Genetics can be complicated. The more you know about what's going on under the hood, the better decisions you will be able to make the next time you plan a litter. 

This would seem obvious, but in fact there are many nuggets of old "wisdom" that get passed around and around that are, well...not true. Yet, like a fly in the kitchen, it seems no amount of swatting at these untruths will get rid of them. 

Breeder! Unburden yourself of these myths! Embrace truth and science! Read on!

Common Breeder Myths
You've probably heard all of these. You've probably even repeated some of them. We will examine each of them. 
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Breed only BEST to BEST
Look, don't breed the dogs that have no good points. But, just like in school, realize that there can be a lot of merit in "above average". In fact, if the parents of a litter were quality dogs, then the offspring inherited quality genes, but perhaps not always in the best combination. Don't toss out those valuable genes - mixed a bit differently, they could produce the next superior animal. Remember: Improvement through selection requires genetic variation. Keep a good variety of ingredients in the genetic pantry to choose from!

Inbreeding is required to fix type
The genes for breed type should be fixed in the first few generations after breed formation. Once the breed has the qualities that define it, further inbreeding simply increases homozygosity in the other "dog" genes, for things like toenails and kidneys and glucose metabolism and saliva. If there are some mutations among the thousands of genes in the dog (and of course, there are!), then inbreeding will inadvertently produce paired (homozygous) mutations for some genes. For these, whatever the normal gene is supposed to do will be broken.

​Other domestic animals have clearly recognizable breeds with much lower levels of inbreeding than are typical in dogs. Most purebred dog breeds have average inbreeding in excess of 12%, and about half of the breeds are greater than 25%. In horses, most breeds are less than 12%.

Close the stud book to protect the breed
If the stud book is closed, genes will be lost from the gene pool through selective breeding and "genetic drift" (chance). If you start a breed with a founder gene pool, then lose genes every generation that cannot be replaced, eventually the gene pool will be depleted. You can easily test this with a bowl of M&M's on the coffee table. Grab a few when you need that chocolate fix, but don't put any back. Eventually, the bowl will be empty. 

The rule of thumb here: Animals in closed gene pools go extinct.

Really? Is this always true???

In fact, no. There is a very famous herd of cattle in England, the Chillingham cattle, that has survived for centuries as a closed gene pool. They are the iconic exception.

But every other closed population has gone extinct, and yours will too. You can count on it.

I know what's in my line
You probably know about dominant alleles. They mask the expression of recessive alleles. You cannot know what recessive alleles are lurking in your gene pool as long as expression is masked by a dominant allele. You could unmask recessives using inbreeding, because as we saw above, inbreeding breaks things. Or you could avoid inbreeding, not worry about the recessive lurkers, and keep that doggy working like a well-oiled machine.

Outcrossing introduces new diseases
Outcrossing does not "introduce new diseases". It introduces new alleles, some of which will probably be recessive mutations. But single mutations do not usually produce disease. In fact, as noted above, most recessive mutations are masked by dominant, normal-functioning alleles and produce no ill effects. Eliminate this problem by following a simple rule of genetic management: keep recessive mutations rare. So no popular sires! 

And remember from above: Inbreeding breaks things.

Hybrid vigor doesn't apply to dogs
Hybird vigor results when you "undo" inbreeding by mating two animals that are relatively unrelated. Inbreeding applies to dogs. So hybrid vigor applies to dogs. 

No, it hybrid vigor not require different species. In fact, most interspecific hybrids are infertile and not terribly vigorous.

Nothing will make you look dumber than declaring that hybrid vigor doesn't apply to dogs.

Do yourself a favor. Look this one up. So you never forget.

If you're a dog breeder and you believe in genetics (of course you believe in genetics!), you know that there is a certain predictability in breeding that is the result of genes being passed from parent to offspring. You take advantage of your understanding of the process of inheritance when you breed for certain colors, or you use a taller sire to put a bit more leg under your next litter. 

On the other hand, as most breeders will tell you, "breeding is a crap shoot". You are trying to breed for one a particular trait in your puppies and get instead a litter of puppies with something else or, even worse, a mish-mash of variety that beggars your belief in genetics.

Of course, the problem here isn't that understanding genetics is worthless. It's that you are trying to select a breeding pair based on the genes you would like them to pass on to their offspring. You are trying to select for particular genes, but you are assessing the genetic merit of a dog for a particular trait based on its phenotype - how those genes are expressed in a dog. This method of selection - evaluation of phenotype - only works well if phenotype is a good indication of genotype. As anybody who has ever bred a litter of dogs knows, for some traits phenotype is a good indication of genotype, and for other traits it isn't.

The most important concept in selective breeding is "heritability". If you ask 10 breeders to define heritability, I can almost guarantee that most will get it wrong. Most people will define heritability as the inheritance of a particular trait by a dog.

​But actually, heritability is a concept from population genetics. Heritability tells you how much of the variation in a trait in a group of dogs is the result of differences among them in their genes.

