Line Breeding versus Out Crossing

Dr. Angella Hughes from MARS veterinary USA will discuss a new genetic tool which allows breeders to choose potential breeding mates by measuring breeding coefficients of their breeding stock. This test provides breeders with a better understanding of the specific chromosomal patterns (haplotypes) their dogs carry, allowing them to use that information in their breeding decisions and work to maximize the genetic diversity or heterozygosity in their puppies.

Dr. Angela Hughes Podcast with Pilar

Optimal Selection - genetic breeding analysis

These educated idiots have no idea on how to breed performance bred canines. This is the exact opposite of how you should breed. No wonder, so many working canine breeds are absolutely pathetic. Thank God for euthanasia.

A very liberally edited version of an article by Jerold S. Bell, D.V.M. that appeared in the September 1992 American Kennel Club Gazette, "The Ins and Outs of Pedigree Analysis, Genetic Diversity, and Genetic Disease Control" ... followed by some personal observations.

Without exception all breeds of dogs are the result of inbreeding. Inbreeding has either occurred through natural selection among a small isolated population (i.e. the dingo) or through the influence of man breeding selected animals to derive specific traits. Either way intensive inbreeding is responsible for setting enough of the dominant traits that the resulting group breeds true to type. At which point a population of dogs can be said to be a breed.

Dogs actually have more genes than humans. Tens of thousands of genes interact to produce a single dog. All genes are inherited in pairs, one from the sire and one from the dame. If the inherited genes from both parents are identical they are said to be homozygous. If the pair of inherited genes are not similar they are said to be heterozygous. The gene pairs that make a German Shorthair breed true to type are obviously homozygous. However, variable gene pairs like those that control coat color, size, scenting ability, etc. are still heterozygous within the breed as a whole.

Line-breeding concentrates the genes of a specific ancestor or ancestors through their appearance multiple times in a pedigree. When a specific ancestor appears more than once behind at least one animal on both the sire's side and yet another animal on the dame's side homozygosity for that animal's traits are possible.

However, if this specific ancestor appears only through a particular offspring of the ancestor in question then the Breeder is actually breeding on this offspring of the ancestor rather than on the ancestor itself. This is why having many "uncovered crosses" to a specific ancestor (those that come through different offspring of this specific ancestor) gives the Breeder the greatest chance of making the desired traits of the specific ancestor homozygous.

Homozygosity greatly improves the chances that the resulting pups will in turn pass on the desired traits of the specific ancestor to their pups. When selecting pups from a line-bred litter the Breeder must choose pups that display the desired traits of the specific ancestor or they have accomplished little. In fact, if these traits are not present in a line-bred pup it is very likely that it inherited its genes from the remaining part of its pedigree and will be unable to breed true to type. Because the Breeder selected “out” for the pups that didn’t display this original ancestor’s traits.

Inbreeding significantly increases homozygosity, and therefore uniformity within a litter. One of the best methods of evaluating how successful a line-breeding has been is to gauge the similarity of the littermates as compared with pups of other litters with similar pedigrees. Considerable similarity among littermates tells the Breeder the genes have "nicked" or paired together as anticipated. The resulting pups will likely be able to pass these genes to the next generation.

Undesirable recessive genes are always masked by a dominant gene. Through inbreeding a rare recessive gene can be passed from a common ancestor on both the sire and the dame's side creating a homozygous recessive offspring. The resulting offspring actually displays the trait neither of their parents displayed (even though both of them carried it). Understand that inbreeding does not create undesirable genes it simply increases the chance that traits which are already present in a heterozygous state within the breed will be displayed.

Too many Breeders outcross as soon as an undesirable trait appears, blaming the problem on breeding "too close." Nothing could be further from the truth. In fact out-crossing insures that the undesirable trait will be carried generation after generation in a heterozygous recessive state only to rear its ugly head again and again. Therefore the Breeder who turns away from breeding “close” is simply passing a known problem on to succeeding generations and future Breeders.

