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

Betting on Innovation: Horse Ancestry with Dr. Samantha Brooks

January 08, 2024 Etalon Equine Genetics
Genetics Unbridled - Horse DNA & Technology Powered by Etalon Equine Genetics
Betting on Innovation: Horse Ancestry with Dr. Samantha Brooks
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Ever placed a bet that revolutionized an industry? Explore the intersection of horse genetics and innovation in the latest Genetics Unbridled podcast with Dr. Samantha Brooks. In this episode, we delve into ancestry testing in horses such as, thoroughbreds, sport, and stock horse breeds. The cutting-edge testing platform from Etalon Equine Genetics was born out of a bet with an Irish sport horse enthusiast.

Join us as we trot alongside Dr. Brooks, focusing on genetic diversity and the 'Find My Herd' initiative, working to reunite horses with their genetic kin. We delve into the critical role of heterozygosity in horse populations, discussing how these genetic insights reshape breeding and selection strategies. This episode offers essential genetic insights for decision-making, celebrating the interconnected histories of horse breeds worldwide. Prepare for an enlightening and entertaining exploration into the intricacies of horse DNA!

Lauren:

Welcome back to Genetics Unbridled. On this part 2 episode with Dr Samantha Brooks, we're working to answer all of your questions about ancestry testing. In this episode we'll discuss Find my Herd Horses Like Me, genomic Inbreeding, thoroughbredblood and so much more. You may be thinking I know my horses breed, so why would I need this technology? This is a whole new way to connect you with your horses, herd and fellow equestrians. Keep listening to learn how ancestry is a practical tool for all horse owners, and this one I'm excited to talk about because we've just been talking about the power of ancestry for so long and I think people are finally starting to realize it. On our first episode we had a mystery horse that we found the first degree relative, which was really exciting, and since then we've had some clients say okay, I've got questions about ancestry, you need to break it down for me All right.

Christa:

So we have just for people who haven't done ancestry we have this really crazy platform, and I'm going to say crazy because I know that I founded this company. I have several partners in crime One of them may or may not be involved in this podcast right now and we all have our pet projects and I love the diagnostics and I really love behavior, which is something we have recently talked about. And at one point along the line, while we were developing these products, one of us may have had a bet for a beer with an Irish sport horse rider about whether or not we could actually tell what the percent blood was in their animals and by percent blood they mean percent thoroughbred and that set a fire under one of our scientific advisors and we were working on this platform and that was like our sole litmus test. Can we do this, can we do this? And lo and behold, it turns out that we can, because thoroughbreds are so inbred that they have a unique genetic signature and they're one of the few breeds I guess that you can genetically test for and I'm going to watch Samantha come through the camera and strangle me for saying anything like breed test and so that worked really well, and on top of figuring out what percent thoroughbred you had in an animal, you could also see that in breeding, in a few other things. And then we started offering it to clients and every day same question Do you have a breed test? Because I've been doing this breed test and blah, blah, blah, blah, blah. So before we go down the power of ancestry, two questions. One, did you ever get your beer? Yeah, no beer. And two, why can't you really offer a definitive horse breed test? Like how come somebody can't send us a sample and we can tell them oh, it's a quarter horse, or it's a Shetland Cross with an Arabian, or a Shetland Cross with a Piri. Why can't you do that?

Dr Samantha Brooks:

Oh boy. Well, let's take the second part first. The biggest reason there really isn't anything that can be called a breed test in the horse, although genetics is phenomenal for tracking ancestry is because we as horse owners and breeders cannot decide what a breed is. We really make these definitions often based for political or historical rationale that doesn't always line up with the biological truth. So, for example, the difference between American Quarter Horse American Paint Horse Registries culturally are huge. These people don't want to have their horses confused, but there is a lot of shared ancestry there and they both belong genetically to the stock horse group. In most cases it's pretty hard to tell the difference, especially since horses have a long generation interval, takes a long time to get from parents to offspring relative to some other critters, and the history on a lot of our breed registries is relatively short. Especially here in the United States it's hard to find many breed registries that go back more than 100 or 150 years. So there's just not enough time for us to create these distinct gene pools that have enough opportunity to diverge to the point where there actually is different genetics between them. Now there are significant differences in the long-term ancestry of horses. So the difference between the Shetland pony and the Clydesdale are kind of obvious from the outside, but also fairly easy to determine from the genetics, because those horses had fairly different geography and much different selective pressure for thousands of years, and so that gave time for biology to really separate the two populations. And a good thing too, because you wouldn't want to breed two Shetland horses together and accidentally get something that looked like a Clydesdale right. Those gene pools have started to diverge.