Now, let's say we could create an exact clone of each of those puppies and raise that duplicate litter separately. Each puppy goes to a different home, is fed differently, exercised differently, and raised under conditions that are unique to that puppy. Now when you measure the weight of each puppy at 1 month, you will probably get different numbers compared to each pup's clone, and there will probably be more variation in the litter. The pups have exactly the same genes, but ended up at 1 month with different phenotypes. We know that genes are important to weight, but in this case there are clearly effects of environment.

Here is where most people get tripped up on the definition of heritability. In the first example, the heritability of weight will be equal to 1. In the second example, the heritability of weight will be less than one, perhaps something like 0.3. Same trait, different heritabilities. Why? Because heritability is not about a particular trait in an individual, but rather tells us about the trait in a population of dogs. Here's why.

The phenotype of most traits depends on both genes and environment. We could write this in shorthand as

So for our example of weight in puppies above, the puppies in first litter were raised in identical environments, so the "E" term in our little equation is 0; there is no effect of environment on puppy weight, and all the variation you see among the puppies is due to genetics. So for these puppies, the heritability of weight is 100%.

I don't want to get into the details of heritability and how it is determined (these are things we discuss in the ICB courses). Rather, I want to make a simple but extremely important point. 

When you assess particular breeding combinations, you use whatever information you have about phenotype of the parents or relatives to make assumptions (or guesses, really) about the genes each parent is likely to pass on to each puppy. If the heritability of weight at 1 one month is 1.0, as for the first litter, you know that 100% of the variation in weight from pup to pup is due entirely to genetics. If you wanted smaller size in your next litter, you should keep one of the smaller puppies to breed and you should also get the genes for smaller size.

But what about the second litter, for which heritability of weight was only 30% because there was lots of variation in how they were raised? If you want smaller pups in your next litter, you can't assume that you are correctly selecting the genes you want for size just by the weight of the puppies. Some pups might have had more to eat, some might have been couch potatoes and put on some puppy fat, some might have been slow eaters and never got as much to eat as the others. In this case, phenotype is not a very good indication of genotype; there is lots of variation in phenotype because the "E" term in that simple equation above is not zero.

Okay, here's the rub. For most of the traits you want to select for (or against), there will be multiple genes involved as well as non-genetic factors that will affect phenotype. If you select the pick of the litter based on phenotype alone, you will not necessarily be selecting the puppy with the best genes for that trait. For puppy weight with a heritability (in our example) of 0.3 (30%), most of the variation in phenotype (70%) is because of things that have nothing to do with genetics. If your strategy for selection relies heavily on the phenotype of the dog, you are more likely to be wrong than right. 

If you don't know the heritability of a trait you are trying to select for or against, you are likely to make a lot of incorrect decisions based on phenotype alone. If you're assuming the heritability of a trait is 1.0 - i.e., what you see is what you get - you are going to have a lot of those "breeding-is-a-crap-shoot" experiences, selecting for one thing and getting something else. On the other hand, if you know that the heritability of a trait in dogs raised in uncontrolled conditions (different households, various diets, variable amounts of exercise) is 0.15, then you should understand that phenotype is not a very good reflection of the genes for that trait in an individual puppy and that you will not be very good at selecting the puppies with the genes you want. On the other hand, if the heritability of trait is typically 0.8, then phenotype will be a decent reflection of the genes for that trait inherited by that dog.

The critical point here is that heritability tells you how much of the variation in a trait is due to variation in genetics. If heritability is low, efficient selection will be difficult because phenotype is a poor reflection of genotype. If heritability is high, more of the variation in the trait among individuals is a result of genetics, so selection based on phenotype will be more effective.

There are ways to get around the limitations of selection when heritability is low. One is to use information about the relatives of a particular dog. If the heritability of hip dysplasia in a breed is usually about 0.2, and you found a sire you like but his hip score is mediocre, have a look at the hip scores of his litter mates, his parents, and, if he has already been bred, his own offspring. All of this information will provide clues about the genotype of that sire you like. If his relatives have good hips and he is the outlier, you can have more confidence that he probably has good genes, but perhaps he had an unfortunate experience as a puppy or was overindulged by an owner who fattened him up by rewarding everything he did with a cookie. You can do this assessment statistically using something called "estimated breeding values" (EBVs), which does some fancy math and comes up with a number that tells you about the quality of genes in a dog for a particular trait. (Some kennel clubs now provide EBVs for hip dysplasia.)

Hate that "crap shoot" part of breeding? You can reduce the guesswork in breeding by understanding heritability. Know the typical heritability of the trait you are selecting for, and take that into consideration when you evaluate phenotype. And also make use of information available from the ancestors, siblings, and descendants of a dog, because those animals share many genes and can help you decide how much weight to put on your assessment of phenotype when you are trying to select for particular genes.

Breeding will always have an element of chance, because that's how genes are inherited. But it doesn't have to be a crap shoot. Understanding how to use some simple tools like heritability can help you make better decisions and result in more predictability and consistency in your puppies.

To learn more about the genetics of dogs, check out
ICB's online courses

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