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Twenty key elements of a successful breeding program

3/29/2016

 
By Carol Beuchat PhD
When I first started reading about the genetics and breeding of dogs, two authors affected me profoundly. One was the late Dr John Armstrong, a Poodle lover who began writing about dog genetics after he retired in the 1990s from his university faculty position in genetics. He founded the original Canine Genetic Diversity group that has continued to discuss topics of interest long after his death. The other was Jeffrey Bragg, who is not a professional scientist but whose grasp of the finer points of genetics as relating to dog breeding is exceptional. Bragg has devoted himself for a half century to the preservation of the Seppala sleddog, a line of outstanding working dogs descended from the famous dogs bred by Leonhard Seppala in the early 1900s.

​The Seppala story is fascinating and worth a visit to the Seppala Kennel website. But there is also a collection of articles by Bragg that should be required reading for anybody who aspires to produce dogs that are beautiful, functional, and sound in mind and body for generation after generation. That Bragg has preserved the legacy of these dogs and successfully implemented sound breeding practices is evidenced by the dogs he produces, which are working sled dogs that routinely live well into their mid-teens. I think so highly of the knowledge he has to offer that I have compiled his collected articles into a single document, which you can download from the ICB website under "Resources: Essential Reading" (or more conveniently from here).

I have copied for you below what I think is the most valuable of his essays, because it is simple and to the point. If you grew up learning how to write with Strunk and White's Elements of Style under your arm, you will appreciate how a few pithy statements can have a far greater impact than pages of prose ("Omit needless words!"; "Use active voice!"). Bragg provides the details here, but he encapsulates the essence of his points very simply:
  • Maintain balance of sires and dams
  • Eschew incestuous matings
  • Understand and monitor coefficient of inbreeding
  • Pay attention to the trend in COI
  • Calculate number of unique ancestors
  • Know the genetic load but don't obsess about it
  • Use pedigree analysis
  • Conserve sire and dam-line diversity
  • Practise assortative mating
  • Maintain high generation time
  • Avoid repeat breedings
  • Ensure sibling contribution
  • Monitor fitness indicators
  • Attempt founder balancing
  • Consider outcross matings
  • Monitor population growth
  • Seek balanced traits
  • Avoid unfit breeding stock
  • Avoid reproductive technology
  • Restrict artificial selection
How different is this list from the one you got from your mentors? "Breed only the best to the best". ""Let the sire of the sire become the grand sire on the dam's side". "Inbreeding is necessary to expose deleterious mutations". "DNA tests are necessary to produce healthy dogs". "The coefficient of inbreeding is just theoretical". "The goal is to remove all mutations from the gene pool". "Outcrossing will ruin your line." I'm sure you know many more.

​Sit down with a cup of tea, Bragg's essay, and a highlighter. This is the syllabus for a graduate degree in dog breeding. Most of what I have said in my dozens of blog posts is communicated here in a document you can read from end to end in ten minutes. Read it, then read it again. Absorb the lessons. These are simple truths that  will make you a more successful breeder if measured by the soundness, health, and happiness of the puppies you produce.


Population Genetics in Practice:
​Principles for the Breeder

J. Jeffrey Bragg (copyright 2009)
ALTHOUGH THE SCIENTIFIC DISCIPLINE of population genetics has existed for the better part of a century, its penetration into the world of the dog breeder is only just beginning, despite its importance and relevance to that world. Often I have heard dog breeders wish for an understandable guide to practical dog breeding, drawn from the principles of population genetics -- a set of guidelines for dog breeders that would show the way to a healthier way of breeding than the harmful methods of inbreeding and selection now practised by the vast majority. As things stand with traditional dog breeding, the competitive struggle for individual excellence has harmful consequences for breed populations. What is needed is for breeders to think in population terms, to look at each breed genetically as a population and each breeder involved with that particular population as a conservator of that breed in partnership with others.
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At the present time, after twelve or fifteen years of existence of the canine diversity movement, most available discussions of dog breeding as a discipline still recommend linebreeding (a euphemism for inbreeding), breeding only "the best to the best," together with stringent artificial selection and multiple screening for genetic diseases. That is still the old way. Those are the methods that brought genetic crisis to the world of purebred dogs in the first instance.
​
Two and a half years ago on the Canine Genetics email list, I asked whether we could not collaborate to write down a set of rules, guidelines or principles aimed at breeding according to the principle "primum non nocere" -- "above all, do no harm!" Although a few people acknowledged the desirability of such a document, we never managed to mount a thorough discussion of which principles should be included. In the end I drew up my own provisional list of principles for 21st- century dog breeding, which I never published as I never was able to put it into a final form that I thought adequate.
The release of the sensationalistic one-hour video entitled "Pedigree Dogs Exposed" commissioned for the B.B.C. has galvanised the discussion of 21st-century dog breeding somewhat, through the threat of repressive regulation from government and kennel club authorities and the advance of the "animal rights" agenda. Nevertheless the futile wrangling between advocates of inbreeding and diversity advocates still continues unabated on the email lists. One cannot help feeling that, although a certain level of awareness may have been raised, perhaps we have not yet really gone anywhere since the mid-1990s when Dr. John Armstrong made his pioneering efforts to raise questions of canine population genetics on the Internet.

​Meanwhile the exigencies of the Seppala Siberian Sleddog Project (a Canadian bloodline conservation and breed development initiative under Ministry of Agriculture charter) required that I "wing it" as best I could, creating for purposes of the Project a coherent body of breeding practices for conservation and development of the Leonhard Seppala sleddog strain. Lacking time to make extensive research of other rare or developing breeds, I worked mostly from my own knowledge of population genetics, within the parameters of our evolving SSSD breed, with relatively little light shed on our problems by the practices of other breeders in similar situations. 

Not every breed may be in a position for its breeders to do some of the things we do in the SSSD Project -- breeders of Chinooks, for example, cannot avail themselves of landrace stock from the "country of origin" of their breed, both because the breed is synthetic in origin and because its original component canine strains are not completely known. With the strong caution, then, that not every single measure here recommended may be possible or appropriate for all other breeds, for every situation, or for any given breed other than the Seppala Siberian Sleddog, I offer for consideration the following guidelines drawn from my own limited knowledge and experience.
Please realise I do not say that you (as an individual dog breeder) must necessarily do any or all of the things discussed in the following paragraphs. Still less would I wish to see any such guidelines imposed by government as laws or regulations upon the dog breeding community; I do not feel that breeders can be coerced to breed healthier dogs. I do suggest that if you are concerned about inbreeding, inherited illnesses, and lack of genetic diversity, you might wish to consider implementing some of the following principles whose observance we have found useful in the Seppala Siberian Sleddog Project.

​
Maintain Balance of Sires and Dams 
Breeders should make a great effort to maintain a reasonably equal numerical balance of sires and dams; it is unwise consistently to use fewer individual sires than dams. The so-called "popular sires" syndrome, in which a small number of elite show or trial winners sire grossly disproportionate numbers of progeny in a breed population, has received much discussion and attention. What may not be so well realised is that this selfsame syndrome is repeated in miniature in most kennels, where one or two of the "best" males cover all the bitches, sire all the litters. (How often has one heard it put forth, and not only by novices, that "the best males should sire all the litters!") Any significant imbalance between the number of sires and dams automatically restricts the effective breeding population. In order to avoid such needless reduction, just as many individual males as bitches should contribute to the population; this holds true whether we speak of the breed population as a whole, or of the population within a single kennel.
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Eschew Incestuous Matings
As controversial as this advice may still be, I nevertheless advise the breeder to do no incest breeding whatsoever (even if you would rather call it "linebreeding" or inbreeding). Just about all purebred dog breeds demonstrate serious and sustained inbreeding when the full known pedigrees are considered. There is little excuse for inbreeding to be continued in the first four generations of pedigree if it can possibly be avoided. Matings of related individuals closer than cousins ought never to be contemplated unless that should become absolutely necessary to prevent loss of a rare bloodline. That means: (a) no brother/sister matings, (b) no father/daughter or mother/son matings, (c) no half-brother/half-sister matings (i.e., sire and dam share one parent in common), (d) no grandsire/granddaughter or grandson/granddam matings, (e) no uncle/niece or nephew/aunt matings. Why should a practice universally decried with respect to our own species be so common in dog breeding? The principles of genetics are the same no matter whether humans, dogs, or other species are considered.
​

