Gemma Genetic Testing Results

About a month ago I ordered a full genetic panel to be run for Gemma… we pulled out some mane hairs, filled out the form, sent in the sample, and proceeded to wait. I’m of the opinion that it’s always a good idea to get the most holistic view possible of any horse you’re going to use for breeding, and indeed all the WTW mares have had full genetic profiles run. The most crucial thing to know is whether or not they’re carriers for Fragile Foal Syndrome (originally thought to be limited to warmbloods but has recently popped up in thoroughbreds as well), but it’s also nice to know their color genetics and if they show any predisposition to other health issues. The more you know about a horse, the better breeding (and care) decisions you can make. And while, as of right now anyway, we’re not planning on breeding Gemma anytime soon, I’m just super curious.

my clever girl

So, let’s get into the results. Gemma’s color panel came back as ee AA.

Since she’s chestnut we already knew she was ee – every chestnut is ee. Chestnut is recessive, therefore in order for a horse to show as red, it cannot possess any E (black), only two e (red). If you want more deep-dive info on this, most commonly called “Extension” or “Black Factor” or “red/black”, there’s a longer explanation here. But basically ee = chestnut, Ee = heterzygous black, EE = homozygous black. Every horse is some combination of such. With a black-based horse, like a bay or a buckskin or a grulla, you have to run the test to see whether or not they have one copy or two copies (Ee or EE). But with a chestnut there’s only one option: ee. They’re red-based, not black-based. A bay/black horse can carry one copy of the red gene, since it’s recessive, but a chestnut horse can only possibly have two copies of red.

The thing you don’t know just by looking at a chestnut is their agouti status – that AA part. Agouti is what’s responsible for making an Ee or EE horse present as bay instead of black. The way agouti works is that it restricts the black pigment to the “points” of the horse’s body – ears, legs, mane, tail, etc as you see on any bay horse. So a true black horse will have an agouti status of aa – totally recessive for agouti and therefore the black is not restricted at all, but rather covers the entire body. A bay horse will either be Aa, heterozygous for agouti, or AA, homozygous for agouti. You can’t tell by looking – there’s no difference between Aa and AA in how the horse appears physically. Since a chestnut doesn’t physically display agouti on their coat at all (since, remember, they don’t have any black and agouti only expresses on black), you have to test in order to know which of those three combinations it carries. Gemma is AA meaning she’s homozygous for agouti, which means that any foal she has will carry at least one copy of agouti. This means that she cannot produce a true black offspring – only some form of bay (or chestnut) – all depending on the stallion she’s crossed with.

For another example, Presto’s sire Mighty Magic is EEAA – homozygous black and homozygous agouti. This means he can ONLY produce bay offspring, since he will always pass an E (black based) and an A (agouti). The caveat to this is if he’s bred to a gray mare or a dilute mare and the mare passes one of those genes – known as modifier genes – on top of the bay… but that’s getting a lot more complicated and off topic so lets not go there today.

Anyway, back to Gemma. I also was interested to see what her test results would be for splash or KIT (also known as Dominant White) genes – the ones responsible for white markings. Given her high jagged front stocking, ermine spots, and flat top on the hind sock, I thought it was possible that she might carry one of the genes responsible for amplifying or adding more white markings. She has some very typical physical characteristics of both, but not ALL the physical characteristics of either. I was actually surprised that all of these tests came back negative – no splash, no KIT.

To give an example of how sneaky these genes can be, WTW broodmare Peyton is actually a carrier of W20, a gene responsible for amplifying white markings. Peyton herself has one teeny tiny sock, but we did see that W20 gene at work on her 2020 foal Remi, the chestnut with 4 high whites and a blaze even though he had two pretty plain bay parents. Sometimes Peyton will pass it, sometimes she won’t, sometimes it’ll be very obvious, sometimes it won’t. Genetics are fun like that. It’s also worth noting that while there are 4 known splash genes and over a dozen known KIT genes, we do also know for sure that there are a lot more out there that just haven’t been identified well enough to develop a test for yet. Probably lots more. So while Gemma doesn’t have any of the known ones, it doesn’t necessarily mean she doesn’t have any.

Moving on past the color stuff and into the health stuff – she’s negative for all the immune diseases, muscle disorders, endocrine disorders, ocular disorders, and hoof & connective tissue disorders, including FFS. All good news. She did pop up as a carrier for RLN (roaring) which has pretty much been the case with every Thoroughbred we’ve tested. None of them have actually been roarers, and neither is Gemma, but they do carry an increased risk – not surprising for the breed. Just something to tuck into the back of my mind when making breeding decisions. She also has one marker (of a possible 8) for Lordosis – not enough to warrant being labeled as a carrier, but something else to keep in mind. I would not cross her with any lines known to carry Lordosis, just to be on the safe side.

