Breed Surprises! Why don't my dog's breeds match their appearance?

Sometimes looks can be deceiving. And breeds may not equal appearance

A more detailed version of this article was originally published on Embark's blog and can be accessed here: https://embarkvet.com/blog/whats-in-your-dog/.

Appearance in mixed-breed dogs is governed by several genotypes and not by their composite breeds per se. If you have access to your dog’s trait results, you may be interested in reviewing these to understand your dog’s appearance in the context of its genetic results.

The TLDR: A summary of what's below:

While it’s fun to guess which breeds might make up your dog, it’s important to realize that visual breed identification is notoriously unreliable-even shelters and veterinarians get it wrong 75-80% of the time, as their classification is generally a best guess based upon appearance rather than genetic results. Less than 1% of a dog's 20,000 genes impact appearance. There is so much variation among dogs in general that visual or behavioral ID is generally an unreliable way to diagnose a dog's ancestry.

The Details:

What makes a dog breed a dog breed? Let’s pick one of my favorite breeds, the adorable Corgi. Most Pembroke Welsh Corgis come with that fantastic natural bobtail, a result of a mutation in the T-box gene! That’s right, a genetic mutation creates that natural bobtail.

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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.

It is quite simple when dealing with a purebred animal. On our genotyping platform, a purebred's DNA will closely identify to the purebred DNA in our reference panel of dogs. But what if you have a mixed-breed dog 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?​

Naturally, the first inclination is to say, well, we must have contaminated the sample. However, 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), we know that more than one dog’s DNA is in the sample. As a result, we will issue you a replacement then and there. (There are rare instances when a dog is aneuploid, meaning the dog has an abnormal copy number of any given chromosome. With extra scrutiny, Embark can decipher this, as well.) 

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.

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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 the 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.

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Among other things, Yorkies are prized for their lap-friendly size. An allele of the IGF1gene is known to cause small body size in dogs, including the Yorkie. Going through the same calculations as above, the 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 the 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 seen below are between 18% and 23% Chow Chow:

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The vast majority of our DNA doesn’t code for genes, but it is highly informative of ancestry.

So, our hypothetical Embark dog didn’t inherit a size allele from the Yorkie. 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. 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 is largely regulatory in nature. Of the 200,000+ genetic markers that we use, roughly 10% of them fall in the 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 it may not directly impact what a 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.

An open mind is important when looking at canine traits. Some preconceived notions about your dog’s breed are bound to vanish when you have as high resolution of a genotyping platform as we have. 

The value of the DNA test is not only to figure out who your dog is; 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 are exceedingly common in shelters today, and studies suggest that the reliability of visual identification of dog breed is low, especially Staffy-type dogs. This is why understanding breed-specific conditions and diseases is so important.

We choose our dogs unscientifically. Some of us have a few criteria of what we want: breed, size, or color. But ultimately, whether you’re searching via a breeder or a shelter, you’re going to be responsible for this dog for the rest of his or her life. It is invaluable to know what kind of breed-specific disease and trait alleles are part of your dog's breed mix for your peace of mind and your dog's health.

• 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.