That does not mean that first-cousin matings (sire and dam have different parents but the same grandparents) are okay or recommended, either; it is simply a case of having to draw the line somewhere, at a given degree of consanguinity, in order to say "anything closer than this is quite beyond the pale and should not even be considered." (Otherwise excuses will inevitably be found even for full-sib -- brother/sister -- matings.) If the available pedigree diversity within your own breed allows you to draw the line further out, so much the better.
Inbreeding cannot be practised with impunity, without consequences. Inbreeding depression may not be dramatically visible to most breeders, but that is only because it is subtle, incremental and widespread. It is a proven fact that longevity, reproductive success, and the immune system are all negatively affected by even "moderate" degrees of inbreeding. Survival fitness has already been compromised in many breeds. For breeders blindly to continue down the path to destruction whilst telling themselves that they are merely "fixing type and exposing undesirable recessives" is inexcusable.

Understand and Monitor Coefficient of Inbreeding
To avoid frankly incestuous matings within the first three generations of pedigree is not sufficient in and of itself. The Coefficient Of Inbreeding (COI) must also be monitored, preferably over ten generations of the known pedigree, with a view to keeping it as low as possible. To calculate COI over more than two or three generations requires the use of computer software such as CompuPed, Breeder's Assistant, BreedMate, FSpeed, etc., in conjunction with a reliable breed database. It cannot be done easily or accurately without computer assistance; fortunately a good number of applications are available that meet the purpose.

These days every breeder should understand clearly what Coefficient of Inbreeding is and just what it tells us. Unfortunately that is still far from the case. Wright's Coefficient of Inbreeding (the only scientifically acceptable version, though there is at least one specious version in popular use) represents the statistical probability that the alleles contributed by sire and dam at any given gene locus will be identical by descent . It may also be regarded as the percentage of multi-allele genes that are likely to be homozygous by descent for a particular mating. Therefore COI is the principle measure of the degree of inbreeding and its effects on the genome.

To calculate a four to six generation COI only gives a false sense of security; usually such a COI fails to tell the whole story and the ten-generation COI will be found to be dramatically higher. Many popular writers, of whom Dr. Malcolm Willis is probably the best known, speak as apologists for inbreeding at one moment, at the next moment attempting to assure us that the average COI in most breeds is quite low. That is simply not the case. In the first place, a true average COI for an entire breed is not easy to determine. People assume that such things are known, but they are not, because the requisite research simply has not been performed. But the assertion that the COI in an "average pedigree" is something on the order of four to six percent is ludicrous, something that can be disproven readily by anyone with a breed database and one of the above mentioned pedigree software applications. The four to six percent contention, when examined, will usually be found to be supported by pedigrees of four or five generations only. Such calculations fail to take into account the background inbreeding inherent in the breeding history of every dog breed; ten generations is the generally accepted standard for comparison. In some breeds even ten generations may not tell the complete story and whole-pedigree COI will need to be examined before breeders can truly know where they stand.

Another specious argument often voiced is that "inbreeding should be defined as any mating in which the COI is higher than the overall average for the breed." This is an unscientific and somewhat circular definition. It is ridiculous on the face of it, as COI is not a static measurement but a dynamic one, a new story each time a new sire is mated to a new dam. As mentioned, the average for most breeds is not known. Moreover, distinctly different "average" levels may obtain in different sectors of some breeds (as, for example, show dogs, working dogs, and pet stock). In any case, inbreeding is never defined by reference to a population; it is always a function of the relationship between the sire and the dam of a litter or an individual. Inbreeding exists when genes held by both the sire and the dam of a litter are identical by descent. It is certainly a truism that all present-day dog breeds are "inbred," or, more accurately, that inbreeding has occurred consistently throughout their history. That is why we have acute problems with genetic diseases in our dogs. For that very reason, one of our major objectives ought to be to lower the average COI of every breed by reversing the inherent bias of our present system towards inbred matings. But to speak of an "inbred population" is at best shorthand. Inbreeding has meaning only with reference to a specific mating. It results in an increase in homozygosity (and a corresponding decrease in diversity) which is the permanent effect of the inbreeding.

In a purebred dog breed COI can hardly be too low; almost always it is far too high! It is safe to say that most breeders are totally unaware of their own dogs' Coefficients of Inbreeding. Ignorance is no excuse. COI is the best tool the breeder has to assist in the conservation of genetic diversity. Without it he stumbles in the dark down the slippery slope to canine genetic depletion.

Pay Attention to the Trend in COI
It is impossible to recommend an arbitrary figure for maximum allowable percentage COI, as the situation of each breed is likely to be different. Probably anything greater than 5% constitutes a threat to genetic health, yet to set the bar at 5% would be virtually impossible in many breeds. It is easy to point to specific individuals in numerous breeds with COIs of 70% or more, but in many breeds it would be a real challenge to discover examples of less than 5% COI. There are breeds in which breeders would have to make great efforts to obtain COIs as low as 20%; in at least a few breeds 20% would be alarmingly and needlessly high.

Breeders should at least endeavour to grasp what the average 10-generation COI level probably is for their breed, at any rate in bloodlines with which they are familiar, and to seek to keep their own breeding well below that level! Otherwise the COI will continue to increase indefinitely, steadily, year by year.

One should take care that the COI trend in one's own breeding is never upward, but always either downward or at worst neutral. This is done by averaging the individual COIs of sire and dam (add the sire's COI to the dam's COI and divide by two) and then comparing this average with the COI for the trial mating or litter that would result from mating those two individuals If the litter COI is higher than the average of the parents, then obviously you are increasing the overall level of inbreeding by performing that mating; ordinarily the greater the positive disparity between the two figures, the more the mating should be deprecated. (This rule of thumb has distinct limitations, though. When a low-COI bloodline or a frank outcross is being integrated with an existing high-COI bloodline, it may still be quite desirable to perform matings in which the mating COI exceeds the parental average, since the end result will still be a desirable increase in diversity for the high-COI subject bloodline.) Conversely, a litter COI lower than the parental average is desirable. As far as I know, despite some claims to the contrary, there is no danger in an abrupt decrease in litter COI from parental levels.

You may also wish to look at the same data from a different perspective by calculating (with the same pedigree software) the Coefficient of Relationship (RC) when examining trial matings, the more easily to ascertain which of two or more alternative matings has the least-related parents.

Calculate Number of Unique Ancestors
A deep and reliable breed database, used in conjunction with a pedigree and COI application such as Breeder's Assistant or BreedMate, is a basic tool to explore COI and trial matings. That is far from its only use, though. The database and pedigree application should also be used to study the number of unique ancestors in the known pedigree. By that I mean the number of actual individual dogs showing in the full pedigree, as against the number theoretically possible in each generation; invariably the number of actual ancestors will be radically smaller than the number theoretically possible. Next you should determine the number of ancestors in common between sire and dam, and finally the number of ancestors unique to each parent. These figures are useful to assess the potential diversity of a projected mating and will tell you more than the simple COI (which, after all, is only a percentile probability figure predicting the likelihood that alleles at the same gene locus contributed by the sire and dam will be identical by descent). One of the best guides to the probable genetic diversity available in any particular mating is the number of ancestors not common to both parents. You will find that this tool dramatically points out genetically impoverished matings, and conversely that it easily isolates matings that are markedly superior from a diversity standpoint. This technique is one of the most valuable tools in actual practice, yet few make use of it.

Actual numbers of unique ancestors will vary from one breed to another, particularly in response to the depth of known pedigrees. It is of little use without a complete breed database; pedigrees in which some lines have not been researched beyond the usual four generations will distort results.

