.

Reference: RH Schaible et al. J Am Animal Hosp Assoc 33:379-383, 1997

IV. Diversity and the Purebred Dog

(The Poodle and the Chocolate Cake)

by John Armstrong


The Nature of Diversity

Think of genes as recipes. They carry the instructions for the various components that go into making up an organism. Each recipe specifies a particular component, and different individuals may carry different versions of the same recipe. (In the jargon of genetics, we say that they carry different alleles of a particular gene.) Individuals within a population often carry similar or identical recipes, for example, chocolate cake for a Poodle, lemon cake for a Beagle, and white cake for a Samoyed. A different canine species might be represented by a fruit cake. When you consider animals that are quite different, such as frogs and chickens, you will generally find "homologous" recipes, say for pies or puddings. Thus, there is more diversity among mammals than among carnivores, more among the carnivores than among the Canidae, and more among the Canidae than among the wolf group.

An organism carries a collection of recipes, and the collection defines the organism. The great diversity in the possible collections of recipes is the reason for the great diversity in the animal and plant kingdoms. The more closely related two individuals are, the greater the similarity in their collections. The number of combinations is huge, and during evolution, the recipe collection was undoubtedly reshuffled many times. The combinations that worked well survived and multiplied. Those that did not work quickly died out. In theory, one may make a meal of Champagne with tacos and Yorkshire pudding, but they don't really belong together. As time passed, exchange of recipes became difficult between animals that differed substantially in their physical and behavioural characteristics. Different groups, therefore, became constrained to work with only a subset of the total possible collection of recipes.

One definition of a species is that members of two different species bred to each other cannot produce a fertile hybrid. However, a more modern definition is that two species are geographically, physiologically, or behaviourally isolated such that they do not normally produce hybrids. Additionally, they should have features that differ sufficiently to allow them to be distinguished from each other. The domestic dog, wolf, coyote, and jackal can all mate with each others (barring size constraints) to produce viable and fertile hybrids. Yet, they have been considered different species (within the genus Canis) because they normally live in different places, behave differently, and can usually be told apart. (Though there has been a recent move to change Canis familiaris to a subspecies of Canis lupus.) However, a jackal will not mate with a dog unless they have been raised together from pups (presumably due to a learned behavioural difference). Furthermore, no Canis species can produce a hybrid with a fox. This is not because the kinds of genetic recipes are greatly different, but because foxes do not share the same number of chromosomes. (In other words, their recipes are filed under a different, incompatible system — somewhat akin to filing one under DOS and the other on a Mac.)

Genetic recipes may get modified when they are passed on. Many of the modifications will make no noticeable difference, or only a very subtle one. Some may improve the recipe and others will not. If we are making a chocolate cake and a critical ingredient is forgotten, or the cake is baked too long or at the wrong temperature, we end up with a disaster. (If we don't understand what has gone wrong, we will likely throw out the recipe and look for a new one.) We may even make deliberate modifications in an attempt to get a more memorable cake. Among the "chocolate cake" population, there will be a variety — or diversity — of recipes and, therefore, of cakes.

This, I would say, is a "good" thing. Do we always want the same chocolate cake? Surely we will tire of it, and even if we don't, we lose the pleasure of anticipation. If, for some unforseen reason, everyone suddenly loses their taste for THE chocolate cake, it will surely go extinct. To have the potential for evolution and adaptation, we must risk the possibility of the bad. That is the "cost."

In a large, naturally breeding population, we will end up with a number of versions (alleles), some so slightly different that we will never notice, some perceptibly different (but still functional), and some that just don't work at all. However, if we remove the diversity we lose the potential for evolution and for surviving unexpected change. To have the potential for evolution and adaptation, we must risk the possibility of the bad. Geneticists call that cost genetic load. (This "bad" group persists because every individual carries two copies of every recipe, and often having just one "good" copy is enough for normal function.) In most populations, every individual carries a portion of the load — three to five bad recipes out of several thousand. The load is so well distributed that if two individuals compare their recipe collections they will generally not have two copies of the same bad recipe.

Loss of Diversity

Suppose we start a new population with only six or eight founders. (A number of breeds have started with that few.) We will get rid of hundreds of bad recipes, but the remaining dozen or two will be encountered much more frequently. Furthermore, if there are several good or excellent recipes, the chance of dropping one of these from the collection grows greater as the number of founders diminishes, and the risk of losing one remains high as long as the effective population size remains low. Working with small numbers will inevitably decrease the diversity, simply because individuals do not pass on their recipes equally to the next generation and some recipes are accidentally lost. This has the superficially desirable result of giving a more reproducible phenotype, but at the expense of an overall reduction in quality, health, and longevity.

