Equine Genetic Testing

If any of you are even remotely involved in breeding, you’ve probably heard about Warmblood Fragile Foal Syndrome. It’s a relatively recently-discovered genetic defect found mainly in warmbloods, and is fatal to all affected foals. Over the past year or so warmblood breeders (well the responsible ones anyway) have been testing their stock to check for carriers. WFFS is recessive, so lots of horses can be carriers and be completely unaffected, but breeding two carriers together results in a 25% chance of an affected foal. For breeders this is a big deal, since obviously you don’t want to breed two carriers and risk getting an affected foal that won’t be viable. There is still a lot of widespread testing being done, but the initial estimate was that between 6-12% of the warmblood population are carriers, and the current trend is more toward the higher end of that.


Several of the warmblood registries have moved quickly to require stallion owners to test and submit the results of their stallions, so that it can be public knowledge. Most mare owners are doing the same as well, to identify any possible carriers amid their own stock. My friend Michelle at Willow Tree Warmbloods wanted to test her mares for WFFS of course, but rather than opting for just that test, she decided to go “all in” and get a full genetic panel of each of her mares from Elaton Diagnostics.

everything included in the full panel

It tests a wide range of each horse’s genetic makeup, from their color genes to their susceptibility to West Nile Virus, the presence of alleles that could lead to metabolic issues, roaring, lordosis, laminitis risk, Uveitis risk, etc. I guess the easiest comparison would be to think of it as an equine version of 23 and me.

Of course, some of this research is more confirmed, while some is still in “discovery” stage and the information may not be super reliable yet. All of the details and reliability are broken down on this page. Researchers have even found genes relating to temperament, gaits, and speed (all explained here). If you’re a nerd, it’s SUPER interesting.

Michelle has a wide range of mares that she tested, from traditional european warmbloods, to ponies, to a stock horse, to a full TB, to a half TB, to an Irish sporthorse. It’s possible that I spent a while paging through the results and trying to interpret what all of it might mean. To give you an idea of just how much is included on each horse:


It’s A LOT! And admittedly, I had to google several things because I had no idea what the heck it was.

But let’s start in the easiest place, with the color results. Chestnut is recessive, so all the chestnut mares obviously only have two red genes. The bay/black mares were more interesting, seeing who has a red hidden in there… only one of them is homozygous black (that would be Inca), the rest all carry red and could produce a chestnut foal with another red carrier. Some of them have a genetic predisposition to produce more white markings, as well. The most interesting result from all of the color stuff (to me anyway) was this note on the Irish Sporthorse mare’s panel.


Even the ponies and stock horse mare didn’t have anything like “non-dun primitive markings” show up. Is it from the Irish Draught part of her lineage maybe? Interesting!

For a lot of the stuff under the health category, horses can have a couple of alleles (or even more, in some cases) present without actually being affected by said thing at all. This is NOT a diagnostic, in any way, but merely showing where there might be more genetic susceptibility.

A couple of mares showed a slightly higher susceptibility to West Nile, for example. The one with the fewest alleles present on any of the stuff in the health category was Peyton, the full TB mare.


She is the only full TB mare in the bunch, so I’m kind of interested in seeing what other TB mares might look like in comparison. For a TB she has relatively little inbreeding (only Nijinsky II), which I also wonder how much that contributes to how all this stuff shakes out.

Luckily nothing major showed up in any of the mares as far as being carriers, everyone is WFFS n/n, and it’s good information to know which ones might show slightly more genetic susceptibility to certain things. Not only does it make you a little bit more informed as a horse owner, it’s obviously important in a breeding program as well. Of course, like I said earlier, some of the test results are known to be more reliable than others, but still… more information can’t be a bad thing.


I admit, even though I own two geldings I’d be super curious to see their results as well. It doesn’t matter for the breeding side of things, but I would definitely like to know if they show markers for metabolic issues, or are more predisposed to vision issues or roaring or laminitis or West Nile or anything like that. Seems like really good information to have!

In case anyone else out there is interested in the service, Michelle did report that Etalon was super helpful and easy to work with. She’s got a call lined up with them later to ask some questions and get more details about certain things (especially what the stuff in the performance category really means!). I’m super intrigued to hear more.

Would y’all find something like this to be interesting and valuable for your own horses?

21 thoughts on “Equine Genetic Testing

  1. wow that is cool!! I am toying with the idea of doing the genetics dna stuff for our new dog Bernie. I think it is so interesting what they can do nowadays with testing. I am glad Michelle did this for all of her horses. Such a great owner she is.

    AND YOU TOTALLY SHOULD DO BOTH Henry and Presto. hahaha it would be very interesting!!


    1. I am not sure about the performance part of that test. I would need to see more test results to believe that this is more than a horsy version of “Oh, you’re a Virgo. Of course you are *this and that*”.
      As far as a genetic predisposition for cerain diseases: heck yeah, sign me up for that test! Super interesting!
      Also: I am very happy that publishing the stallions’ results are mandatory for wb breeders. Needs to be like that for mares, too.