Know the Genetic Load but Don't Obsess About it
By "genetic load" we mean the total complement of genes within a population that can negatively affect the fitness of individual animals. Some of these genes are known; many remain poorly understood or unknown. The breeder should at least be well aware of genetic problem areas within the breed. Some will be breed-specific (syringomyelia in Cavalier King Charles Spaniels, the purine metabolism defect in Dalmatians); more will be common to most or all canine breeds (epilepsy, canine hip dysplasia) but in some breeds may be associated with particular bloodlines.

Breeders are told that to produce animals with genetic defects marks them as "bad breeders," so they tend not to share information about such defects. They are also told that their objective should be to "eliminate" these genes, which is used as justification for inbreeding and expensive screening programmes. This kind of advice builds up an obsessive attitude towards genetic load. People spend endless time discussing specific defects, individual animals, screening programmes and the like, whilst ignoring the true causes of genetic disease.
It is unlikely that canine genetic load can be effectively eliminated, at least at the present stage of genetic knowledge. Not until the functions and interactions of all genes in the dog genome are fully known, and gene surgery commonplace, would that become a real possibility.

It is therefore important that breeders share knowledge about genetic load within their breeds, so that they can avoid unfortunate breeding combinations. Authors such as Malcolm Willis and Jerold Bell insist that outbreeding "covers up" recessive defects. Indeed it does and indeed it should! That is exactly what nature itself does, and no one criticises natural evolutionary processes or recommends that natural populations should be inbred instead of mated naturally. The fact that inbreeding "exposes" recessives is not necessarily helpful, because in most cases it is impractical to remove or "eliminate" the "defect" genes. Rather, breeding should be guided in such a way as to avoid reinforcement of known recessives whilst maintaining genetic diversity in the population.

Screening and selection can never succeed as a strategy for the "elimination" of genetic disease. As one defect is eliminated, others will be reinforced, and the latter state of the breed will be worse than the former. The genetic load must be known, tolerated and managed; to obsess about its elimination will lead only to disaster.

Use Pedigree Analysis
Every breeder should also carry out in-depth pedigree analysis for each prospective mating, listing the major ancestors on which inbreeding occurs in that mating, noting the number of occurrences and the generation number of each occurrence. This analysis should be carried back for at least six ancestral generations, ideally for eight. This practice will alert the breeder to undesirable "pile-ups" on key animals and therefore to potential genetic problems (where these are known to be associated with such individuals) in the planned mating. This can be done entirely without computer software. However, an alternative or supplementary approach is to use the "percentage blood" function of pedigree software such as Breeder's Assistant. The percentage blood function, in contrast to COI, illustrates just where in the pedigree major inbreeding problems may be occurring, whether just in a handful of key animals, or more broadly throughout the entire pedigree.

Conserve Sire and Dam-Line Diversity
There are two unique points of canine pedigree diversity that are not always paid much attention. These are the topmost and bottommost lines of the pedigree -- the tail-male or sire-line and the tail-female or dam-line. They represent unique genetic content, held by the mitochondrial DNA and the sex chromosomes, much of which is transmitted only by those pedigree lineages. Given the intense preoccupation among breeders with both stud dogs and brood bitches, what I am going to say may seem surprising: diversity in sire and dam lines is often quite scarce in purebred dog genomes.

In the case of the Siberian Husky (one of the breeds most familiar to me) there are two major founder sire-lines and two major founder dam-lines, along with perhaps one or two others that are well on the way to extinction. I have every reason to believe that most other breeds are in similar case, due largely to hazard, simple chance. Since these lines are not consistently scrutinised and conserved by breeders (because they are unknown if the breeder has not researched the pedigree all the way back to breed foundation), they are subject to changes in the frequency of their occurrences, exactly similar to the changes in gene frequency that occur due to random drift. Most breeds begin with a fair number of unique sire and dam lines. But some drift into prominence and others into obscurity, scarcity, and finally extinction.

These lines are important, particularly the dam-line with its association with mitochondrial DNA. This kind of DNA is held outside the cell's nucleus, in the cell mitochrondria within the cytoplasm. Since the spermatozoon has no mitochondria it plays no part in the transmission of mitochondrial DNA, which is inherited only from the dam. Mitochondrial DNA is directly involved in energy metabolism and is therefore vital to performance in working dogs.

The breeder should know the available unique sire and dam-lines in her breed and within her own kennel, and should make every effort to conserve them. That means ensuring that the sons of sires contribute to the next generation, likewise the daughters of dams. It is all too easy to neglect this vital point. Loss of tail-male and tail-female lines within kennels leads quickly to their loss within breed populations.

Practise Assortative Mating
If the breeder should wish to emphasise or fix greatly desired traits, she should consider the use of assortative mating (mating unrelated parents who are phenotypically similar for the desired traits) instead of inbreeding. Assortative mating is much less dangerous than inbreeding and will accomplish much the same ends. It should be obvious that to breed "like to like" for given desired traits will tend to yield more of what is desired, but if the parents are not closely related, there is a greatly reduced chance that other unconsidered traits will be unknowingly reinforced by such matings.

Maintain High Generation Time
Genetic losses occur infallibly with almost every generation of purebred dogs. This happens through a variety of causes -- random drift, from too few progeny contributing to the next generation, from the inbreeding/selection cycle, bottlenecking, etc.. For that reason, the fewer the intervening generations between foundation stock and current stock, the less genetic diversity is lost. Breeders should therefore maintain a high average generation time (age of the sire at mating plus the age of the dam at mating, divided by two) for each litter produced: four years should be considered an appropriate minimum floor level, five or six is better. It is helpful to calculate a running average generation time for your kennel throughout its history, by keeping a grand average of the average generation times of all litters produced.

Far too little attention is paid to generation time by breeders. Many flagrantly disregard the question. How often have we seen the bragging advertisements in dog magazines: "CHAMPION (subject to CKC confirmation) Frou-Frou, finished from puppy classes at 10 months! Offered at stud to approved bitches only. Puppies from Ch. Frou-Frou are eagerly awaited next month!" The dog that is capable of finishing a title at ten months of age may turn out to be anything at all when mature; to mate such a dog at less than one year of age is breeding blindfolded. Often serious genetic diseases do not manifest until three or four years of age. To maintain a high average generation time gives the breeder a distinct advantage when it comes to producing healthy stock, and makes breeding results more predictable, as well as minimising generational losses of genetic diversity.

Avoid Repeat Breedings
Many kennels make a routine practice of repeating favourite breedings over and over again. Do not always use the same sire for a particular bitch (or vice-versa)! Take care to maintain diversity in your matings. Endless repetitions of the same matings greatly reduce the available breeding combinations both within the individual kennel as well as for the breed at large. This principle would seem quite obvious on the face of it, yet how many people ignore it as soon as they find a "nick"!

Ensure Sibling Contribution
The breeder should strive to ensure that at least two of every litter (unless it should happen to be one of those litters that really had best be forgotten) contribute to the next generation; half the litter should be the ideal, though perhaps a difficult one to maintain. In every instance in which only one progeny from a given mating contributes to the next generation, automatically and infallibly half of the available genetic diversity in that line is lost permanently! If two progeny contribute the theoretical average loss is reduced to 25%, still less if more littermates contribute. This single point is a major source of losses of genetic diversity among purebreds, yet it often goes totally unconsidered by the breeder.

Monitor Fitness Indicators
Breeders should not fail to monitor key indicators of survival fitness in their canine stock. These are nestling viability, absence of stillbirths, birth weights, fertility (percentage of successful matings), fecundity (average litter size compared to the norm for your breed), survival to adulthood, and longevity; be sure that your breeding programme does not trend toward the reduction of any of these.

Attempt Founder Balancing
It may be valuable to attempt to balance the relative contributions of founders (where possible and appropriate), particularly subsequent to founder events or genetic bottlenecks. This is routine practice in zoological park captive-breeding programmes, yet virtually unheard of in a canine context. "Founder" is a not an absolute, but rather a relative term. If a breed has a long pedigree history with original breed foundation stock at thirty or more generations remove from current stock, it may well prove impossible to balance the contributions of the original breed founders, whose relative contributions may already be set in stone for all practical purposes. But founder events tend to occur repeatedly within the history of a breed, not only when the stud book is first opened. Bottlenecks occur with dismal regularity. At least the breeder can pay attention to the most recent founder set that is clearly identifiable, attempt to prevent the loss of individual bloodlines that are seriously under-represented, and seek to balance the relative contributions. Clearly this is no simple matter and to suggest that it be applied consistently may be a counsel of perfection. At least it is one more possible tool in the breeder's armoury against diversity losses.

