Genetics Unbridled - Horse DNA & Technology Powered by Etalon Equine Genetics

Exploring Equine Colors: Where Do Bays Come From?

October 09, 2023 Etalon Equine Genetics
Exploring Equine Colors: Where Do Bays Come From?
Genetics Unbridled - Horse DNA & Technology Powered by Etalon Equine Genetics
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Genetics Unbridled - Horse DNA & Technology Powered by Etalon Equine Genetics
Exploring Equine Colors: Where Do Bays Come From?
Oct 09, 2023
Etalon Equine Genetics

Ever pondered why horses flaunt such a myriad of coat colors? What makes a horse black or bay? We've got answers! Sit tight as we embark on an enlightening journey into the world of horse genetics. From explaining the role of Agouti, a significant factor in determining horse coat color, navigating the complexities of the gray gene, to giving insight into why genetic discussions often meet with dismissive responses on social media, we're covering it all.

In the second half, brace yourself for a deep dive into the reference genome horse, Twilight. We'll throw light on how the traditional rules of genetics are constantly changing as new mutations surface. If horse breeding interests you, listen in as we talk about the role color plays in it and introduce you to Etalon's innovative 'Build a Horse' tool, a fascinating game-changer that could help you predict your horses' colors and more. We're here to make genetics enjoyable and accessible, so let's hit the round pen!

Show Notes Transcript Chapter Markers

Ever pondered why horses flaunt such a myriad of coat colors? What makes a horse black or bay? We've got answers! Sit tight as we embark on an enlightening journey into the world of horse genetics. From explaining the role of Agouti, a significant factor in determining horse coat color, navigating the complexities of the gray gene, to giving insight into why genetic discussions often meet with dismissive responses on social media, we're covering it all.

In the second half, brace yourself for a deep dive into the reference genome horse, Twilight. We'll throw light on how the traditional rules of genetics are constantly changing as new mutations surface. If horse breeding interests you, listen in as we talk about the role color plays in it and introduce you to Etalon's innovative 'Build a Horse' tool, a fascinating game-changer that could help you predict your horses' colors and more. We're here to make genetics enjoyable and accessible, so let's hit the round pen!

Lauren:

Welcome back to Genetics Unbridled. On this episode, we're breaking down complex topics to give you a quick and easy explanation. We're calling these short segments Lunge Lessons in Genetics.

Christa:

The same questions, that we have only started this out. It's just not really explained very well anywhere.

Lauren:

I'm looking at my horse's results and the first thing I see is the letter A. They all have either two big as, two small as, or one of each. When I hover over that on my Etalon report, I see the word agouti. What the heck is agouti?

Christa:

Okay, so then should we take a Lunge lesson in agouti? Absolutely Get our butts in the round pen and see if we can figure this out.

Lauren:

Let's do it so, Christa, what can you tell me about agouti?

Christa:

Well, agouti, found in the ASIP region, which is agouti signaling protein, is actually a modifier. It controls where black pigment is distributed in the horse and if you're reading in your variant summary, your agouti will be the capital A or the lower A. Capital A means you have a form of dominant, agouti means the code is there. Lowercase A means the code is missing. It's the recessive form of agouti.

Lauren:

So let's say I have a horse with a big A. Big A in its variant summary. What does that mean for my horse?

Christa:

Nothing without extension. What's extension? Okay, so we don't want to go down a rabbit hole because we're in round pen and we need to stay focused, but extension is the base coat color of the horse Black, capital, E or red lowercase E.

Lauren:

So, in the effort of keeping things simple, we're going to talk about black-based horses, because black is what agouti affects visually. We don't have any known effect of capital A on red, so this means if a horse is red you can't tell the difference right Until.

Christa:

maybe you can further into the research, but presently there is nothing that shows an effect of capital A agouti on a red-based horse. So let's talk about black. We love our black horses.

Lauren:

We do.

Christa:

I mean I love my black horses. I think it's just gorgeous, gorgeous, gorgeous. But how did they get that way? Well, the funny thing about agouti is, again, the definition is agouti gene capital A controls the distribution of black pigment and determines whether a horse will have a bay or black coat color. It's what's known as a primary modifier. Okay, so what it does is if you have a black horse, capital E, one copy or two, doesn't matter if it's capital E, capital E or capital E, literally that would be a recessive form of red. What you'll have.

Christa:

There is an animal that has, by default, black pigment across its entire body legs, mane, tail, nose, ear, everything it's all black. But capital A, agouti, restricts that black pigment. It moves the black pigment off of the main part of the body and you end up with a black mane and tail, sometimes the legs, ear tips, so on and so forth, the outer regions of the body. So that modifier pushes black pigment away from the center of the body and leaves it only on the outer edges of the body. Agouti exists in many mammals. It exists in dogs and mice and even people, and it controls a lot of the pigment in those animals as well. So here's where it gets interesting. So if anybody suffers these lovely social media forums where we talk about Coke Color, have you ever dared to ask a question in one of those forums?

