Commentpalooza part 2: Inbreeding dogs (redux) and a whole bunch of bolding.

While I agree with you generally, your take on COI is off. Outcrossing decreases “genetic diversity” by melting all of the strains and family types of a breed into one pot. The problem is you gloss over the negative recessive traits and those traits come back to haunt your breed, you have no repository of “clean” genetics to turn to.

I totally agree that breeders need to know what they are doing and why they are doing things. You can’t ethically breed dogs by following a recipe, and you should have a strong idea of where you are going not only in this generation, but for several generations to come.

Please Google “Of Peas and Pups” as it is the best free source of information on the topic.

Hoorah! I get a chance to re-address this topic.

Let me say first that I am thrilled beyond belief to see any breeder making decisions based on more than just “Well, her grandfather had two BISS wins, and I certainly want a piece of that, so I think I’ll breed to him.”

The article “Of Peas and Pups” was written in ’63 by a German Shorthair Pointer breeder who was very influential in the breed. It is ABSOLUTELY worth reading. When I summarize it, I’m doing so not because I don’t want you to read it on your own.

Of Peas and Pups is maybe the best example out there of the reasons that breeders stick within very, very tight pedigrees. The point of the article is, in short, predictability is good. Maximum predictability is better. Perfect predictability is best of all.

This is a quote:

We also learn that only pure parents produce pure offspring…Our dogs of course, are not genetically pure and never will be, but whatever minute contribution we can make toward that goal of genetic purity, will be to the everlasting advantage of the breed in the generations to come….

We can see that (in most instances) hybridizing or outcrossing , whether it be of breed or strain or type, complicates our genetic arrangements…..Ideally, we want HOMOZYGOSIS or the homozygous state for every allele. This is a dream not to be realized unless this old world spins a lot longer than it has already.

The author gives examples of the things you want predictability on. Nose, instinct to run, size, shape, fearlessness, etc. He strongly asserts that if you do a lot of outcrossing (breeding to unrelated dogs) you may get a few really able dogs but you won’t be able to reliably count on the outcome. You’ll be breeding somewhat blind because the dogs will be quite different from each other. Maximum homozygosity (where all the genes are the same, no recessives–or ALL recessives, depending on the gene you’re talking about) leads to maximum predictability.

YES. YES YES YES.

This is EXACTLY my point. Only I want you to imagine it like this:

You’ve got seven three-foot lengths of yarn in a rainbow pattern. There are lots of colors in repeating patterns down the entire length, in a random order (so sometimes it’s blue-red-orange, sometimes blue-red-red, etc.). These seven pieces of yarn are your seven breeding dogs.

You also have a paper towel tube–that cardboard insert thingy–with six small holes drilled in it. These holes are just big enough for you to see inside the tube.

Now use an imaginary Sharpie pen (which is all I ever have around here in real life, since my kids steal them constantly) and mark the holes with your six top priorities in breeding. Let’s say tracking ability, dark eye, tight hips, good bite, running drive, angulation. All of these are really, really good things to have in a dog, and I am all for making these predictable.

Now drop the ends of all your pieces of yarn through the paper towel tube and get ready for the magic.

Looking ONLY through the tiny holes, carefully pull one piece of yarn past the other pieces of yarn (or vice versa) until what you are seeing through the holes is exactly lined up. Through the dark eyes hole you see red-green-yellow or what have you; through the tracking hole you see blue-yellow-red, etc. In each hole you see all the identical pieces of yarn making the same pattern.

Hallelujah! You have just successfully inbred (or linebred; it’s the same thing when it comes to this experiment) a perfect breeding population according to Of Peas and Pups. No matter how you breed these seven dogs together, you will ALWAYS get a dog with dark eyes, tight hips, lots of nose and run, good angles, good teeth. Absolute predictability, absolute prepotency (prepotency basically refers to how much influence the parent generation has on the offspring generation–a numerical prediction of how much the kids will look like and act like the parents).

Unfortunately, that’s where Of Peas and Pups ends. It’s all a rosy glow of predictable production of perfect puppies with nary an outlier in the bunch.

Unfortunately, it completely forgets the rest of the yarn.

When you develop perfect homozygosity for traits, you’re developing perfect homozygosity for traits. The six–or ten, or twelve, or fifteen–you can see, the ones you’ve been trying to influence, you really can get just about perfect. And for many breeders, these are not just looks or ability. They inbreed to avoid health problems too, and they do a very good job of it. You really can develop a population completely free of, say, von Willebrands, or PRA, or other simple genetic diseases (simple meaning that the gene means the dog gets the disease, that there’s not an environmental component). You can even make a lot of headway against disorders with a major environmental trigger.

Unfortunately, even if you can manage, say, fifteen holes in your cardboard tube–and that would be an INCREDIBLE number to succeed in as a breeder–the VAST majority of the genetic code (those repeated strands of yarn) is still hidden from view.

And some of the stuff you CAN’T see, and may not in fact see for generations, would be labeled something like “resistance to parvovirus strain CCXI” or “production of tumor necrosis factor under specific conditions” or “unique myelination of nerves.” Hundreds and thousands and quite possibly millions of these traits are ALSO being made completely homozygous.

