What makes a dog breed a dog breed? Let’s pick one of my favorite breeds, the adorable, inquisitive Corgi: Behold, those huge, pointed ears! That questioning facial expression! That Corgi butt, which in most Pembroke Welsh Corgis comes with that fantastic natural bobtail, a result of a mutation in the T-box gene! That’s right, a genetic mutation gives the Pembroke Welsh Corgi that natural bobtail.
Another mutation, one in the FGF4 gene, gives the Corgi those disproportionately short, sturdy little legs, a condition known as chondrodysplasia. It’s the same mutation that causes short legs in the Dachshund and the Basset Hound.
This leads me to my first point: dog breeds are defined by specific, characteristic physical and behavioral traits. Breed-specific traits are coded for by DNA variants that are at incredibly high frequency in a dog breed 1. That’s why if I breed a Corgi to a Corgi, I’m always going to get a litter of Corgis. And what if a long legged Pembroke Welsh Corgi does somehow show up one day? It's possible, because those long legs are driven by genetic changes. But it won’t meet breed standard, and old antelope-legs’ genes will be bred right back out of the breed.
It’s the DNA that defines the breed. And what we report on is the DNA.
So this is all well and good when you have a purebred animal. On our genotyping platform, a purebred's DNA will closely identify to the purebred DNA in our reference panel of dogs. That’s exactly what you'd expect: done and done. But what if you have a mixed-breed dog, one that isn’t clearly the product of two purebred dogs, but has mixed-breed ancestry one or two generations back? How do we explain the 40-pound black Labradorish mutt with Corgi and Yorkshire Terrier grandparents, like in our hypothetical dog family tree below?
Naturally, the first inclination is to say well, we must have contaminated the sample. A sample contaminated with another dog’s DNA will fail quality control: if we get more than two different copies for a segment of your dog’s genome (called a haplotype), barring the unlikely event that the dog is aneuploid (with an abnormal copy number of any given chromosome), we know that more than one dog’s DNA is in the sample and will issue you a reswab then and there.
Now that we’ve cleared that up, let’s talk about genetics.
Genetics is a game of chance.
First, we’ll address our hypothetical dog’s Corgi maternal grandparent.
This grandparent carries characteristic Corgi DNA variants like the aforementioned FGF4 mutation for chondrodysplasia. Our Embark dog has a 50% chance of inheriting the allele from the mother. This also means he has a 50% chance of not inheriting this Corgi allele from his mom. If your dog does inherit the Corgi allele, he may have intermediately short legs. If he happens to inherit a matching allele from his dad, he'll get fully short legs.
Let’s make it a little more complicated and address a trait affected by many genes through examination of our hypothetical dog’s Yorkie grandparent.
Among other things, Yorkies are prized for their lap-friendly size. An allele of the IGF1 gene is known to cause small body size in dogs, including the Yorkie. Going through the same calculations as above, your dog has a 50% chance of inheriting this Yorkie allele. Even then, the effects of this allele will be modulated by the variants at other size-influencing genes identified in the dog, as well as those that haven't. Depending on what your dog has inherited from his mom AND his dad’s side at those other loci, his size may not ultimately reflect the Yorkie size that the IGF1 allele confers.
This is all a game of chance. This is why mixed-breed dogs of similar breed composition can be completely different in body shape, size, and coloring. For example, all three of the Embark dogs below are between 18 and 23% Chow Chow (That's my pooch Shiloh; thank you, Tamara Reilly and Clay Gray for their photos of Molly Malone and Bosley!).
The vast majority of our DNA doesn’t code for genes, but is highly informative of ancestry.
Okay. So, our hypothetical Embark dog didn’t inherit a Yorkie size allele. He also didn't inherit a Yorkie black-and-tan agouti coat color allele (Or did he! Coat color in dogs is influenced by more than seven genes, some of which actually mask the effects of others). Maybe he didn't get the Yorkie excitedly-barking-at-nothing allele, either 2. So what’s that 25% Yorkie DNA doing? Don’t forget that only 2% of our DNA codes for genes, which make the proteins that eventually lead to phenotype. The rest of it, which I won’t go into for sake of brevity, is largely regulatory in nature. Of the 200,000+ genetic markers that we use, roughly 10% of them fall in coding sequence. The rest is in highly conserved DNA that doesn’t code for genes. This is incredibly useful for high-resolution breed identity, but may not directly impact what your dog looks and acts like. It's the DNA that defines the breed, and what we report on is the DNA.
DNA makes the dog, but so do you.
So, guys, come into this with an open mind. Some preconceived notions about your dog’s breed are bound to go out the window when you have as high resolution of a genotyping platform as we have. Ultimately, does your dog’s breed composition change who your dog is to you? Nope: you were the one who taught Fido to sit, to go nuts for peanut butter, to love playing tug of war. Perhaps Fido has Labrador in him, and that’s why he likes to swim. Or maybe it’s because you threw him in the lake when it was hot out one day and he figured out that water is awesome.
The value of the DNA test is not only to figure out who your dog is: you already know this. It is also the ability to anticipate breed-specific conditions and diseases. For example, Staffordshire Bull Terriers are known to experience a condition known as Staffy Cramp, a neuromuscular disorder that arises from a mutation in the L2HGDH gene. Dogs of the Staffordshire Terrier group (which includes the Staffordshire Bull Terrier, the American Staffordshire Terrier, and the American Pit Bull Terrier) are exceedingly common in shelters today (though studies suggest that the reliability of visual identification of dog breed is low, especially Staffy-type dogs).
We choose our dogs unscientifically. Some of us have a few criteria of what we want: breed, size, whatever. But ultimately, whether you’re searching via a breeder or a shelter, it’s the dog that looks at you with those big eyes that say, “Hey! You’re my human,” that comes home with you. You’re going to be responsible for this dog for the rest of his or her life, and it is invaluable to know what kind of breed-specific disease and trait alleles are coming with those soulful eyes.
A note from our science team: Many breed specific traits are dictated by single nucleotide polymorphisms, or SNPs. These usually segregate in two forms or alleles such that the frequency of one can be inferred from the other. Traits driven by structural variants may have more allelic diversity. ?
I love Yorkshire Terriers. ?