When an undesirable trait is "unmasked" the Breeder who does his breed a real service is the one that stays with his line long enough to rid it of the undesirable trait. By controlling which specimens within their line are used for breeding in succeeding generations this Breeder can eliminate the undesirable trait. Once the recessive gene is removed it can never again affect the Breeder's line. Inbreeding doesn't cause good genes to mutate into bad genes it merely increases the likelihood that they will be displayed. 

The “inbreeding coefficient” (or Wrights coefficient) is an estimate of the percentage of all variable genes that are homozygous due to inheritance from common ancestors. It is also the average chance that any single gene pair is homozygous due to inheritance from a common ancestor. Our pedigrees display the inbreeding coefficient for each dog in the first 4 generations of a specific dog's ancestry. Each inbreeding coefficient is calculated from that dog's 10 generation pedigree.

Note: Inbreeding does not cause good genes to somehow mutate - it only increases the likelihood that existing genes will be displayed - allowing the Breeder the chance to eliminate what had previously been unseen in their particular line although it was always present.

At Westwind GSPs we gauge the amount of homozygosity in an animal using their inbreeding coefficient (or Wrights coefficient) - which can be seen as an estimate of the percentage of all variable genes that could be inherited from common ancestors. It is also give us a mathematical value for the average chance that any single gene pair is homozygous due to inheritance from a common ancestor.

Our pedigrees display the inbreeding coefficient for each dog in the first 4 generations of a specific dog's ancestry. However, the inbreeding coefficients displayed for each dog in our pedigrees is in turn calculated from that particular dog's 10 generation pedigree. We can trace most of our dogs back more than 20 generations - some as far back as 35 generations.

Our German Shorthairs

Four generation pedigrees that contain 28 unique ancestors for the 30 positions in the pedigree would obviously generate a low inbreeding coefficient. Yet a ten generation pedigree for the same dog might look quite different. If this dog were to have say 700 unique ancestors filling the 2048 positions in the pedigree the results for the same dog would be a much higher and truer inbreeding coefficient. Sometimes what appears to be an out-bred mix of genes in the first few generations (especially with owners naming their own dogs) ends up being a fine example of line-breeding when the pedigree is extended.

However, it must be remembered that simply knowing the inbreeding coefficient of a dog does nothing to help us understand which ancestors the dog is actually bred on. We know that the animal in question has many crosses to the same ancestors but we don't know which ancestors they are. To understand this, and to unlock the secrets of a dog's pedigree, we must do a homozygosity study.

A homozygosity study is not a percent blood calculation. The percent blood of a dog and its immediate ancestors is relatively easy to estimate but not that important. In fact the dog will have 50% of its blood from it’s sire and 50% of its blood from it’s dame. But if these two dogs have no common ancestors the inbreeding coefficient would be 0%. Homozygosity is far more important in determining what traits a dog is capable of passing on to its offspring than percent blood but it is extremely difficult to calculate without the use of a computer.

So while knowing a dogs inbreeding coefficient is important in accessing its potential to throw its type we still need to clearly understand which dogs behind a particular dog are the most influential. Simply knowing how homozygous a particular animal is does nothing to help the conscientious Breeder understand this. To understand this and to unlock the secrets of a particular dog's pedigree we must do a homozygosity study. We need to know which ancestors the dog in question is bred on.

On more than one occasion we have seen pedigrees in which the most influential ancestor for a homozygous trait doesn't even appear in the first three generations. In this type of situation it is not unusual for this particular ancestor to contribute 50% of the homozygous genes of the dog in question. In this case if a dog is 16% inbred one ancestor would be responsible for 8% or 50% of the dogs homozygosity. It is of paramount importance for the dedicated Breeder to know not only the inbreeding coefficient for the resulting litter before the mating is done but also which dogs in the pups pedigree are influencing their genetic potential.