If breeders had the ability to recognize each individual recipe and choose only those that were excellent, breeds could be produced with a small number of individuals that lacked genetic problems. However, what we see (the phenotype) is the product of all the recipes and, for the most part, we cannot distinguish the individual recipes. Moreover, we do not have the option of selecting recipes individually. When we select an animal for breeding, we are forced to accept a complete set. Even in those few cases where we now have a DNA test for a bad recipe (allele), we do not possess the ability to correct or selectively discarded it. We are therefore forced to work around it, or to discard the whole collection, with the attendant risk of discarding something excellent along with it.

The common practice of almost everyone rushing to breed to the currently-popular male show champion is probably the most significant factor reducing whatever diversity remains. Consider your own breed (the situation for most breeds is similar). Can you find one or more males that appear in most pedigrees? Almost everyone decides they like the recipes of (insert name) — or at least the ones they can see readily — and abandons other recipes with little thought to the eventual consequences. In a few generations, almost everyone has a substantial number of his recipes, though not necessarily his exceptional ones, and many excellent alternatives are very hard to find.

How precious is the individual that comes along with some of the missing recipes and relatively few of the "popular" collection? Do we hesitate because there are also a few bad recipes in this alternate collection? Are we now so accustomed to dealing with the more-popular collection that we have lost the vision of the "memorable" chocolate cake?

Population Genetics and the Breeder

What is often called Mendelian genetics deals with the outcome of specific crosses. Population genetics deals with the distribution of alleles in a population and the effects of mutation, selection, inbreeding, etc., on this distribution. As a breeder, you are a practicing geneticist. A knowledge of both Mendelian genetics and population genetics is critical, not only to your own success, but also to the survival of your breed.

Because many early geneticists believed that there were only two possible alternatives for a gene — "good" alleles that functioned normally and "bad" alleles that didn't — they expected to find little genetic variability in a population. The majority of individuals were expected to be homozygous for the good allele for most genes.

But with the advent of modern biochemical and molecular tools, geneticists studying populations found far more variability (diversity) than they had expected. There are a number of possible reasons for this, and even the experts are not in total agreement on the most likely reason(s). However, geneticists have also discovered that populations lacking genetic diversity often have significant problems and are at greater risk from disease and other changes in their environment. The conclusion is that genetic diversity is desirable for the health and long-term survival of a population.

Are purebreds dogs genetically diverse? Some may regard that as a contradiction in terms. The very concept of creating a breed with characteristics that are distinctly different from other breeds implies a certain limitation on diversity. Nevertheless, within the standards for a breed, diversity should still be possible for genes that do not affect the essential characteristics that distinguish one breed from another. If, in order to maintain breed identity, one has to compromise on genes that relate to general structural soundness, good health, intelligence, and temperament, perhaps this breed should not exist. However, as long as these essentials are not compromised, I see no reason why one cannot have different breeds with different appearances and different talents.

For those genes that establish breed identity, there will be markedly less variability within a breed than within Canis familiaris as a whole. The tricky bit is restricting variability for those genes that make a breed distinctive without sacrificing the variability/diversity that is necessary for good health and long-term survival of the breed. In many cases, this has not been achieved, and we are now paying the price in terms of high incidence of specific genetic diseases and increased susceptibility to other diseases, reduced litter sizes, reduced lifespan, inability to conceive naturally, etc.

Why has this happened, and do we have to accept it as an inevitable consequence of creating a breed? I don't think we do.

The principal reasons for limited genetic diversity are:

  1. Many breeds have been established with too few founders or ones that are already too closely related.
  2. The registries (stud books) are closed for most breeds; therefore you cannot introduce diversity from outside the existing population.
  3. Most selective breeding practices have the effect of reducing the diversity further. In addition, the wrong things are often selected for.
  4. Even if the founders were sufficiently diverse genetically, almost no one knows how their genetic contributions are distributed among the present day population. Consequently, breeding is done without regard to conserving these contributions, which may be of value to the general health and survival of the breed.

A role for the breed clubs

Each breed needs a database with all the breedable animals recorded with all their ancestors back to the founders. This would most appropriately be the task of the breed club. Are any actually doing this (outside some of the rare breeds)?

Such a database would enable breeders to identify which individuals are most likely to carry the genes from each founder. At the level of the individual breeder, it would enable him/her to make intelligent, informed choices when selecting mates. Measures might also be considered to re-balance the breed, in order to ensure that the remaining diversity is more evenly distributed and that, therefore, there is less risk of loss.

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Hartl, D.L. A Primer of Population Genetics, Sinauer, Sunderland, MA, 1988.

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A population is regarded as genetically diverse if a substantial proportion of the genes are polymorphic. A polymorphic gene is one for which the most common allele has a frequency of less than 0.95 (95%). Mammals are about 15% polymorphic.

A gene that is not "polymorphic" is called "monomorphic", but this does not imply only one allele. Most monomorphic genes have rare alleles, generally occurring at frequencies below 0.005.

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John B. Armstrong, 1998 with permission.

Revised July 22, 1998

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