Lauren:

Well, I have seen these Facebook groups and personally stayed away because I've seen how people can just be ridiculed for asking questions. What about you? Have you ever joined the conversation?

Christa:

So I have early on, and I've had friends who have done it and I've seen some of our clients do it. Yeah, and it's an interesting thing because, well, a lot of the science is straightforward and it's complex to think about and it's complex to read about. In asking a question, you're attempting to do your homework and try to understand each piece and what ends up happening when they ask questions Say what does a goody do? Well, first you get the ones standing on the podium screaming from the rooftops oh well, this is what it does, and how could you be so stupid and how did you not know that? And then any further conversation descends into Bay is the original color. What does that even mean? Bay is the original color. So if we just talked about the fact that capital A restricts black pigment and causes Bay horses, what could they possibly mean by Bay is the original color? I have no idea.

Lauren:

Well, don't ask. Well, and that's the thing you know. We always talk about questions being so important. That's the only way we grow, we learn. We have to be curious, we have to be willing to ask those questions and have a safe space to do so. And that's why we have consults, so that you get your results and you're able to go okay, my horse is red, but there's something on here that says a goody, so what does that mean? So that's why it's so important to have these conversations, because everybody's going to have that big A or little A or one of each, and it's on all of these results that they get back and they go. Well, what the heck does that mean?

Christa:

Right, and a podcast is a really safe place to to approach for information, because we're unable to officially bully you from this position and if you don't like what we're saying, turn it off. Yeah, nobody cares, we'll be fine. We're still going to babble on and on about horse genetics. Whether you leave it on or off, we don't care. The end of the story here is what they mean by Bay is the original colors, that the original horses had a piece of code in the ASIP region, so they were all. If they had any black base in them, they all appeared Bay. So the ancient horses none of them appeared black, they all appeared Bay. What's weird to think about is at some point somebody mutated.

Christa:

There became a mutant present.

Lauren:

Which doesn't necessarily mean a bad thing, which we've learned.

Christa:

We all have mutations. Everybody's got mutations. Your parents do, your grandparents do. They may not do anything that you've seen. You may not see them immediately, but they are there in everyone.

Christa:

But in this case a mutation happened in a Bay horse and that passed it on to the babies. And what happened is when a foal eventually got two copies of the mutation, they appeared black. Why? Because this particular mutation in the ASIP region was a deletion. That means you have the genetic code, all these letters A, c, t, g, g, blah, blah, blah, blah, blah.

Christa:

I'm not even going to pretend that I have the Agouti genome memorized, but let's just say you have this series of letters, and these series of letters equate to the capital A. Right, you've got your dominant Agouti. At one point it disappeared, it deleted. It's called a deletion. So you're going along the genetic code. You get to the ASIP region, where Agouti should be, and it's missing. It's not there, it's just blank. So what ends up happening is the default pigment of your horse. Now as well, there's nobody around watching, nobody to restrict me. There's no big A around to tell me what to do. So I'm going to get black pigment everywhere and you get this beautiful black horse. So yes, black horses contain a mutation or a deletion of the ASIP Agouti signaling protein region and that's why you can see the black Interesting.

Lauren:

I'm learning things now too. This is great. Well, and so does that mean the same thing for red horses when they have the recessive lowercase, lowercase? Is that why? Because that wasn't the original, like you were saying that, deletion, okay, so they are also missing a chunk of code out of the ASIP region.

Christa:

Got it, but you can't tell. You can't tell by looking at them. So one of the useful things about genetic tools is if we're doing testing and we have a homozygous black horse and we know that black is dominant to red, so I want to breed my black horse to this red horse, so I get black babies because that's what I prefer. If that red horse is hiding copies of capital A or Agouti dominant form, then there's a chance I'll get a B, depending on how many copies. If the red horse has two copies big A, big A that means she'll always throw a copy of big A. That means no matter how many times you breed her to that black horse, you're going to get a B every time. Interesting.

Lauren:

Well, that's good for our Bay lovers out there. I know we definitely have fans that love their Bay horses. But going back, you said a, b or Agouti is a primary modifier. Is that what you? Is that your? It's a primary modifier.

Christa:

Okay, so the Agouti modifies the pigment. It modifies the pigment distribution on the body of the horse. The pigment distribution is a black. Base or extension. Extension is either black or red. Okay Okay.