Far too many matings have been done only on the basis of physical appearance with little if any regard to the sire's and dame's respective pedigrees or the interplay between the two. Novice Breeders don't realize that individual dogs may share desirable traits but inherit them differently. This is especially true of polygenic traits, such as ear set, bite, or length of forearm. And many Breeders fail to understand that breeding dogs which are phenotypically similar but genotypically unrelated won't produce the desired traits in the current litter - and will actually reduce the chance of these traits being reproducible in the next generation.

Conversely, individual German Shorthairs with the same pedigree do not inherit exactly the same genes and will not breed identically. Dogs in a litter are no more similar than brothers and sisters in a human family. Think about it. If dogs have more genes than people and they are as dissimilar as human siblings need we worry so much about the “too close” we hear sounded by all those who know little or nothing about linebreeding.  At Westwind GSPs we regularly breed litters with a Wright’s Coefficient of more than 20% with superior results. There have been examples in German Shorthairs of fine animals with inbreeding coefficients as high as 65%.

The secret is that all line-breedings must be made on a combination of performance, appearance and ancestry. If a Breeder is going to be successful in solidifying a certain trait they must rigorously select breeding specimens which display the desired trait and have similar pedigrees. In so doing Breeders have a chance of making this desired trait homozygous over time. This is the one key to successful line-breeding that is most often missed by unsuccessful Breeders.

In choosing a line of dogs within any bred it is wise to choose a line with "critical mass". Find a line within your breed where the most pre-potent individual was mated many times and produced many superior offspring. Without enough genetic diversity it will be more difficult to find animals within the line that do not also share the faults of the pre-potent individual. These are the faults the Breeder will have the most difficulty in eliminating.

No matter how limited the critical mass the Breeder must never breed animals that are poor examples of what the Breeder is trying to produce simply because they share common ancestors. Breeding “paper” is the quickest way to ruination and is largely responsible for the negative attitudes people have toward line-breeding. To a Breeder no dog is worth more than what it is able to produce. No amount of titles can overcome an animals inability to reproduce its own great traits. Look at the lack of production from Secretariat (a thoroughbred race horse).

Most beginning Breeders suspicion they should start with a brood bitch of a particular line and they are correct.  If at all possible the new Breeder should obtain females that come not just from the same important stud but actually come from the same Motherline that is behind the stud in question. Instead of trying to get a bitch as close to the stud in question look for a pedigree in which the mothers of the sires are themselves from the same genepool. This is the female who will likely produce great pups.

Motherlines in German Shorthairs

In all mammals the females are "X" "X" and males are "X" "Y" which means that only females carry the genetic code particular to the part of the gene string that is missing in all males. Horse Breeders refer to it the "X Factor" and have demonstrated that the gene responsible for the large heart so many great racing stallions have can be traced back thru their motherlines to a single mare that lived more than 100 years ago. If a stallion has an oversized heart - like Secretariat - this particular mare will show up in his motherlines over and over again. The mares themselves don't have the large heart but they carry the gene for it on their “X” chromosome. Likewise the stallions do not throw the large heart themselves.

And so it is with German Shorthairs. The bitches are far more important than the studs in carrying particular genes forward. Understand that this is true even if the genes most sought were originally found in a pre-potent male. The key for any successful Breeder is to isolate those females that carried his traits and breed off of them. It has been our experience that many important traits are indeed sex linked and carried by the dames from generation to generation.

Successful Breeders realize they are fighting "the drag of the breed," which is the tendency for all animals to breed back toward mediocrity. If it didn't work this way super species and super races would have developed long ago in every animal on earth. For instance in human beings it is impossible to breed parents with high IQs together to produce higher IQs. Even when two genius have children the average IQ of their children will be half way between normal and the average of their IQs.

By the way Einstein himself was the off spring of parents who were themselves first cousins - and he married his first cousin. So much for the tails of woe you heard in school about the effects of inbreeding. In fact the history of the German Shorthaired Pointer is replete with many examples of intensive inbreeding that produced some of the more influential dogs in our breed.

