Horse genetics in real life vs EV

On Equiverse we use a genetics system that doesn't quite reflect what happens in real life, although most of the time it is the same or at least very similar. New theories and genes are always being found, and sometimes old ones get amended or discarded. I wanted to share some of the information I've collected, and also get a discussion going about all the latest discoveries, and what EV's genetics system might look like if it adopted all/most of these. (Maybe one day years from now we'll get another recode, and some of these will be adopted, but I didn't want to create this as a suggestion topic, as such an endeavour would be a mammoth task that wouldn't be plausible or even possible any time soon, if at all.)

Just as a reminder, here's what our current genetics system looks like:

So to briefly summarise, if all the above genes were adopted here, it might look something like this:

This is a very fascinating read. 

Great read! You make it all so interesting and much easier to understand than other sites :) Thank you! 

Last edited on 2017-05-30 at 18:36:30 by Entium

Thanks! I'm glad you found it interesting. :D

I wouldn't include the "brindle 1". It's little more than a genetic defect that's so common in that one horse family because of immense inbreeding. It's not a color or pattern in the normal sense.

The affected gene, in humans, is known to cause several severe skin disorders.

Do you mean I shouldn't include it in these discussions? Or that we shouldn't add it to EV?

On a related note, the genes that cause white spotting in horses are known to cause some severe issues in humans and other mammals but there's no evidence of any such conditions in horses, despite these genes being common. Just because it does something in other animals is no guarantee the same will occur in horses.

Shouldn't be added to EV. It's literally a defect and localized to one severely inbred horse family (I've chanced across one of the breeder's websites and she employs a ton of linebreeding).

*cracks knuckles* Oooooh yeah. This is my place.

Extension: Those discussions are incorrect. Extension has been fully mapped. There are only E and e. Dominant extension E allows both red AND black pigment into the hair shaft, while recessive extension e only allows red pigment into the hair shaft. And, yes, I say dominant extension and not dominant "black" because a horse with at least one E can still be bay, which is a base color and not a modification (bay dun was the original color of ancient horses; non-dun, black, and red mutated from that).

Agouti: Correct. The A^t test was reverse engineered using the genotype of black and tan mice and really had no standing in horse DNA at all. The man who engineered the test and ran the lab even admitted that the test was faulty before shutting down. The agouti locus has also been entirely mapped by geneticists and only A and a exist there. I believe either UC Davis or Animal Genetics are currently looking into potential genetic causes of the seal phenotype. The entire geneticist field doesn't accept A^t at all.

Cream: Correct again. Cream is incomplete dominant and pearl is recessive, on the same locus.
nn = no dillution
prln = no dilution
prlprl = apricot-toned dilution to the coat
Crprl = similar to a double cream dilute
Crn = NO effect on black pigment at all
CrCr = extreme dilution on all bases, overlapping phenotypes (no visual difference)

Dun: Mostly yes. Homozygous nd1nd1 can cause very SLIGHT dilution in addition to primitive markings, but not as dramatic as actual dun dilution.

Sooty: Little to no scientific research has been done on sooty. Cannot say whether it is polygenic or what. I wouldn't doubt it though.

KIT: Basically yes. There are also likely multiple roan mutations that haven't been pinpointed which cause the differences between "classic" roan and frosty roan as well as a different variation of roan in a European draft breed, which does appear to be homozygous lethal. KIT is also linked to extension, which is another crazy thing that would be insane to include in the game XD

Splash: I believe SW2 has been confirmed homozygous safe. One horse, undisclosed by the lab, was tested positive homozygous SW2.  SW1 and SW3 are on the same locus. SW2 is Quarter Horse exclusive to the Katie Gun line. Likewise SW3 is Paint exclusive to the TD Kid line. "Macchiato" also counts as a splash pattern, but nobody really cares about it anymore because it only existed in one horse who never procreated and was gelded, and has passed.

Leopard and Patn: PATN2 is a theory, but the patterns blanket and snowcap are thought to be additionally polygenic from researching pedigrees and phenotypes.
lplp = solid horse
Lplp nn or LpLp nn = without a pattern gene, varnish and appaloosa characteristics (mottling, white sclera, striped hooves)
Lplp PATN1_ = leopard or near leopard.
LpLp PATN1_ = few spot or near few spot
No known difference between PATN zygosities

Brindle: Not really. Chimerism is EXTREMELY rare in horses. Most cases of "brindle" phenotype are actually due to skewed roan or skewed grey patterning along the lines of blashko. There is a form of genetic brindle, which is really just a skin disease called Incontinentia Pigmenti and is lethal to male fetuses.

Mushroom: Yeah, basically.

Tiger Eye: Nothing much to say on that.

Random fun fact, the silver gene in horses is on the same locus as merle in dogs.