Christa:

Can you imagine a Shetland temperament on a Clydesdale?

Dr Samantha Brooks:

Oh goodness, now that would be selected out of the pool pretty quickly because it would be so obnoxious. That'd be challenging.

Christa:

So each of our mom's day?

Dr Samantha Brooks:

I probably would. The Shetland I own is peering in the window at me going. Are you talking about me? I'm talking to people like well, so what we call breeds often is very specifically tied to paperwork but not always specifically tied to biology, and different types or uses of horse often contain the same ancestries as another group of horses but in a slightly different mix. So this is where the thoroughbred blood question comes in because, as you say, the thoroughbred blood has had a closed studbook, documented closed studbook, longer than most other horse populations on record. So if you look back at the records at Weatherbees we say at least 200 years, barring fraud. So they have developed a fairly unique genetic selection compared to genetic signature, compared to all the other breeds, just because they have been isolated and under pretty specific selective pressure for racing ability. Because of that selective pressure for racing ability and the reputation that they have gained for excellent performance, they have also been used to help to develop many of our sport horse breeds. That includes not only the European warmbloods but also our American stock horse breeds. So they have significant thoroughbred ancestry as well as the Arabian. So the Arabian I have to give them some credit. They were also used for many of these things and they have a pretty decent genetic signature too. But so the story. The story came out that no, I have not yet gotten my beer, but I may have to go to Ireland to collect that. So sport horse breeders for years have recognized that if you're in a sport like three day eventing, the horses that have a little bit more thoroughbred or light horse so thoroughbred or Arabian ancestry tend to be a little quicker on course and a little lighter over jumps versus the horses that have a little bit less thoroughbred or light horse ancestry or maybe a little bit better suited to say upper level dressage, where they need a little bit more balance, a little bit more focus and not so much athletic ability for speed. You know there's not too many grumpy pre dressage classes that gauge your hand gallop in any particular test Maybe there should be, there should be. Maybe there should be Maybe so much more fun. I know it goes right along with the heirs above the ground that we tend to do in dressage at the training level, but that's okay, that's, my horse will deal with him. So so we had an esteemed scholar of the horse named Chris Ryan come to one of our USCA future event, horse symposia, oh, a number of years ago, and his his. The focus of his talk was how breeders could use this percent thoroughbred blood predicted from the pedigree as a way to improve the performance of their young horses. So a way that they should. They could use the pedigree to calculate an estimate of what a potential offspring's percent blood would would be, which I found phenomenal. I happened to be sitting in the back row and they were. He was showing a pedigree of Fisher Rucana I'm almost certain that's who was one of Mikkel Young's horses, and and he looked at it and he said you know, she has such incredible speed. Her pedigree doesn't entirely make sense to me because it seems to say that she has less thoroughbred blood than her performance speaks to, and I thought this is great. I raised my hand, I said I have the answer and the the answer is that your pedigree is only an estimate of the genetic contribution that you receive from your ancestors. So every generation, each individual gene on a chromosome has a 50 percent chance of transmission and that means over time, for any little thoroughbred gene sort of tracking along the family tree, there's a 50 percent chance that it'll fall off and go one way or back or be transmitted to the, to the offspring, and over time the accumulation of that 50 percent chance over branches of the tree can lead to a lot of drift away from what the predicted percentage might be. So so our bet was I said, you know, I bet, if you can get me a DNA sample from Fisher Rucana, that I'll bet you again this that she actually has more thoroughbred ancestry than her, than her pedigree will speak to. And unfortunately we were never able to get that DNA sample. We did try.

Christa:

Weird so. So let me see if I can. Can I? All right, I'm going to try to say this in horse human terms. So, if I understand you right, the basis of the math model on the pedigree is that you inherit 50% from each parent. Except, what that doesn't account for is how related each parent is for their backometry and what chunk of the 50% they got from their parents. In other words, two horses can be full siblings and be 50% thoroughbred, but they can be two entirely different chunks of their bread. Is that right? So like a mixed bag and you don't know what you're going to get. Is it like a box of chocolates?