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​Consider Outcross Matings 
The great majority of dog breeds have been bred within a completely closed studbook for sixty to a hundred years or longer, with little or no fresh genetic input throughout the entire period from breed foundation to the present. In most cases the stud book was opened for a year or two, a small number of founders, often closely related to one another, were registered, and the stud book was then closed. Thereafter, only dogs descended from the founders could be registered. And for those sixty to a hundred or more years, artificial selection, random drift, bottlenecking and other forms of attrition took their toll of whatever genetic diversity was present in the founder group. It is exactly as though a bank account had been established with a single initial deposit (the genetic diversity of the founders), with no further deposits permitted; meanwhile bank fees and direct debits (diversity losses from drift, selection, etc.) chiselled away at the balance. It is a sure and certain recipe for bankruptcy. 

Similarly, many individual bloodlines have been treated in exactly the same way, bred in relative genetic isolation from other bloodlines -- except that in this case additional deposits are at least allowed, in the form of bloodline outcrosses. Therefore each breeder probably ought to consider the desirability of locating and using a true outcross within his or her own breed (unrelated to one's own stock for at least ten to fifteen generations) at least once and to integrate the resulting progeny into one's kennel bloodline. 

This cannot be done uncritically, outcrossing just for the sake of outcrossing. Some bloodlines might be an outcross to your own line, yet be worthless for the purpose. Generally, lines that come from the same ultimate foundation, but contain less diversity because they have been bred in a closed stud book for more generations, or have been heavily selected for cosmetic traits, will tend not to yield useful results. 

If there is any possibility whatsoever to import unrelated stock from a breed's country of origin, one ought seriously to consider doing just that. This is mainly possible in the case of landrace breeds, in which an autochthonous regional population remains in the country of origin, independent of exported stock that may have become a registered breed in other countries. Examples of such situations would be the population of desert-bred coursing sighthounds in the Near East, relative to the Saluki breed in Europe and North America, or the relict populations of autochthonous arctic spitz-type sled dogs relative to the modern Siberian Husky, Alaskan Malamute, Samoyed, et al. 

It would be difficult to overestimate the genetic value of a single import animal, unrelated to the registered breed population for scores of generations but stemming from exactly the same fountainhead. This I would term the Holy Grail of the diversity breeder -- the ideal controlled-outcross situation in which an immediate significant increase in healthy genetic diversity may be obtained at little to no cost in terms of breed type and purpose. (That the Canadian Kennel Club rejected this option for the Siberian Husky in 1994 demonstrates, I believe, the true extent to which the umbrella all-breed registries represent an obstacle to genetic health and true breed welfare and improvement.) 

In cases of small, highly-inbred populations for which there is no landrace resource, it may become necessary to consider an outcross or outcrosses to similar breeds to relieve inbreeding depression and restore healthy genetic diversity. If so, this ought to be faced squarely and proactively by the breed club concerned and breeding subsequent to the breed outcross should probably be a collective endeavour, shared for purposes of more thorough integration and to reduce the work-load on any one breeder -- because, no question about it, the integration of a breed outcross is a major task that can hardly be undertaken alone by the average breeder. (The Backcross Project in the Dalmatian breed was an excellent example of a breed outcross well-purposed and superbly integrated; but the reaction of the breed club was deplorable.) 

Monitor Population Growth 
In the case of small, developing breed populations, it should be regarded as important to monitor and control the growth in number of the population such that there is steady expansion of the population within the limits of breeders' kennel capacity and the demand for progeny. Growth by fits and starts, with periods of rapid overexpansion followed by sudden cutbacks or population collapse, is very bad for genetic health. It is difficult to impossible wholly to avoid population bottlenecking, but its existence and ever-present threat should be recognised. To whatever extent may be possible, breed clubs and individual breeders should do what they can to ensure smooth, steady population expansion and to minimise cutbacks and consequent genetic bottlenecking. 

Seek Balanced Traits 
One ought always to evaluate breeding stock for balanced characteristics: health, vitality, temperament, working ability, intelligence, structure, type. Breeders should aim to maintain the balanced characteristics of a total dog, not just to produce winners at dog shows, field trials, races, etc. An all-round, balanced dog will be a much better hope for the future than a highly-selected, over-bred animal thought to be "best" due to its possessing exaggerated traits in one or two areas, whether it be a "perfect head," a showy gait, a faster racing speed, or whatever. First, every individual needs to be a good dog, and that should come ahead of specialised breed considerations. 

Avoid Unfit Breeding Stock 
It ought not even to need saying -- but in these days in which extensive, heroic and expensive veterinary measures are routinely used to save otherwise doomed animals, it does need saying: the breeder ought never to breed from dogs that would not be alive but for such interventions (excepting, of course, survivors of physical injuries). It should be obvious that if we circumvent the operation of natural selection, many of the animals that we use for breeding purposes are likely to pass on various genetic weaknesses.

Avoid Reproductive Technology 
Breeders should also consider whether it is in their breed's interest routinely to use elaborate reproductive technology to produce litters. These days various and sundry technical means are available which circumvent natural mating and whelping. Some breeds, indeed, cannot either mate or whelp a litter without veterinary intervention -- already! If we use artificial insemination and hormone assay to effect mating combinations that cannot be brought about by natural mating, along with routine C-section to deliver litters, we may rapidly find ourselves in the position of having created strains that cannot reproduce naturally without technological support. We should also consider whether it is really a good thing to freeze the semen of outstanding males and thus extend their breeding life decades into the future; this practice seems to be universally approved, while no one appears to have examined the effects such extension of the influence of individual stud dogs might have on breed genomes. If the "popular sire" syndrome constitutes a serious risk factor, frozen semen can only ramp up the risk level another notch. 

Restrict Artificial Selection 
Restriction of the use of artificial selection may really be the most important principle of all, and the most difficult for the vast majority to accept. Breeders really should avoid all extremes of artificial selection! When one comes to consider the problem of lost genetic diversity, inbreeding by itself is less than half the story. The hard truth is that breeders’ selection itself is just as great a culprit, if not worse. Inbreeding and selection combine in a cyclical fashion in the dog world, to cause the systematic depletion ("depauperisation" to the geneticist) of purebred genomes. From the professional geneticist's standpoint, present-day purebred dog breeds are virtually all depauperate to a significant degree, therefore lowered in fitness, vulnerable to genetic disease and inbreeding depression. This situation is due to excessive artificial selection more than any other single factor. 

When this goal is discussed most breeders react with dismay, asking "but how else can we set type?" If "type" has not already been "set" in breeds held within closed stud books for the better part of a century, then it never will be set. The truth is that selection is now used by dog breeders to create bizarre exaggerations of type, often unhealthy in themselves to the dogs. (Some examples, such as the nearly muzzle-less Pekingese, the respiration-challenged Bulldogs and the cerebrally-deformed Cavalier King Charles Spaniels, are already notorious in the dog world.) The desire for a cookie-cutter "consistency of type" causes healthy genetic diversity to be discarded intentionally at an alarming rate. (An example of this desire is the person who declared at a Chinook specialty show that he saw at least five different types represented there, and that "they had better get themselves a geneticist or they will never have a standard type." The Chinook is a working breed with a dangerously low population and a perilously narrow genetic base; the kind of diversity that engendered that comment is hardly to be deprecated in such circumstances.) 