      Liked by 1 person

  2. I’d be super interested to do something like this with Frankie at some point! He’s a lifetime horse, so it would be fascinating to know if there are susceptibilities we should keep our eye on when he gets older.


  3. I have 3 horses I’d be interested in testing for various reasons. My 2 retirees at home are draft crosses and I’d love to know more about their genetic make up. Does this test go in to breeds or is that more of the Texas A&M test? Then I have a full tb mare that I’d love to get more info at a much more detailed level like this test provides as I plan to have her for a very very long time (she turns 9 tomorrow!).


  4. This is SO cool, I love it. Although I did read ‘Gait’ as ‘Goat alleles’ and that was amusing for a minute or two. I’d love to see what Lucy’s looks like even though she’s retired (the farrier referred to her as a propane tank on legs last week…) in part because she’s a minimal white overo and the paint color markings are so interesting.
    Would have loved one on my old mare too, since she was born/registered Buckskin, turned bay w/a dorsal stripe and then roaned out around 12-13. Weirdo.


  5. We did disease focused genetic testing of the human variety before I got pregnant with our first child, through a company called Counsyl that tested for something like 175 genetic problems. Based on cost ($350 per person at the time) we only tested my spouse, and from that I can confidently say he’s excellent breeding stock; carries no known genetic deficiencies. 😀


  6. Do you know what they are classifying as warmbloods? I am breeding my mare this spring. She is arabian on her sire side and (we think) ISH on her dam side (no papers). I am wondering now if I should have her tested. I guess I will at least reach out to the stallion owner (Oldenburg w/ a lot of TB) so see if he has been tested! I’d be curious to know cost & contact info! Thanks!


    1. It has been identified in some TB lines as well. I don’t think its a bad idea to have any mare tested, but as long as the stallion is n/n you would not get an affected foal. If your mare is a carrier you could still get a carrier. If you want only the WFFS test there are a few different places offering it, just google.

      Liked by 1 person

  7. Very interesting! It brings up the whole responsible breeder thing too, which, as we know in many breeding situations isn’t always the case. I have QH/stock types and the amount of HYPP still being bred is so disappointing. You really have to watch out for it in certain bloodlines.


    1. As well as the amount of PSSM horses being bred because they’re ‘just carriers’ (thats not how this one works!?!).


  8. OMG I nerded out so hardcore with this post lol. I LOVE genetics! So fascinating! That panel really does look interesting. I may do it just to know for Amber. And I agree with you that it would be interesting to test Peyton against some other full TBs to see the difference. I was an intern for a place that line bred their QHs, and it really baffled me. They kept trying to tell me it’s LINE breeding not INbreeding, but it looks the same to me. And I have never otherwise seen purposefully bred horses where 95% of all foals had a defect in some way – most of them conformation, but some definitely had personality issues. It’s getting close to line/inbreeding in reining horses too, and it makes me worry. Ah, sorry, a bit of a tangent, but basic point – genetics is fascinating! lol


    1. Ah yes, the wonderful world of AQHA breeding… don’t EVEN get me started. If it’s not HYPP it’s the impossibly straight hind legs, or tiny feet, or crazy brains, etc. Oh, and let’s over-breed, too and just dispose of the “bad” ones. All of that linebreeding and “own son” crap drives me crazy as well. I’m not saying other breeds don’t do bad things, too, and not all QH breeders are bad but some – especially the conformation breeders whose manta seems to be the more deformed/useless/crippled young the better – are just the worst. Horrible.

      Amanda, I didn’t know you could get such a thorough profile done these days. Really amazing! Assuming that Michelle tested Sadie, were you surprised at anything that came up? I think it would be way cool to get your boys done, too!


  9. Genetics is super cool, but also kinda confusing to me. Maybe it’s because I fell asleep in high school bio 😬. I would love to be able to do a full genetic work up on some of the horses at my barn, there are few I’m curious about as well as a few rescues I wonder their history. Either way I’m poor and most aren’t mine so 🤷🏻‍♀️


    1. Ooh Ill have to research the UCDavis pannel. I geek out on genetics so this is cool, I wish the breed ones were more accurate because Id love to tease out if Appy pony is mixed or not, but even just the colors should be entertaining with an Appy. I think any animal breeders should be more responsible and genetically clear their lines as possible. If your gonna play god, do it right.


  10. I find this super interesting. Especially the predisposition to certain health issues, since as it happens, I’ve dealt with quite a few… What’s the turnaround time on results? Wondering if eventually this sort of panel would show up on a PPE. I feel like if you’re an area that is more prone to things like west nile, or lyme, or epm (or whatever) it might be useful to know if your horse is more likely to be infected genetically. Thanks for sharing this! I saw Michelle post that the mares were all negative, but I didn’t actually know what it was they were negative for, and wasn’t in a position to go googling when I saw it.


  11. So very interesting! I am definitely tempted to have my mare tested even though I probably won’t breed her. I’d be really curious to see what it says about her personality- she is bossy and vigilant about her herd! She’s a German Riding Pony Thoroughbred cross, so an interesting mix to look at dna-wise too.
    Hmm… budgeting, budgeting.


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