Useful information on Motherlines

This article was originally written in the 1930s by Dr. Kleemann (by whom the German Kleemann Seiger or KS tests were developed and for whom they are named. It was first reprinted in the Kurzhaar Blatter in August of 1962 then subsequently translated into English and reprinted in the GSP News in 1963. Once again it has been reprinted here (after being edited for brevity) for your review.

What is the meaning of "Motherlines?" The idea is too often confused by breeders with "motherside" or the bottom side of a pedigree, but Motherlines is the whole of the bloodlines of all the mothers, including the father's mother and the other mothers on the father's side of the pedigree; but always the mothers.

[the success of Motherline breeding comes from utilizing very important sex-linked genes present only in the additional DNA of the X chromosomes of great producing (Stamm) females. Since a male dog has 76 paired chromosomes plus an X and a Y chromosome the only place a male can inherit these important sex-linked genes is through his mother. Therefore, when this son becomes a father only his resulting daughters (never his sons) get this valuable X chromosome back again (along with another X chromosome from their own mother)

In turn, when these resulting grand-daughters become mothers the art of breeding lies in selecting only the male offspring that inherited this valuable X chromosome (as these great-grandsons will be able to pass the important sex-linked genes on to their get) In so doing we bring the influence of the Stamm female (through this valuable X chromosome) to the topside of the pedigree and dramatically improve our chance of producing great pups true to type when we breed to quality females from the same Stamm line. Thus the importance of having an unbroken Motherline on both sides of the pedigree]

Pedigrees only serve as a guide to show us what "blood" could be carried by certain animals. Only through careful study of a particular animal's offspring and intimate knowledge of its ancestors can we determine what "blood" an animal is actually carrying. It is necessary to breed both according to bloodlines and performance to achieve success. We are looking for animals who are outstanding performers within the same bloodline.

It is only by inbreeding that we can double up on the good and bad qualities so we can see what we are dealing with. When faults in the line come to the surface we can skim them off and get rid of them. By out-crossing we only cover up the faults and reduce our knowledge of what to expect in subsequent litters. Anyone who condemns inbreeding must in turn condemn the detective who brings crimes to light as well as the messenger who brings bad news.

A good brood-bitch is feminine, of finer build, a light and pretty head with a smaller and thinner neck, lots of nobility, but also depth for growing pups. You should be able to recognize a good brood-bitch at 100 meters and not find it necessary to look between her hips to tell her sex. Often I have seen young bitches which looked like grown males receiving much attention and being considered as future outstanding brood-bitches. These bitches never lived up to expectations.

And then there is Herta von der Maylust who was considered a "cat" at shows because of her fine build and light bone structure and was advised not to be bred because (it was thought) she would only produce poor small puppies. Yet Herta is a Stamm (original ancestor) mother behind many of our great dogs today.

If you have a bitch you must select a stud with complimentary motherlines. It is much simpler if you have a bitch from a great motherline so that you can profit from the long experience of breeders in that motherline and have little difficulty in choosing a good stud dog. With a little known motherline it is difficult to find the proper mate since there is but a small number of dogs to choose from. Look for a pup with a continuous motherline from known performers.

When sire and dame have the same motherlines you can generally count on outstanding pups and you will have classy breeding stock. To improve your motherline, you must bring together matching bloodlines holding fast to the good qualities and abolishing the bad. You then breed for performance, boldness, conformation, nose and waterwork. The Shorthair must be able to hunt for hours without tiring, he must have an outstanding nose and never give up on the retrieve of wounded game regardless of the distance.

Our German Shorthaired Pointers

Dr. Kleemann had been dead for 20 years when this article was first published, which was nearly 40 years ago. We all owe a great debt to Dr. Kleemann for his artistic ability to pick the right breeding stock when the breed was still very young and his willingness to put his keen observations in writing for the rest of us to follow.