This is what makes an intensely homozygous population–your seven dogs, and in some breeds virtually the entire population of forty thousand dogs or four hundred thousand dogs–INCREDIBLY vulnerable.

Here’s how it works: Your population of predictably beautiful and birdy dogs chugs along pretty happily for a while, but then a new environmental threat or pressure comes to bear. Very often this is a disease, but it can also be a diet change (the way we feed dogs has flip-flopped in an incredible way over the last 50 years, with generations being fed almost entirely differently than the prior ones and differently from the subsequent ones) or a husbandry change (more weight, less exercise), or a vaccination change, or any number of things.

In a maximally heterozygous population, where the yarn doesn’t match up on almost any region, the dogs’ individual bodies will respond in many different ways. If the threat is a virus, some dogs will have genes that code for a protein that does a better job than the other dogs’ proteins at sticking to the viral coating and therefore coding for an antibody. So those dogs will get over the disease much faster. Other dogs will have a greater fever response, a more labile body temperature. So those dogs will spike a fever instantly and possibly kill more viral particles. And some dogs will have a sluggish reaction and very little immune response and they’ll die.

When you have a homozygous population, there’s no ability for some dogs to zig and some dogs to zag. Every single dog will respond the same way to the threat. And for some threats that’ll be a good thing, because they all survive (that’s how you breed plants resistant to certain fungi, for example). But for other threats it will be a catastrophic thing.

It is VERY well established that homozygous populations are super vulnerable to what are called plague diseases–not “the plague,” but a term that population ecologists use to refer to any disease or threat that sweeps through the entire population.

The second huge threat to very homozygous populations is that of polygenic disease.

Genetic disease is very, very rarely a simple thing. There are a few diseases that have a one gene equals one disorder formula, but this is only a tiny minority. Most diseases have a complex recipe of genes interacting with each other, with the eventual symptoms triggered by environment.

So, for example, the gene sequence for osteosarcoma might be RSTAUU, where each letter represents an entire gene (a sequence of many base pairs).

If you look across the entire population of dogs, a whole bunch might have RS, a few have TA, a very small number have RSAUU, a proportion has UU, etc. It’s pretty rare that they all occur together in one dog.

But what happens when you align all those yarn pieces, when you remove heterozygosity, is that those cancer genes get aligned too. The dogs that tended to be just UU also had iffy bird sense, so they were selected against and disappeared from the population. The dogs with just RS had light eyes, so they’re gone too. The result is a ton of dogs with RSAUU and another ton of dogs with TA.

A dog with RSAUU won’t get cancer. Neither will a dog with TA. Nobody INTENTIONALLY bred cancerous dogs. They looked like two entirely healthy populations.

But when they came together, a population with a huge proportion of dogs that will get the entire RSTAUU sequence was created. And that is something that is INCREDIBLY difficult to undo.

And we have precisely that situation in Boxers and Goldens and Flatcoats right now–such enormous cancer rates that the effective lifespan of the breeds has been cut nearly in half. Breeders are aware of the issue, appalled by the cancer rates, and are working like the dickens to reduce them, but when you have a polygenic disease it’s very difficult. You don’t know if the reason Ch. Besom’s Big Boy was cancer-free until old age was because he actually didn’t have cancer genes, or if it was that he was TA. You don’t know whether your lines have TA or RSAUU, so if you breed your cancer-free Ch. Lori’s Twinkle Toes to him you could end up with a super healthy litter or you could end up with a disaster. And even if you do end up with a healthy litter, you might wreck it all in the subsequent generation.

In other species, when you find yourself in a corner you either kill every member of your breed and start over (this is what happens in plants–you let Soybean Strain WW23, which turned out to be vulnerable to a certain insect, get plowed under and you buy WW24 from the seed company the next year) or you breed your way out by accessing completely different genetics. You take your Alpine goats that are producing an uncomfortably large proportion of skin diseases and you breed to Saanen bucks for a year, then breed those kids back to your Alpines. The ADGA (the goat version of the AKC) has a specific provision for this; as long as you use registered animals you can cross-breed and then breed back into purebred status with a letter attached to your registration number.

The AKC has no such plan or provision except under VERY specific circumstances. I applaud every breed club that has gone that route and has sought out alternate breedings when it became clear that they had bred themselves into a corner; I sincerely wish more would follow suit.

But the point is that with an almost entirely closed studbook (i.e., we can’t breed into different breeds or to unregistered dogs), we remove genes at our own great peril. We do not have any idea, and probably won’t for another fifty or a hundred years, what protective or preventive genes we lose when we move toward maximum homozygosity.

It is well worth considering that a huge proportion of all behavioral adaptations on the part of complex animals, from fish to humans, are designed to get you away from breeding with your relatives. Losing heterozygosity is a quick trip to species death.

Because we control our dogs’ breeding decisions, we can do a great deal of good, we can select away from disease, we can select for traits that maximize the dogs’ abilities to do their jobs. And we MUST do those things. But I strongly suggest that we treat a high coefficient of inbreeding with no little caution, and we move toward maximum heterozygosity wherever it is possible. For the long-term health of our breeds, far beyond next year’s sweep of the trophies, it’s something we must consider.

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