We hear endless discussion about inbreeding and its evils, and rightly so; yet we hear very little about the dangers of sustained extremes of artificial selection, which are if anything yet more dangerous than inbreeding. Together these two factors become an engine for the destruction of genetic diversity. People's constant obsession with having the "best" dog and with "breeding only the best to the best," whether in dog-show terms, in dogsled racing, or whatever, creates a situation in which the best is definitely the enemy of the good. The endless repetition of the inbreeding/selection cycle in the quest for a dog that is better than last year's best, has systematically stripped away most of the healthy genetic diversity from today's purebred dogs. Stringent, sustained selection for cosmetic ideals (shape, number and intensity of the Dalmatian's spots; shape and chiseling of the poodle's muzzle; subtleties of colour and markings in an endless series of breeds) or narrow ideals of performance or athleticism (top sprinting speed in racing greyhounds or racing sleddogs) have for many decades taken absolute precedence over breeding to provide the kind of "genetic outfit" that will allow the dog to be healthy and hardy. 

Now that canine diversity has been stripped to the point that homozygous recessive "defect" genes are everywhere apparent, the dog fancy proposes to remedy the situation by embarking upon a new level of elevated selection, armed with DNA marker testing to enable the wholesale "elimination" of "defective" genes. This new wave of super-selection on top of the already extant depauperisation may well become the killer wave that will sink the ship of purebred dogdom, AKC, CKC, and The Kennel Club with it. DNA testing has become a growth industry. This all may be more about corporate profits and grant money, than about canine genetic health. It is up to breeders to have the common sense to realise that what is being proposed is a losing game, that already depauperate purebred breed genomes will not support further massive artificial selection and the consequent wholesale elimination of yet more genetic diversity. The "defect" genes cannot be excised with a scalpel; many other genes that happen to reside on the same chromosomes will go right along with the defects, with totally unforeseeable consequences.
​ 

Conclusion 

In conclusion, let me say that, although this set of guidelines cannot be made into hard and fast rules or (worse yet) regulations -- because the situations of each individual dog breed and even each breeder are different -- yet I believe we all need faithfully to attempt to apply such principles as those discussed above, in order that our dogs may have long, healthy lives upon the earth. We have made them whatever they are today; we are responsible for and to them. We should therefore strive to be faithful and responsible stewards of the genetic heritage of our canine friends. In that way we may hope that our bloodlines will endure longer in the dog world, and in the end we may even be remembered as pioneer 21st Century dog breeders who strove heroically to correct the errors of the past in the light of better knowledge of population genetics. 
​

If you saw my posts summarizing the DNA data on the genetic diversity of terriers as well as dozens of dog breeds across all the groups, you realize that for many breeds the situation is grim. Many breeds with multiple, serious genetic disorders to deal with lack the genetic diversity to be able to select away from the problematic genes. Yet the prevailing notion is that "health testing" - by which we mean DNA tests - will produce healthier dogs. It hasn't and it won't.

Every breeder, through the dogs they produce, affects the quality of the shared gene pool of a breed, so it behoves all breeders to not just understand the basics of population genetics themselves, but to make sure others in the breed do as well. We are entering a new era in the breeding of purebred dogs, where the quality of the breed as a collection of animals must be the goal instead of the progress of an individual breeding program.  The principles to do this are grounded in population genetics, which provides the concepts and tools necessary to protect and preserve the genetic resources of our purebred dogs. Bragg has collected here the essential elements necessary to produce healthy dogs, generation after generation, from a properly managed gene pool. Embrace them.
If you're ready to adopting sound genetic management strategies in your breed, the place to start is with the online courses offered by ICB.

​"Managing Genetics for the Future" is a great place to start, and a class is starting on 2 April 2022. You can get more info about the course and register on the ICB  website.
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Breeds with the BEST & WORST genetic diversity

3/28/2016

 
By Carol Beuchat PhD

Carrying on from my blog post "What are we going to do about Terriers" (which you will need to read in order to understand the rest of this), I decided to post the pages for all of the groups that I had compiled.

From these, I have now gathered together a page of "best" and "worst" breeds that will make it easier to get a sense for which breeds are in the most trouble. Note that I did not include all breeds for which there are data on the MyDogDNA (MDD) website, and for some breeds there aren't enough data to display. So if you don't see your breed on the "worst" list, don't take that to mean that it's in robust genetic health. Go see if there are data available that I didn't include.
Here's a quick primer about how to interpret these data.

For each breed there is a scatter plot and a line graph. The scatter plot displays the data points for the individual dogs. They are usually color coded by country, and on the MDD website there are sometimes options to display these data by use (e.g., show, work, companion, etc).

Note that the scatter plot is not a typical graph: the x-axis is labeled "genetic relationships", and the y-axis has no label at all. This is because the graph was created by taking all of the data for a breed and asking the computer to find some characteristics in the DNA data that would separate all of the individuals along a gradient in the horizontal direction, then do the same thing in the vertical direction. This will separate all of the data in a way that displays the degree of genetic similarity (or difference) between individual dogs as proportional to the distance between their points. Then if you code the points by country of origin, you might see that the clusters correspond to different countries (like these data for Golden Retrievers). This is useful because it can tell you whether there are clusters of genetically distinct subpopulations in a breed, which would be handy if you wanted to outcross to improve genetic diversity in a litter. Because we don't really know what the actual differences are that separate these groups, the axes of the graph are usually labeled as "principal components"; in this case, "genetic relationships" is similarly vague.

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You will also see plots like this of multiple breeds. For these, you need to be very careful about interpretation. A group of breeds that clusters one way in one analysis, might cluster very differently if a few breeds are added or removed. This means that you might think that breeds A and B are very similar genetically because they cluster near each other on a graph, but find them far apart when they are displayed in a different mix of breeds. So for example, among the sporting dogs, the Toller seems to be very similar to the Chesapeake Bay Retriever (upper figure), but in an analysis of breed relationships, the Toller doesn't even cluster with the retrievers, never mind the Chessie (lower figure).
​
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Shannon et al 2016. Genetic structure in village dogs reveals a Central Asian domestication origin (supplement)

​The line graph below displays the data for percent heterozygosity, which is the proportion of loci that are heterozygous (the two alleles at the locus are different). Higher numbers are better (in the "green-is-good" zone), and lower numbers correspond to low heterozygosity (= higher homozygosity = higher inbreeding).

The median value for Goldens is low (32.0%), but there is a tail in the "good" direction (representing dogs that are less inbred) and, as you can see from the scatter plot above, there are genetically distinct subpopulations that could be exploited to improve heterozygosity.
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Note that the orange line is not a depiction of "normal", or "good", or even adequate. It simply represents all of the dogs in the database, and you will note that the peak is down where green is fading into a moldy-looking yellow. A genetically healthy breed will have high heterozygosity and therefore a low incidence of disorders caused by recessive mutations because they must be homozygous to be expressed. The DNA testing we do is not "health" testing; it is mutation testing. If we want to have a health test, it should be the measurement of heterozygosity, which will suit for ANY recessive mutation, known or otherwise, and we could toss the mutation-specific tests. It would also reflect the genetic health of the immune system, which under natural selection is maintained as the most diverse part of the genome.
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Bear in mind when you look at these data that they are not part of a formal study. The data are from whatever dogs are submitted for testing. It's tempting to say that they're biased, or not representative of your breed, or skewed towards show dogs, or too heavily influenced by dogs from Finland (which is where MyDogDNA is), or whatever. Don't do this. More data might shift some curves around a bit, but for most I suspect things won't change enough to matter. There are only a few breeds that can burnish their diversity credentials. For the rest, breeders should consider how they can minimize loss of the diversity they still have and make better use of it to improve the health of the next letter.
If you sailed through the explanation of the graphs, head over to the page of "best" and "worst" breeds.

And if you're not happy about the data for your breed, join one of the ICB courses that teach you the basics of population genetics and how to breed to produce healthier dogs by protecting the health of your gene pool. (The next course starts 4 April.)

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What are we going to do about Terriers?

3/25/2016

 
By Carol Beuchat PhD
Update (27 March): There was so much interest in these data that I have created a page on the ICB website with links to all of the pages that I compiled from the MyDogDNA data. You can find that here.