A History of German Shorthairs

Unsuccessful Breeders regularly overlook an animal that has a great trait because it also has a minor fault in favor of an animal that has no faults but no great traits. Successful Breeders use specimens within their line that have at least one truly great trait and breed them with specimens that in turn are great where the other dog is weak. This is the "secret to line-breeding" the only way to successfully fight off the drag of the breed.

In so doing it is possible to line-breed offspring that are better than both the sire and the dame. Mathematically ¼ of the resulting pups have the possibility of getting the great traits from both parent. Plus, the resulting specimens in turn can pass these great traits on to the next generation, unlike the F1 hybrid animal that results from out-crossing that carries the same traits. This is how a successful Line-Breeder can actually improve his line as he condenses his gene pool.

So much is made about the perceived problem of a limited gene pool in pure bred dogs it has caused some "experts" to advocate out-breeding of all dogs. However, studies in genetic conservation of rare and endangered species have shown this practice actually contributes to the loss of genetic diversity. If we were to uniformly out-cross all "lines" in any breed we would eliminate the differences between the lines and therefore reduce the diversity between individuals within the breed. The process of breeding toward genetic purity of any particular line of German Shorthairs will in fact contribute to genetic diversity within the breed itself.

In fact what few people understand actually happens is that as a line is successfully bred over the years a concentration of good recessive genes is happening. Assuming the Breeder is a person of integrity and doesn't knowingly breed animals that have disqualifiable faults or traits. Over a period of time this Breeder will clean up his gene-pool. While it is true that line-breeding gives the opportunity for the worst traits to display themselves in any individual animal, it is not true that the Breeder is required to use that animal in his gene-pool. In fact if the Breeder is concerned with his gene-pool and not just about producing pups he actually has the opportunity to clean up genes that would go unnoticed in an outcross breeding.

What actually happens in a successful line-breeding program is that over the years the dominate genes in the line tend to lessen in number. This is because unless a dominate gene was selected out for in each successive animal it can never "reappear" in the same way that a recessive gene can. Obviously if neither of the parents displays this dominate gene then none of the offspring can - because it no longer exists in the gene-pool.

Dominant genes are either displayed or they don't exist. And it should be noted by any serious Breeder that the "Original Animal" his particular line was built on was the only animal in his line to carry all of the dominate genes originally possible. From that point in a truly closed breeding program there is only the chance that the number of dominate genes will decline as they are slowly being replaced on each point of the gene string by recessive genes. There is no other possibility unless a breeder outcrosses.

Therefore if the Breeder isn't skillful in accessing and selecting offspring they will lose some of their precious dominant genes over time. Often we hear Breeders say they are “needing an outcross”; what they are really saying is that they have lost their original dominant genes and have no other means of getting them back. These could be some of the most cherished traits of the Fountainhead Animal.

If possible it is wise for you as a Line-Breeder to freeze semen on old stud dogs in your gene-pool who are known to throw the dominate genes you value. This gives any Breeder the ultimate insurance policy, the ability to "outcross" within their own gene-pool if they were unfortunate enough to lose valued dominant genes over time. We have made good use of frozen semen on a number of occasions.

Our GSP Puppies

One of the more interesting things about a line-bred gene-pool is that it is difficult if not impossible to pass a line-breeding program on to another Breeder. Lets assume that you have put in the work and made the difficult decisions not to use certain specimens (even those with highly touted titles and awards) because they pass on undesirable genes. Let's assume you have managed to clean up your gene-pool. At the point another Breeder is lucky enough to bred to some of your best specimens it will improve virtually anything the other breeder has.

Unfortunately, while those who outcross to your line will improve their genetic structure the genes of your inbred line will tend to vanish because these genes will very likely be more recessive than the outcross genes.  In effect the outcross gene-pool will "cover up" your more recessive inbred genes. And there is not much either breeder can do about it, even if you wanted to. Unfortunately many breeders do this to themselves.