For the performance part of things, she has the markers (aka “likely affected” status) for the Endurance gene. Yes, they can test for sprint vs endurance genes! She falls into the “generally has less speed, but greater stamina and endurance” category. She was never really tried at longer distances on the track, her longest races were only one mile (granted, she had her best finish at this distance) but she was more of a come from behind type rather than a first-out-the-gate type, so it does line up in that regard. Maybe we’ll get to find out more about that one in her eventing career.

They also have a test (not quite in the “high confidence” realm of research, but in the “moderate confidence, findings replicated in multiple species”) for curiosity vs vigilance. Basically they define curiosity as an interest in novel objects and a willingness to approach them vs vigilance as the tendency of a horse to examine its surroundings carefully and from a safer distance. I was interested to see what this one would say, because to me she’s a bit of both. Definitely VERY curious, and I would say leans more toward curious than vigilant, but she’s also careful and intelligent about her surroundings. Like for instance, I haven’t tested Presto or Henry but I would be SHOCKED if Presto wasn’t Curious and Henry wasn’t Vigilant – like if that wasn’t the case the test would just be garbage IMO. Gemma though… I could argue both for her. So it’s kind of funny that she indeed came back as having markers for both. That tracks.

she wants to touch everything with her nose

The last test is for height, also known as LCORL, which she’s heterozygous for. This is very typical for a TB or a more moderately sized warmblood – meaning that they carry one copy of the gene for increased height and have a 50% chance of passing this to any offspring. So basically, I should expect her to produce to her height (16h) or larger, barring any extenuating circumstances or environmental influence of course.

All good information to know! None of it really changes the list of stallions I had picked for her, but it does give me more things to consider.

11 thoughts on “Gemma Genetic Testing Results

  1. I love genetics. That is super fascinating about the endurance gene in TBs and how that can affect their performance. I am very curious as well about the curious vs vigilant test – that might be fun to get Amber tested to see which one she is. I’d say she’s in between like Gemma, but potentially leaning more towards curious. Gemma sounds like a super contender as a broodmare, and I’m excited as well to see how her endurance gene will factor for eventing!


  2. I really enjoy how you break down & explain the genetic testing. Its an interesting science and would help mare owners clarify which stallions to select for their mares. In hindsight, if you knew that Sadie & Mighty Magic had a propensity to produce height, would you have still matched them? We all adore Presto, but he is definitely on the tall side.


    1. I feel like MM tends to produce pretty average height, I haven’t seen anything majorly giant from him. Back when we did Sadie’s testing the height variant wasn’t part of the panel, but I would be interested to see what her results show. We know that she tends to produce her own height or larger… but I still would not have chosen a different stallion for her.


  3. Curious, has the “endurance” been tested in other breeds? The science part of my mind (which is most of it, ha) wonders what would happen if you tested a bunch of Arabs who do everything from never leave the show ring to the 100-mile endurance rides and see if there’s a correlation between performance and genetics. Arab breeders certainly want you to think there is, but that doesn’t mean there ACTUALLY is.


  4. I just sent in hair for my horse because he has no history. I did both Texas A&M (cheap) and Etalon (not so cheap). Texas came back with South American gaited breeds (WTF??) so very curious to se what Etalon says.


    1. Texas A&M’s testing is notorious for being wildly inaccurate so I wouldn’t put a lot of stock in what it said. I know someone who tested a few horses, including a registered QH as a “control” and that horse came back Trakehner, Mustang, and something else random that I don’t remember. Doing breed ancestry DNA is still pretty difficult in horses, the science isn’t as far along and a lot of them share some common roots that are difficult to decipher. I’ve yet to see any that was super accurate.


  5. SO interesting – thank you! I have 2 half brothers (same sire different dams) and they are polar opposites on the curiousity v vigilance scale so finding out there may be a gene for that was super cool.


  6. This is all so interesting! Not that I think it would be in my best interest to ever breed my pony, but now I kinda want to test her anyway. Plus, we all know doing what’s best isn’t always what I do…
    I can’t wait until you can start Gemma back. Really excited to see what she turns into. And then also for when she starts making babies. She’s so beautiful, I’m sure she’ll make beautiful foals!


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