This morning at the top of my Facebook news feed was a post by a long-time terrier lover and "dog writer", Billy Wheeler, about the potential demise of the Sealyham Terrier, which suffers from declining popularity and diminishing numbers.

​Over the last few weeks, I've been gathering up information from various sources about the genetic diversity and population numbers of dog breeds. While I'm still dredging for data, the information for terriers had already caught my attention. Although I didn't yet have things properly organized and documented for public review, Billy's post has prompted me to share with you some of this information. As I said, I wasn't planning on putting this out there now, but sooner is definitely better than later, and with apologies to the reader for rough edges, I share with you my response to Billy.
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Billy's post:
The Sealyham Terrier is almost extinct. AKC why do you not publish registration numbers? Dog lovers, show this photo of Cruft's winner, CH Efbe's Hidalgo at Good Spice (beautifully captured by 
Lisa Croft-Elliott) to your friends, relatives, and neighbors. Tell them a breed once owned by the British Royal family and movie stars is almost gone. It is estimated that there are less than 500 in the world today. That's way less than Gray Whales, Lowland Gorillas, or Polar Bears.

My response:
​Billy D Wheeler - I sat down at my computer this morning and saw this post, and I could kiss you. I've been working for a while on evaluating the genetic status of purebred dog breeds, and there are many breeds in peril, but as a group there is none worse off than the terriers. The information I'm pulling together isn't ready for prime time yet - I haven't written nice descriptions and the other text that should go with this stuff, but I'm going to offer it up for you to look at and I think you can figure it out well enough.

There are two things that are critical indicators of the genetic status of purebred dogs - the level of genetic diversity in a breed, and the population size. The latter is important because low population size results in a faster rate of inbreeding - there just aren't enough dogs to breed to, and inbreeding results in the expression of deleterious mutations that compromise health.

Here are some data in a number of forms that you can evaluate.

First, I have gathered up the breed-specific data for genetic diversity and population structure from DNA analysis on the MyDogDNA website (www.mydogdna.com) and organized them here -

http://www.instituteofcaninebiology.org/mdd---terrier-breeds.html

At the top of the page (and included below) I have posted the heterozygosity data for all breeds (the breed names will be way too small to see, but you can download a larger file at the bottom). The horizontal line is the median heterozygosity for all dogs in their data, and the green horizontal line is the median for mixed breed dogs. High heterozygosity (low inbreeding) is to the right, low to the left. Below this graph I have enlarged just the left end (and turned it vertically) so you can read the breed names and I've highlighted the terriers among this group.
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Below this are the data for each breed. You will see a scatter plot on the left that might be color coded by country or other criteria, and on the right you will see the frequency graph of genetic diversity (heterozygosity) for the breed in blue, and the lines for similar or related breeds (green), and all dogs (orange). Healthy breeds will be to the right, genetically impoverished (i.e., low heterozygosity, high inbreeding) will be to the left. Just scroll down the page and you will see the blue curve shift right and left. Note that for some breeds there aren't enough data to produce these curves (e.g., Sealyham, unfortunately).
Breeds with robust genetic diversity include the Rat Terrier and Jack Russell. Breeds falling off the genetic cliff on the left include the Airedale, Bedlington, Bull and MiniBull Terriers, Dandie Dinmont, Manchester, Scottie, and... well, just scroll through. ​
Jack Russell Terrier
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Scottish Terrier
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​Some of the breeds with low heterozygosity might not seem from general impressions to be in such dire straits, but you need to consider these data together with the other information available. For instance, Bull Terriers have very low genetic diversity, and this has been confirmed in other studies as well, including the data just published last year by the UK Kennel Club, which I have compiled here.

http://www.instituteofcaninebiology.org/terriers-select-breeds.html

If you look at the graphs below for Bull Terriers, you will see that it not only confirms the high inbreeding coefficient (that's the blue line zooming past the horizontal red line on the graph to the right), but it also shows that the trajectory of the breed appears to be going ever skyward - AND the registration numbers in the graph on the left are dropping like a rock. As the population size declines, this will necessarily increase the rate of inbreeding.

In the right hand graph, the red squiggly line is the inbreeding level that would be possible if the dogs were breeding randomly and the blue line above this indicates that dogs being bred are more closely related than average. The green horizontal line is inbreeding of 5%, the red horizontal line is 10% - this is inbreeding that has accumulated just since 1980. I hope this is enough explanation to give you a sense of what this means.
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Billy, breeders are understandably trying to improve health by identifying specific mutations and breeding away from them one at a time. But heterozygosity is the only true "health test" - because it is for ALL genes and mutations - and most of these breeds are headed in the direction of extinction.

I have talked here about the risks that come with small population sizes:

http://www.instituteofcaninebiology.org/.../the-trouble...

To the biologists, the future of many terriers breeds is in clear jeopardy (and again, the worst off aren't even on these graphs because of low numbers and not enough data - Sealyham, Cesky, etc). As I put the data together for terriers and the other breed groups, I struggle with finding a way to communicate this information to breeders in a way that will encourage them to look past the ribbons and litter of adorable puppies and recognize that we need to take action if these breeds are still going to be around 25 or 50 years from now. Many are on the UK KC's list of vulnerable breeds, but there is no plan to do something about this.

I had no trouble at all convincing canine geneticists that we should study the DNA of these breeds now before we lose them, and we will be working on getting that project going in the next 6 months or so. This information could also form the basis of a genetic restoration plan if such a thing could be organized. But those that love these breeds need to recognize that there is a serious problem, and hunker down and make a plan to not just improve numbers but also adopt breeding strategies that will preserve and improve the existing gene pools.

I would have no trouble at all getting canine geneticists and population biologists interested in working on a plan to address these problems, but the interest and support must come from the breeders.Unfortunately, I despair that breeders won't take this seriously.

I would love to hear your thoughts.

You can download a copy of the graph of heterozygosity for all breeds here:
_-_mdd_genetic_diversity_by_rank_copy_2.png
File Size: 134 kb
File Type: png
Download File


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Evaluating the genetic status of a breed using both pedigrees and DNA

3/20/2016

 
By Carol Beuchat PhD
​
There's a nice little paper just out about the Bullmastiff that provides a useful discussion of how both pedigree information and DNA analysis can be used to assess the genetic status of a dog breed. They worked on the population of Bullmastiffs in Australia, which descended from dogs imported from the UK. Although the breed was recognized by the British Kennel Club in the 1920's, the pedigree data for the animals in the Australian registry only go back to 1980, so documentation of the ancestry of the population is incomplete. This means that pedigree analysis will underestimate the current inbreeding level because it documents only the inbreeding that has accumulated since 1980. While there is much to be learned even from incomplete pedigree data, DNA analyses can complement pedigree analysis as well as fill in some of the gaps in pedigree data.
A nice thing about this study is that they genotyped nearly 200 of the 16,739 dogs in their pedigree database, so the were able to compare information produced on both platforms. They also compared their estimates of homozygosity (inbreeding) for Bullmastiffs with information for 12 other breeds from previous studies. Finally, they examined the genetic relationship between the Bullmastiff and 30 other dog breeds. 
They characterized the Australian Bullmastiff population using standard statistics from population genetics, and they do a nice summary of what these mean in the paper. Those with some basic background in population genetics of dogs will recognize some of these, such as effective population size, effective number of founders, and effective number of ancestors. They also used some techniques specific to DNA analysis such as "runs of homozygosity" (ROH), which reflects the abundance and magnitude of stretches of the DNA that are homozygous. ROH can be used to distinguish between recent and ancient inbreeding (e.g., from the time of breed establishment).
A really cool thing they were able to do with the genotype data is display the relationships among all individuals as a network, with closely related dogs organized as clusters and lines connecting related clusters. This a nice way to convey the complex relationships among animals, especially in populations like dogs where the breeding patterns can be unusual and even involve animals long since deceased.
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Unless you have Bullmastiffs, you probably won't be interested in the details of the results, but this is a great resource for learning about the basics of population genetics and the use of both pedigree and DNA information to reveal the genetic health of a breed. As the authors point out, managing inbreeding and reducing the expression of genetic disorders will require information about the genetics of both the individual and the breed, and you can expect to see more and more of these studies as breeders adopt modern strategies for genetic management. Pedigrees provide a roadmap that documents the genetic history of a breed and the relationships among current animals, while DNA can distinguish between old and recent inbreeding and provide fine scale resolution of genetic differences between closely related animals.