We have seen this many times over the years especially from those who think they can "buy their way in." The fallacy in their thinking is that they can buy a line-breed brood bitch from one line and a line-bred brood bitch from yet another line to breed to their great new Stud Dog, often their first German Shorthair. They think they can start a breeding program overnight from three different gene-pools because the dogs are such fine specimens. Oh, if it were so simple.

Often overly enthusiastic newbies in their over simplified thinking take this exact approach. Unfortunately, it is the third generation where the wheels come off. Why the third generation? Well the first two litters were dynamite because they were both F1 hybrid litters. But when the F1 hybrid offspring from one line-bred bitch are bred to F1 hybrid offspring of the other line-bred bitch things come apart. In fact this "well laid plan" is a sure receipt for breeding straight downhill.

So what is the answer? Wherein lies the truth? It is not what you want to hear but here it is: Years and years of line-breeding by a committed ethical Breeder - someone with a vision of perfection and the tenacity to make difficult decisions. The only way to consistently produce superior animals is to line-breed. Period ... it’s that simple!

Those who argue against line-breeding are inevitably those who have never successfully bred animals themselves; most often they are college professors. The same people who have bred nothing more complicated than fruit flies or no more demanding than lab rats are often the most vocal about how others should breed performance animals. These "know-nothings" advocate the notion that out-crossing is in and of itself good because it produces some thing they often refer to as "hybrid vigor".

To them, and to you, we pose this question: "If out-cross breeding is the answer then why don't the owners of successful herds of Holstein milk cows out-cross to the American Shorthorn milk cow?" In theory this would produce super milk cows by combining a milk cow that has the genes for high milk production like the Holstein with one that has the genes for high milk quality like the American Shorthorn. Oh yes on both paper (the stuff of academia) and in theory this should produce the best milk cows on earth.

But this is where the theory that reigns supreme in the professor’s lab meets the reality of the milk barn. Some of the most inbred animals on the face of the earth are Holstein Cattle. The reality is that dairy farmers know all too well is that they would go broke from the inferior milk production of the resulting out-crossed animals. Crossing to an animal with such poor milk production would be disastrous fore them. And here in lies the rub for all of us ...

Understand something and don’t let anyone sway you again. Outcrossing does NOT produce “more”, the genetic material remains the same. Nor do the qualities of the subject animals it produces multiply. Just as line-breeding doesn’t damage genes, out-crossing doesn’t magnify what’s in the genome. There is no magic in out crossing!

Note: So called "hybrid vigor" is never in and of itself the answer to breeding better specimens. The quality of the specimen used in any breeding is far more important than whether or not a particular animal has a very low inbreeding coefficient or whether the proposed breeding will result in a low inbreeding coefficient.

And for those who continue to stubbornly advocate out-crossing we ask you this final question: "Even if by random chance the outcross breeding in question would actually produce a superior specimen would the animal in question be able to reproduce itself?  Would the greatness be passed on to its get?" No.

The sad fact is that this superior specimen would likely not be able to reproduce itself. It will likely never throw a single specimen as good as it is in its lifetime. This is because by definition this “super specimen” is of the F1 generation and animals of that generation are rarely able to reproduce themselves. So what has been accomplished by even a successful outcross?  Little or nothing other than to put a single animal on the ground.

For fun I would like to invite this no-nothing college professor to the race track where for an afternoon he would have the opportunity to bet on all the out-crosses and I would bet on all the line-bred race horses. I believe we call them Thoroughbreds for a reason don’t we? Oh but I forgot he wouldn’t be the betting kind would he? Not in his lifestyle and not in his career. No, he would be the man of theory. He would be a man who lives in the world of theory.

Not us my friend! No, we both live in the world of fact. Yes, we live in the world of bird hunting where what separates the wheat from the chafe are immeasurable traits like “heart” and “bird sense”. At Westwind GSPs we understand how much is expected of these amazing athletes we call German Shorthaired Pointers. You see we own performance animals not lab rats.