Dr Samantha Brooks:

All of life is like a box of chocolates. Those statements are true, but in this case so when we say that a parent and a child are two siblings. So every time a parent has another generation in the offspring, they have given that offspring 50% of their DNA, but we don't know which at each individual gene. Which version of that got included in that package of 50%, and so two siblings likely share about 50%, but we don't know which 50% that is. So on average they share 50%, but for any given copy of a gene, one copy of a gene, 100% will either be in the offspring or not included in that next genome, and that's a 50% probability. It's not like one chromosome gets completely cut in half and all the possible gametes look identical right, and we know this. Everyone who has a full sibling in this audience. Think about your full sibling and think about all the ways that you are different from one another. Thank God I know right, not conflict. We're all so glad that we are not all identical twins, so the same is true for two offspring of a couple of warm blood parents. While they have the identical parentage, they have identical predicted percent blood, but the two individuals are not at all the same and those differences will equate in every generation into drifts in the distance between your predicted thoroughbred percent blood and your observed or actual genetic ancestry percent thoroughbred blood. And in some of our examples and Krista, you might be able to pull them up right there these differences were sizable, right.

Christa:

Huge, huge. We did do one study with some true caners from Dr Timothy Holkamp, and he provided some familial samples of animals that are the offspring of windfall and two particular athletes that are pretty notable, zetserlegg and Vendiver, and interestingly enough, the genetics seem to indicate one of them would be a little draughtier than the other, probably a little better dressage, but both of them eventers, even though the pedigree analysis indicated one probably wasn't. But the differences between their percent blood were kind of striking, both from their pedigree prediction and from each other, and so that's stuff that we can illustrate. I think we did, we have illustrated that in a few talks and we can probably post that on the website. But what was predicted to be their percent blood and what actually was totally different?

Dr Samantha Brooks:

Right On the order of 10 to 20 percent different.

Christa:

Yeah, quite Wow.

Dr Samantha Brooks:

Which is a big, which is a big span. So you know the pedigree pedigree percent blood has been the gold standard for for breeders to use because it's easily accessible. Challenges those estimates can be missing the mark by 10 to 20 percent. So if you really want to know, you need to ask the DNA.

Lauren:

Really interesting. Okay, I'm going to squeeze a client question in here real quick, because this is somebody that asked early on and they wanted to learn more about this. So she said in a previous episode you explained the difference between the horses like me and find my herd features. I previously thought that these were the same thing. We'd love to hear more about what horses like me really means. What does an 85 percent match actually represent?

Christa:

So this is going to be a little tricky. Okay, and this is just based on observations of the data, the. I'm not going to try to split the difference between horses like me and find my herd. I'm going to let the good doctor do that. But what I can tell you is, when you're looking at percentage of a horse like me, we're going back to this how inbred is or is the horse, or is it not inbred? Because we see that in horses that are highly inbred, a lot of times a horse like me can be like 80 to 82 percent or higher like me and not be directly related, not be a father, mother, sibling, half sibling, but on the average horse, quarter horses, warmbloods. Most horses like me that end up being sort of in the same breed category have the same labels and are in the same registry. The highest we see there is somewhere between 76 and 79 percent and anything above that starts to be closely related. But it's really variable, dependent on the breed that we're looking at or the line of horses. I'm saying breed, right, because I'm going to get in trouble, but talk a little bit more about what's really the difference between horses like me. I'll say we have Two horses like me. Here's my horse, charlie, charlie, charlie horse. Yeah, so my horse Charlie has two animals that are like me, like Charlie, and they're both 81% like me. One of them is a relative, direct relative, like first or second degree, and the other one isn't. What gives. How does that work?