Although many of these tools (and the jargon) will be unfamiliar to some breeders, I think this paper is a great place for the novice to dip their toes into the modern genetics of populations. You will find some basic courses about population genetic on the ICB website, and courses to help breeders understand and use the tools of molecular genetics are coming soon. The next five years or so is likely to see an explosion of breed studies similar to this one as breeders recognize the importance of genetic management at the breed level to the control of genetic disorders.

Mortlock, S-A, MS Khatkar, & P Williamson. 2016. Comparative analysis of genome diversity in Bullmastiff dogs. PLoS ONE 11(1): e0147941. doi:10.1371/journal.pone.0147941 (download the pdf)

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Reprise: The Pox of Popular Sires

3/15/2016

 
By Carol Beuchat PhD
​
In a recent post, I identified three things breeders can do that will improve the health of purebred dogs (Three key strategies to reduce genetic disorders in dogs). One of these was to prevent a few individual dogs from making a disproportionate contribution to the gene pool by having more than their fair share of offspring. This, of course, is the Popular Sire - that top-ranked dog that you're convinced has all the qualities you would dearly love to see in your next litter. Everybody wants a piece of him, and convinced that he has so much to offer the breed that it would be wrong not to use him, breeders rush to get in his date book and the proud owner basks in the glow of his celebrity.

But popular sires destroy gene pools. How could such a beautiful animal be so bad for the breed?

This was first published in December 2013, but if you missed it then or are new to the fancy, here's the story of Hank and his unfortunate genetic legacy.

The Pox of Popular Sires
The most common admonition of the geneticist to the dog breeder is to "avoid the Popular Sire Syndrome". At the same time, the most common advice from breeder to breeder is "breed the best to best". So the conundrum is obvious and the consequence predictable - the "best" dogs are the most sought after, so they sire the most offspring and become popular sires.

The Popularity of Popular Sires
Even a century ago Williams Haynes (1915) was writing about the "Effect of the popular sire", noting that in three terrier breeds that he examined - Irish Terriers, Scottish Terriers, and Fox Terriers - about 40% of the puppies were sired by only 20% of the sires. Back then, "popularity" was quite different than now - his "prolific" dogs sired 5-7 litters, which would be completely unremarkable today. And surprisingly, Haynes thought that popular sires actually benefitted the breed by contributing to the preservation of variability in type.

Superficially it might appear that if approximately 40% of the puppies each year are sired by but 20% of the stud dogs this would eventually result in the greatest uniformity of type. The selected sires are all to a greater or lesser degree exceptional animals, but they are not selected by any uniform system. Most of them excel in some particular physical point, but they do not excel in the same points or in the same degree, nor even, in some cases, in the same direction. Here the personal equation, the ideals of different breeders, is at work, and the result is that since a few males not themselves of uniform type sire a greater-than-average number of offspring they disturb the race average of the following generation and introduce abnormal amounts of variation. The fact therefore, that artificial selection gives to certain selected, but not uniform, males an undue preponderance of influence must always keep the type of domestic animals in an unstable state. This seems to me an important factor in the great variability always noted among domesticated breeds.

Haynes thought popular sires were a good thing, because he thought they were sufficiently different from each other that they prevented the breed from becoming too "uniform". How then did the popular sire go from contributing to the quality of the gene pool in 1915, to the source of a problem to be avoided by breeders 100 years later? What is this "syndrome" that today's geneticists are so concerned about?

Breaking Bad: DNA
To understand the problem, you must understand a bit of genetics. You probably know about mutations - bits of DNA that are not replicated perfectly or are perhaps damaged by some environmental toxin. If the mutation is dominant and affects some vital process, it is removed from the gene pool by natural selection when that individual fails to pass its genes on to the next generation successfully. But many mutations have no ill effects because their paired, dominant allele functions normally. These "recessive" mutations are silent in the genome and can be passed to the next generation the same as any other gene, and as long as the offspring has a copy of a normal allele the mutation remains silent. The mutation becomes a problem when an individual inherits two copies so is homozygous at that locus. Without at least one copy of the normal, unmutated allele, the gene does not function properly, and the consequence can range from something relatively trivial (e.g., a different eye color, or slightly shorter legs) to the catastrophic (e.g, blindness, disruption of a critical biochemical pathway, cancer).

Mutations happen all the time. The ones with immediate ill effects are removed from the gene pool by natural selection, while the recessive, silent ones remain in the genome as the "genetic load". Every dog - in fact, every organism - has its own unique collection of damaged alleles that causes no harm as long as there is also a copy of a normal allele of each that can do the job it is supposed to.
A Star is Born
Now consider what happens in a population of purebred dogs. Let's pretend that this cute collection of dogs represents your breed, with the phenotypic variations among them representing the nuances of type that would be obvious to a serious breeder. We've given each dog a (typographic) recessive mutation, a bit of DNA damage that is not expressed so it has no detrimental effect on the dog. If each dog in our population has a litter of puppies this year, the frequencies of these various alleles in the population will stay about the same in the next generation.

But what happens if one of these dogs wins big at an important event and becomes a star? If it's a bitch, she will have a litter of much sought-after puppies, and it will probably be at least a year before she is bred again.

​

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If our star is male (let's call him "Hank"), he will be bred many times and produce dozens (or more!) puppies in a single year. Hank will pass half of his genes, both good and bad, to each of his offspring, so many copies of his recessive, silent mutations get distributed in his puppies.

As long as Hank's deleterious mutations are paired with a normal allele in his puppies, they are not expressed and cause no ill effects. But if you could view the gene pool of the breed in the new generation, you would see that now it is markedly different.

Hank's mutation has in just a single generation gone from being rare to common, and now lurks silently in the genomes of dozens of his offspring. In this generation, noone is any the wiser. The prized puppies that carry their sire's recessive mutation will appear to be no different than the ones that don't.

​
The Next Generation...
But in the next generation we start to see the first hint of trouble. Perhaps there were a few half-sib matings, or father-to-daughter, and some puppies are produced that are homozygous for Hank's mutation. Perhaps the mutation is lethal and these are stillborn pups, or maybe the puppies are born with a disease. But the breeders will be mystified - they have never had this problem in their line, or even in the breed, so maybe it's just bad luck? Nobody can see yet that this is just the tip of the iceberg.

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In one more generation, however, the trouble really begins. Carriers produced by the first generation will pass on the mutation to half of their offspring, and half-sib matings or line breedings back to the sire will begin to produce affected puppies. Even while the number of affected puppies is still relatively small, the number of carriers will by now be significant, and remember that our popular sire probably continues to produce more than his fair share of the offspring in each generation. You can see where this is headed. The seeds have been sown.
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Every litter produced by this popular sire is one less reproductive opportunity for any of the other potential sires in the breed, so the frequency of genes carried by those unused sires will decline in the population. At the same time, multiple bitches are producing puppies sired by Hank that will be half-sibs to the dozens of other puppies in their generation. The temptation to capture a bit more of that popular sire's star qualities will probably result in a few line breedings that will put carrier with carrier.


Uh-oh, We've Got A Problem
This is about the time breeders begin to notice that there is a "problem" in the breed. It won't take a pedigree sleuth to trace the growing population of affected dogs back to Hank, our popular sire who will now be blamed for introducing this new disease into the breed. Geneticists will be called in to hunt for the defective bit of Hank's DNA and to develop a reliable test. Then breeders will begin the mission of trying to eliminate Hank's formerly valuable genes from the gene pool, with proportional collateral damage to the genetic legacy of all of the bitches he was bred to. The genetic carnage resulting from attempts to purify the breed of the unfortunate mutation will continue for generations. The ultimate damage to the gene pool can be catastrophic.
This happens over and over again in breed after breed. Of course, the problem isn't poor Hank. Wind back the clock, and if the judge had pointed to a different dog at that fateful show - let's say it was Rosco who got the nod - the trajectory of the breed would have been completely different but the consequences pretty much the same. Rosco will leave his genetic legacy behind in dozens of lovely puppies, half of which will have that one nasty mutation that will emerge a few generations down the road to bite the breed. Breeders will eventually catch on, sound the alarm, and the effort to identify and eradicate the offending mutation will begin. The gene pool will be purged, and the next time a big winner appears that happens to be male, the cycle will begin anew.
The Unfortunate Legacy of the Popular Sire
The really unfortunate thing about the Popular Sire is that the negative genetic consquences of his popularity don't begin to manifest for generations, by which time the breed already has a really significant problem.