Lauren:

And then so being a primary modifier, is that part of two, why we see it on all the horses in their results? Or is that because the original horses, like you said, being that's where they started with Agouti Explain a little bit more of like? I mean, I know you said primary modifier and stuff, but like explain more of what that means? Obviously there are a lot of modifiers out there, correct?

Christa:

There are. There are other modifiers. Gray is a modifier right. So what gray does is a baby is born and it's got a copy or two of gray and gray is not a deletion. Gray is what we call a duplication. It's a copy of the same thing over and over and over and over and over in the genome right. And if a baby is born with a copy of gray, you can't necessarily tell when they hit the ground, because they're gonna be black, they are red or whatever default color. They are right. But as time goes on, that gray gene begins to modify the pigment in the skin and the hair and depigmenting it. Over time they become gray and eventually you know white, mm-hmm interesting.

Lauren:

Okay, and then, and because I know there's no silly questions, so obviously Agouti.

Christa:

What you're so stupid?

Lauren:

What the heck are you asking me now?

Christa:

Lauren.

Lauren:

So obviously Agouti is always on horse's results, but gray isn't. Why is that?

Christa:

So, again, because gray is a duplication in the genome, right. So if you were to look at a variant summary, you can. You have a few choices, and this is where it gets really difficult, because this is an emergent science and people haven't been doing this for more than you know, say 30 years at this point, and we keep discovering things literally at a rate of like new mutations every month. So it comes down to how we write or note what the horse's genes look like. In the case of gray, if you don't have the duplication, then you would write by default n slash n, where the gray question is right in the variant summary, whereas in the case of Agouti, the way it was set up was its dominant form or recessive form.

Christa:

So they did a capital for the dominant form or a little for the recessive form. They could have called it a slash DEL for deletion, but they didn't, and I think the default is n for things that are normal, and normal refers to the reference genome. Now this is where it's going to get really weird. But this goes back to arguments like Bayes, the original color. Well, in this case little known fact, maybe to some people who are not complete genetic geeks the reference genome is a horse named Twilight. So that is the. What do you call the basic genome for the horse? Right, the reference genome, the one all others are compared to. Well, she's gray, is gray, then normal, it's not. So do we call it wild type? Because wild type is usually equated with the reference genome, but it isn't in this case, because the reference genome is gray, so she's got the duplication, so she is mutated herself.

Christa:

It gets really complicated and that's why we try to have open discussions with our clients and say well, here's what we know, here's how we write it and here's the history of how this works.

Christa:

And people haven't quite teased it out. I'm sure there is an absolute, perfect, technical, correct solution or explanation, but people haven't made that very clear to the general populace and I don't think we've worked it out in a way that is clear, even if we write it absolutely correct, right? So in my humble opinion, if I were to write something in a variant summary and I said this horse has one copy of Dominic Goody, I would probably have defaulted to say capital A slash DEL for deletion, because it's not there, instead of capital A and little A, because now I'm saying capital A is dominant, little A is recessive, but that's confusing to the lay person, because now capital G is gray and N is normal, but normal refers to the reference horse, which was gray. Yeah, it is getting really messy, yeah, right. So there has to be a little wiggle room on how we follow the pattern of traditional genetics as we discover new things and how we apply those rules now and going backwards. It's really complicated, which is why there are so many questions.

Lauren:

Yeah, color being such a powerful tool in explaining, because you can see the horse, you can see what color, you see their coat, you see all these distinct patterns and markings and sometimes it leads to even more things that you learn about the horse. But it is something clearly visual. You can touch it, you can feel it, you can see it with your own eyes. A lot of these other things we test for you can't physically see, and so it's our job to create these visuals to explain and informational tools. But color is a great point to start out, because you can see it and everybody says they don't care about color Lies, but they do Lies.

Lauren:

Everybody has a favorite color of horse. I'm a weirdo. I like just plain red, but everybody has something that they like and it's everybody's Googling to see, ok, what color is this horse and this horse going to make? Well, we have tools that can help you figure that out. Build a horse, baby, yep, yep, and get all those little predictors there. So, yeah, it's something people definitely care about and we'll definitely have a lot more to dive into on colors.

Christa:

And you're welcome to try out the Build a Horse tools and you can go see what colors you can get from your babies. And guess what? We won't tell anybody. You care about color?

Lauren:

Yep, it's not just the paint people. Everybody says it's just the paint horses that care about all the fun colors. Not true. It's not true. We all have our favorite. Thank you so much for listening to this episode of Genetics Unbridled. If you liked this episode, make sure to leave us a review and give us a follow. For more about Edelon and our latest discoveries, make sure to follow us on Facebook and Instagram at EdelonDX, or visit our website, edelondxcom. We'll see you next time.

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