Dr Samantha Brooks:

Yeah, the challenge here is that. So these percentages are measuring a group of very, very diverse snip markers. So we use a ruler here that has really fine, fine detail to it. So that percentage as if you want to carry it over from one breed to the next, to the next to next isn't very portable because it's a relative measure, right, so it's. It's. It's measuring the proportion of those markers that match between two individuals, horse A and horse B. And in some breeds, like the thoroughbred, most horses are much more similar to one another versus if you look at a population of Mustangs, where those measures will be quite distant, because you can have everything from a little light horse looking pony height thing to something that looks quite drafty among the Mustangs and kind of intuitively know this, there's more diversity in one breed versus another. So the measures you know 2% may be very informative in one group and not tell you a whole lot in the other. So in the find my herd idea you are looking for the horses that have the shortest genetic distance or the highest match who your horse among the whole population of animals there. Those horses likely are among the possible choices in the database most closely related In some breeds that closeness might be enough to signify parentage. In other breeds, where there's a lot of closeness already, they may not have a pedigree connection for four generations back right. This is one of those challenges with working in the horse With people. You could you could make some assumptions depending on which population you're working in. With laboratory mice it would be super simple. But in horses, because some breeds are tightly knit and other breeds are very loosely defined, the measure is a little bit different depending on on the population. So we have to think of it as relative. It's relative to the population structure of the groups you're working with and it's relative to what's available in the database. So if you're working with a rare type of Moroccan horse, there's not a whole lot of those tested yet in the database, or even something like a Felpony, rare breed, small population, even though they're maybe more known. So there won't be many individuals in that population to pair them with to create those measures.

Christa:

So I think, if I'm understanding what you're saying, the difference, the difference could be you could have two horses that were 81% like me and the difference between who is composed like me part therobrath, part Arabian, part Iberian, a little bit of carriage horse, those are all similar in percentage. That still wouldn't meet the requirements to the find my herd horses that are related to me, because it didn't fit the kinship algorithm right. So in the find my herd we're looking for exact markers that could have been inherited or shared versus the overall. Yes, I'm part heavy horse, yes, I'm part thoroughbred, but in the which happens in horses like me, but in the find my herd, which parts of thoroughbred and which parts of heavy horse are we sharing? Is that a better way to say it?

Dr Samantha Brooks:

Yeah, I think that that does a pretty good job. So so let's say you have, you have a warm blood who is a cross between a freezing and a thoroughbred, one of those down the street, right? So so that sport horse, he, if you match him to the parents, obviously those parents are its parents, right? And so if you test your kinship, those are the parents, they will come out as they should. But your sport horse, if you compared it to a population of freezons, doesn't share the same amount of its genome as, say, another thoroughbred compared to a population of thoroughbreds, right? So a thoroughbred offspring, compared to a population of thoroughbreds, is always going to have a higher measure, even if its parent is among the population. Then, if you have a very outbred individual whose parents came from very divergent populations, like they'll be more genetic distance there, and it's actually it's pretty useful because that creates some of our benefits of heterozygosity, that hybrid vigor.

Christa:

Hetero, hetero. What?

Dr Samantha Brooks:

Yes, heterozygosity, so that's a measure of how many sites across the genome have two different versions of a gene instead of two identical versions of a gene. It's what gives us the magic of our our sweet corn that came in a couple months ago and how high it grows and how many ears it makes because of hybrid vigor. And it's also what creates inbreeding, depression or a reduction in performance and health and fertility that results from too much inbreeding in the pedigree.

Christa:

So heterozygosity up means inbreeding down.

Dr Samantha Brooks:

Yes, exactly. Very good, you get an easy way to put it.

Christa:

Why don't we circle all the way back? Oh, all right. So we've got this ancestry and we're looking at these big chunks of genetics from around the world that compose our horse. So we were talking about behavior earlier, and I know that all Arabians are hot and crazy and I know that all drafts are slow and lazy. Is that true? Can we see that in the ancestry, using behavior or anything else?

Dr Samantha Brooks:

Well, as long as there have been horses and horse people working with them, we've definitely formed these stereotypes of how breeds behave. In some cases they're under very specifics for behavior. That's a good thing, because before we had all this magical genetic testing, all we had to go on when we wanted to purchase the horse say we needed a new plow horse is we wanted to look for something that came from a breed or a breeder or a geographic region where they had a reputation for having excellent temperament. If we wanted a hot-blooded endurance horse to go racing across the desert on, then we had to rely on breed trends to inform our choices. It's generalizable that there should be differences in horse senality between breeds, although it's not always well scientifically measured today because we just don't necessarily always have or have not historically had the best tools to measure behavioral traits. But in general, the idea that your ancestry could help you inform a little bit about all of the traits of the horse, especially behavior and performance, it does hold true. This is the way we've been intuitively breeding horses for thousands of years A deep look at the ancestry using genetics rather than a pedigree, especially for our admins breeds like our sport horses and our continental stock horses. It makes sense. It makes sense that we could look at that ancestry and just as for our three-day event horses, where we're going to infer their ability to have speed over a cross-country course, that ancestry may also be useful to help to infer these behavioral traits, especially those that have some well-known stereotypes. So those dressage bred warmbloods probably do have some overrepresentation of having horses in their ancestry and that may also translate to being able to stay a little bit more calm in the ring. But boy would that be great to continue to study that.