​The large number of breed-specific disorders known to be caused by a single recessive gene (175 as of this writing; OMIA) is testimony to the prevalence of the problem (indeed, some breeds now suffer from multiple recessive genetic disorders).
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Of course, it is not just the recessive mutations that are disseminated widely by popular sires. Any genetic disorder can become quickly widespread, especially in the absence of any means of documenting the appearance of a new disease and if breeders are not willing to be completely transparent about issues they are aware of.
Unacceptable aggression in English Springer Spaniels, which used to be one of the most popular family dogs in the US, appears to be genetic and has been traced to one popular sire from a prominant kennel (Reisner & Houpt 2005; Duffy 2008).
​Twenty-five percent of Bernese Mountain Dogs die at an average age of only 8 years old from histiocytic sarcoma (Dobson), a fatal cancer that apparently originated from a single dog in Switzerland, and the flames were fanned by a prolific great-grandson in the US that spread the malignant genes far and wide in the gene pool (Dobson 2013; Moore 1984; Moore & Rosin 1986). Many Dobermans die at an early age from sudden heart failure caused by dilated cardiomyopathy, which can be traced to seven popular sires in the 1950's, three of which died of heart failure. A serious - usually lethal - susceptibility of Miniature Schnauzers to infection by Mycobacteria avium (referred to as "MAC" for Mycobacteria avium complex) is thought to be traceable to a sire popular in the mid-1980s and is found now in dogs all over the world. There are no doubt many other similar examples that I am not aware of or have never been documented.

Leroy (2011) has identified popular sires as the single most important contributor to the dissemination of genetic diseases in purebred dogs. Recognizing this, the FCI has issued a recommendation to breeders that no dog should have more offspring (presumably in its lifetime) than equivalent to 5% of the number of puppies registered in the breed during a five-year period, and a number of national kennel clubs have followed suit (e.g., Finland). But without cooperation of breed clubs, or in the absence of some authority that would oversee registrations and be in a position to police such a breeding restriction, it is hard to see how such a recommendation would have any effect at all on current breeding practices. (Which 5-year period? Which population of dogs - the worldwide breed, or just the dogs in your country? Who does the counting - the owner of the sire, the owner of the bitch, the breed club, the kennel club??).

The only people benefitting from the explosion of breed-specific genetic disorders are the molecular geneticists, who have discovered dogs as an ideal research animal because many of the same disorders occur in humans (Ostrander 2012). But as useful and fascinating as dogs might be for their research, I suspect all would prefer to see dogs that are free of genetic disease, for they have so much more to offer in the family home than in the lab.



  • Dobson, JM. 2013. Breed-predispositions to cancer in pedigree dogs. ISRN Veterinary Science 2013: (doi: 10.1155/2013/941275)
  • Duffy, DL, Y Hsu, JA Serpell. 2008. Breed differences in canine aggression. Applied Animal Behaviour Science 114: 441-460.
  • Haynes, W. 1915. Effect of the popular sire. Journal of Heredity 6: 494-496.
  • Leroy, G. 2011. Genetic diversity, inbreeding and breeding practices in dogs: results from pedigree analyses. Veterinary Journal 189: 177-182.
  • Leroy, G & X. Rognon. 2012. Assessing the impact of breeding strategies on inherited disorders and genetic diversity in dogs. Veterinary Journal 194:343-348.
  • Moore, PF. 1984. Systemic histiocytosis of Bernese Mountain Dogs. Veterinary Pathology 21: 554-563.
  • Moore, PF & A Rosin. 1986. Malignant histiocytosis of Bernese Mountain Dogs. Veterinary Pathology 23: 1-10.
  • Ostrander, EA. 2012. Both ends of the leash- the human links to good dogs with bad genes. New England Journal of Medicine 367: 636-346.
  • Reisner, IR. & KA Houpt. 2005. National survey of owner-directed aggression in English Springer Spaniels. Journal of the American Veterinary Medical Association 10: 1594-1603.
  • Wellman, R. & J. Bennewitz. 2011. Identification and characterization of hierarchical structures in dog breeding schemes, a novel method applied to the Norfolk terrier. Journal of Animal Science 89: 3846-3858.


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That purebred vs mixed breed thing again

3/13/2016

 
By Carol Beuchat PhD

"Health of purebred vs mixed breed dogs: the actual data"

I wrote this last year, but it clearly needs to get out more because every few days I hear somebody proclaim that "Purebred dogs are just as healthy as mixed breed dogs!" 

The latest is in this month's Canine Chronicle, in an argument against the breeding of "designer dogs". The designer dog thing is beside the point here, but what is really troubling is the amount of misinformation that is declared to be scientific fact, of which the mixed vs purebred thing is just one example.
The bottom line is that we can't reduce the alarming prevalence of genetic disorders in purebred dogs if breeders don't know even the most basic things about genetics. If we can't do better than this, I despair for the future of the purebred dog. 
​
How many incorrect statements presented as scientific "facts" in this article can you find? (Hint: I've written about many of them in my blogs on the ICB website, and just scanning the list of titles should turn up a few.)
​
The Canine Chronicle article: 
"Raising the alarm on designer breeds"

Here's the note I sent to Tom Grabe, the Chronicle's  editor:

Hi Tom,

I was so pleased to see Peri Norman's article about the need to preserve the genetic diversity in our purebred dogs for the same reasons that there are now global efforts to protect the "heritage" livestock breeds.

But I'm dismayed to see in this month's issue the piece by Attila Márton about designer dogs that is full of statements that are demonstrably false. Anybody who survived an undergraduate (or even high school) biology class will have learned about dominant and recessive alleles and should be able to explain why breeding related dogs together will increases the risk of producing genetic disorders, because related dogs are likely to share the same mutations. Similarly, breeding unrelated dogs, such as two different breeds, will reduce the risk of genetic disorders.

Not only does that make perfect sense, but it is borne out in the studies the author claims don't exist. The so-called "Davis" study was widely claimed amongst the dog show folks to have proven that purebred dogs are just as healthy as mixed breeds. In fact, it clearly shows just the opposite. Mixed breed dogs are more likely to have three problems: patent ductus arteriosis (an anatomical condition), ruptured cruciate ligament, or injury from getting hit by a car. For all of the other conditions reported in the study, purebreds were worse off, as I have summarized here: Health of purebred vs mixed breed dogs: the actual data.

I won't go through all of the other false claims in that article, but I would point you to my discussions about hybrid vigor in dogs (The myth of hybrid vigor in dogs...is a myth), about why DNA tests will not solve the problem of inherited disorders in dogs (Why DNA tests won't make dogs healthier), about why recessive mutations have become such a problem (Why all the fuss about inbreeding? (Or "Why are there so many genetic disorders in dogs?"), and about why it's impossible for a breeder to "know what's in my lines" (The fiction of "knowing your lines"). I would also point you towards Three key strategies to reduce genetic disorders in dogs and Ian Sneath's commentary about it (The sins of the father are laid upon his children).

I've put down the camera and have spent the last three years doing the much more important work of trying to educate breeders about the genetics they MUST understand if we are to reduce the burden of genetic disorders in purebred dogs. To solve this problem, breeders will have to get the science right, whether they believe it or not. I urge you to use your platform to help clear the facts from the rubble by insisting that those writing about the genetics of breeding know what they're talking about.

With my best regards,
Carol Beuchat

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