Think about it. Those who advocate the out-crossing of birddogs are effectively proposing that bird hunters entrust the development of their performance dogs to the whims of random chance. If you believe this is a wise course then you need to locate another Breeder. May we suggest that you check the want ad section of your local newspaper where you will find many splendid examples of out-cross breeding.

Successful line-breeding is a long and arduous task, one that requires a lifetime's commitment to a particular line of dogs. We have great respect for the few Breeders of German Shorthairs who successfully developed and perpetuated their particular line of GSPs in the past, fighting negative public opinion all the way. Even if we don't have a single dog from their particular line in our pedigrees we have studied their breeding patterns and over the years have developed a deep appreciation for their work.

It is from the legacy of Breeders who refused to settle, who held to their standards when things didn’t go as planned that we owe so much. It is from those Breeders who bred to the brother of the champion because he produced better pups than the titled dog that all of us enjoy a robust GSP gene pool today. To them we all owe a huge debt of gratitude.

Our Breeding Philosophy for German Shorthairs

Although our breeding program remains a "hobby" our commitment to the German Shorthaired Pointer remains strong. We are looking forward to many more fine litters and many more years of great hunting behind our beloved Westwind GSPs. Which remains the single driving force behind our breeding program. Good Hunting.

Reference: Westwind GSP's

The ins and outs of pedigree analysis, genetic diversity and disease

Author: Dr. Jerold Bell

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

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

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

Breeding by pedigree

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

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

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

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

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

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

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

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

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

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

Pedigree Analysis

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

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

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

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

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

Pedigree of: "Laurel Hill Braxfield Bilye" (a spayed female Gordon Setter owned by Dr. Jerold and Mrs. Candice Bell, and co-bred by Mary Poos and Laura Bedford)

1          2      3       4                5

                                             Dual CH Loch Adair Monarch
                            CH Sutherland MacDuff
                            |                CH Sutherland Dunnideer Waltz
                    CH Sutherland Gallant
                    |       |                CH Afternod Kyle of Sutherland
                    |       CH Sutherland Pavane
                    |                        CH Sutherland Xenia
            CH Loch Adair Foxfire
            |       |                        Afternod Fidemac
            |       |       CH Loch Adair Peer of Sutherland, CD
            |       |                CH Wee Laurie Adair
            |       CH Sutherland Lass of Shambray
            |               |                CH Afternod Callant
            |               CH Afternod Karma
            |                                CH Afternod Amber
    CH Braxfield Andrew of Aberdeen
    |       |                                Afternod Fidemac
    |       |               AmCnCH Afternod Scot of Blackbay, CD
    |       |               |                CH Afternod Alder
    |       |       AmCnCH Forecast Trade Winds, CD
    |       |       |       |                Bud O'Field Brookview
    |       |       |       CH Oak Lynn's Bonnie Bridget
    |       |       |                        Borderland Taupie
    |       CH Afternod Ember VI, CD
    |               |                        CH Afternod Simon
    |               |       Afternod Profile of Sark
    |               |       |                CH Afternod Heiress of Sark
    |               CH Afternod Ember V
    |                       |                CH Afternod Callant
    |                       CH Afternod Maud MacKenzie
    |                                        CH Afternod Amber
 LAUREL HILL BRAXFIELD BILYE
    |                                        CH Afternod Callant
    |                       Dual CH Loch Adair Monarch
    |                       |                Loch Adair Diana of Redchico
    |               CH Sutherland MacDuff
    |               |       |                CH Afternod Anagram
    |               |       CH Sutherland Dunnideer Waltz
    |               |                        CH Hi-Laway's Calopin
    |       CH Kendelee Pendragon
    |       |       |                        CH Afternod Callant
    |       |       |       CH Wee Jock Adair, CD
    |       |       |       |                Loch Adair Diana of Redchico
    |       |       CH Afternod Nighean Kendelee
    |       |               |                CH Afternod Simon
    |       |               CH Afternod Wendee
    |       |                                Afternod Dee of Aberdeen
    CH Halcyon Belle-Amie
            |                                Dual CH Loch Adair Monarch
            |               CH Sutherland MacDuff
            |               |                CH Sutherland Dunnideer Waltz
            |       CH Sutherland Gallant
            |       |       |                CH Afternod Kyle of Sutherland
            |       |       CH Sutherland Pavane
            |       |                        CH Sutherland Xenia
            CH Loch Adair Firefly, WD
                    |                        Afternod Fidemac
                    |       CH Loch Adair Peer of Sutherland, CD
                    |       |                CH Wee Laurie Adair
                    CH Sutherland Lass of Shambray
                            |                CH Afternod Callant
                            CH Afternod Karma
                                             CH Afternod Amber