Christa:

That's something we aspire to do and we think that a lot of the secrets are held by the horse people and trying to get the message out of hey, let's all work together on this, it's good for everyone. One more little thing I'm going to circle back to and I'm going to be a real stickler about this. You said another word in there admixture. The heck is that Admixture. Do I use that for cookies?

Dr Samantha Brooks:

You do use it for cookies. You just didn't know. Next time you go make cookies you're going to say admixture on high. So when you're mixing, when you're mixing something, you're doing ingredient admixture. Yeah, it works out.

Christa:

So having a diverse or large admixture would be a quarter horse or a Mustang, and having a low or limited admixture might be an old world Arabian. Is that right?

Dr Samantha Brooks:

Right, right. So we tend to think about admixture events. So opportunity in the history of an animal where two fairly isolated populations might have been brought together to mix? Yep.

Christa:

Your thoroughbred freezing.

Dr Samantha Brooks:

Yeah, your modern thoroughbred freezing. That's a recent admixture event. It probably occurred in the last generation. But let's say, for example, the use of Arabian to develop the saddlebred breed that occurred a hundred years ago, or the contribution of the Arabian to say some of our European breeds, that might have occurred several hundred years ago. So when we talk about admixture, it's just a chance for genomes that otherwise would be fairly different to get together and to mix the populations, gene pools that otherwise would have been very different, to get together and mix.

Christa:

I can think of so many people I want to talk about right now I'm not going to. It seems like, all things aside, that admixture encourages heterozygosity and heterozygosity encourages hybrid vigor, in other words, preparation to handle change. So are you saying pure bread is not really the greatest thing?

Dr Samantha Brooks:

The heterozygosity is great because it gives you a lot of different tools in your toolbox. So one reason our hybrid plants are often quite successful is that they may inherit genes for improved production from one parent and drought resistance from another. And so our horses that have a lot of heterozygosity. They might inherit genes for height from one parent and some extra genes for a strong immune system from the other and then get a lot of diversity in their immune system with two very different parentages as well. But from a breeder's standpoint that can be a challenge right. So in the first generation, that freezing thoroughbred cross, you'll have a pretty good idea of what you'll get. But let's say you take two half-freeze and half-thrower breads and try to breed them together, thinking you'll get a horse that looks the same, and all of a sudden you get this grab bag of diverse offspring that potentially could look very, very frisiany and could look very, very thoroughbredding. So the challenge with these very heterozygos individuals is it's difficult to predict what copy which of the two copies of genes that they'll transmit into the next generation. So it's challenging from a farmer's perspective, whether you're growing corn or horses, because heterozygosity will give you individuals that have a little extra vigor in that first generation, but then it's very hard to repeat that success in the second generation. So this is why our inbred lines of corn and our fairly narrow and closed stud books have been an important tool in agriculture for thousands of years, because the selection increases the chances that you're gonna get what you get in the next generation. They breed true, so to speak.

Christa:

So then, based on this, wouldn't it be awesome if somebody would take the horse project and build tools to predict what you're gonna get when you cross two horses? Imagine that Somebody should do that. Somebody should Do we know anyone, I don't know. I bet we could buy them a beer, yeah.

Dr Samantha Brooks:

What's a girl got to do to get a beer around there?

Lauren:

I know, Thank you so much, dr Brooks, for taking time out of your evening. I really appreciate it and I'm so glad I finally got to meet you, because I hear about you all the time around here.

Christa:

So everything good, it's good. I promise Bye yeah sure.

Lauren:

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 wherever you listen to podcasts. To learn more about Dr Brooks, visit the University of Florida Equine Sciences website For more about Edelon and our latest information. Make sure to follow us on Facebook and Instagram at EdelonDX, or visit our website, edelondxcom, to learn more about our testing. We'll see you next time.

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