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

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

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

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

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

 

 

 

1st Generation

 

Linebred Ancesters

Percentage  of blood

 Appearance in pedigree

Times in pedigree

 

 

 

 

CH Afternod Drambuie

33.20%

6

33

CH Afternod Sue

27.05%

7

  61  

CH Afternod Callant 

26.56%

5

13

 

 

 

 

"Grand-Parents"

25.00%

2

1

CH Sutherland Gallant

  25.00%   

3

2

CH Sutherland MacDuff  

25.00%

3

3

CH Sutherland Lass of Shambray

25.00%

3

2

CH Wilson's Corrie, CD

22.30%

7

200

CH Afternod Buchanon

20.22%

7

48

Loch Adair Diana of Redchic

17.97%

5

12

CH EEG's Scotia Nodrog Rettes

17.76% 

8

181

Afternod Ember of Gordon Hill

17.14%

8

76

CH Afternod Hickory

16.21%

6

27

CH Black Rogue of Serlway

15.72%

9

480

CH Afternod Woodbine

14.45%

6

15

CH Fast's Falcon of Windy Hill

13.82%

8

66

Afternod Fidemac

13.67% 

5

7

CH Page's MacDonegal II

13.43%

7

56

Afternod Hedera

13.38%

7

56

CH Downside Bonnie of Serlway

12.90%

10

708

Peter of Crombie

12.76%

11

3,887

 

 

 

 

"Great-Grand-Parents" 

12.50%

3

1

CH Afternod Amber

   12.50%   

5

5

Ben of Crombie

11.83%

11

7,584

Stylish William

11.18%

13 

23,764

Stylish Billie

11.08%

14

70,542

Stylish Ranger

  10.80%  

15

297,331

CH Afternod Kate

  10.74%   

6

17

Heather Grouse

 10.61%  

16

1,129,656

Afternod Hedemac

10.45%

7

28

 

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

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

Breeding by appearance

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

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

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

Genetic diversity

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

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

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

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

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

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

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

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

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

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

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

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

Putting it all together

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

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

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

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

Further Reading:

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

• Abnormalities of Companion Animals: Analysis of Heritability - C.W. Foley, J.F. Lasley, and G.D. Osweiler, Iowa State University Press, Ames, Iowa. 1979.

• Genetics for Dog Breeders - F.B. Hutt, W.H. Freeman Co, San Francisco, California. 1979.

• Veterinary Genetics - F. W. Nicholas, Clarendon Press, Oxford England. 1987.

• Genetics for Dog Breeders - R. Robinson, Pergamon Press, Oxford England. 1990.

• Genetics of the Dog (equally applicable to cats and other animals) - M.B. Willis, Howell Book House, New York, New York. 1989.

Dr. Bell is director of the Clinical Veterinary Genetics Course for the Tufts University School of Veterinary Medicine and national project administrator for numerous genetic disease control programs of pure-bred dogs. He performs genetic counseling through Veterinary Genetic Counseling and practices small animal medicine in Connecticut. He and his wife breed Gordon Setters.

Reference: SiriusDog.com