@vos
Thanks for the info! A few things to add:

Extension: Actually it's not quite correct to say there are only two alleles on extension (effectively, yes; but genetically, no). I saw a recent paper that found a very rare mutation of e through genetic mapping. I think they named it e^a. Functionally it appears to be identical to e, so this doesn't really change our understanding of extension's role in genotypes/phenotypes. The only real issue was that the genetic tests for extension needed some modification to avoid false negatives, i.e. having a test show a horse had neither E or e alleles, when they effectively had ee (not actually ee, but effectively that as far as the effect of the gene is concerned). So if they've managed to find this, maybe others exist too, even if they're very rare. Or maybe it's on an entirely different locus, and it just overrides extension? I have some strong doubts about dominant black though. It would be worthwhile following up those pedigree studies with genetic tests.

Dun: I didn't know nd1nd1 could have a dilution effect, albeit a tiny one. That's interesting. I'm going to see if I can find photos. Do you have any sources? *edit* I've now found the original article that published these studies. Non-dun1 on bay just looks like a slightly lighter version of bay with a dorsal stripe. Similar story for the other base colours. Source

KIT: The KIT - Extension link is news to me as well. I'll have to look into that.

Brindle: Yes, there's multiple types of brindle. Most are indeed chimeras, so those aren't genetic. The genetic type of brindle you mention is a different one to what I'm referring to though. Brindle 1 is not lethal to males, as several healthy males had tested positive for it in the study I found. They don't display the coat characteristics, just have very thin manes and tails. Incontinentia Pigmenti is actually mentioned in the same study, and they explicitly state they are separate things, with genetic proof to back it up.


@Kuk
Are you sure Brindle1 is a defect? I'm not seeing any reports of any issues associated with it. Is it possible you've confused it with Incontinentia Pigmenti? They apparently have similar phenotypes, and are both found in the same family of horses.

Last edited on 2017-06-01 at 06:40:46 by UlyssesBlue

Dude. The source paper you used for BR1 literally calls it a defect. I mean, it's in the title of the paper: "An Intronic MBTPS2 Variant Results in a Splicing Defect in Horses with Brindle Coat Texture".

From the discussions section of the paper:
"Based on the fact that hair morphology is altered in both BR1 horses and human patients with MBTPS2 variants, we propose that the observed splice defect is actually causative for the BR1 phenotype in horses. The BR1 phenotype is clearly much milder than the different phenotypes reported in human patients with coding MBTPS2 variants. We speculate that this might be due to the specific equine variant and the high proportion of wildtype transcript, which is still expressed in the skin of mutant horses."

I haven't seen that paper. I'll look into that and ask around in a genetics group I'm in (lots of really knowledgeable people, including geneticists active in the field there). I can PM you the group name if you're on Facebook and are interested.

nd1 is the "dun color" found in Andalusians and common in Lusitanos (I do believe actual dun D is found in Lusitanos, but it is very rare; it is not in Andalusians). So "dun" Andalusians are a great example of what nd1 can do, dilution-wise.

It can get very tedious to explain the link between KIT (lumping in tobiano, even though it's a separate locus; it behaves as if it is a KIT mutation and does effect how KIT functions) and extension. It is because they are all on chromosome 3. The simplest I can possibly explain it:

Stallion: ee aa nTo (red heterozygous tobiano)
Mare: EE aa nn (black with no pattern genes)
Foal: Ee aa nTo (black heterozygous tobiano; one possible foal color)

Because we know the parents' genotypes, we can determine that the foal's tobiano allele is linked to his/her recessive extension allele. If the foal is bred and produces foals down the line, whenever it passes e to a foal, the foal will also inherit tobiano; if the horse passes E to a foal, the foal will inherit no pattern. HOWEVER, there is an approximate 3% chance of the extension/KIT link breaking per breeding.

The link can be helpful in determining possible foal colors. Let's say a horse had a red sabino parent and a black tobiano parent and inherited both tobiano and sabino (so this new foal is Ee aa ToSb1). If this new horse is only bred to red horses (let's just use that as a hypothetical) we can assume that all of its red foals will be sabino and all of its black or bay foals will be tobiano, with the exception of the rare link break.

Desperate to learn more about our EV horse & real life horse colors I've once again read something on genetics and I've once again failed miserably at understanding it....

@Kuk
I think we're using different definitions of the term 'defect'. I meant it as synonymous with "negative trait" or "health issue". Again, I'm not seeing explicit evidence of any health issues with Brindle 1. Even so, if there are some, but they're very mild, this would probably be no worse than leopard, which causes night blindness when homozygous, and we're not about to exclude that from EV.

Leopard and BR1 can't be compared. Leopard is found in many different breeds. BR1 is found in one heavily inbred horse family.

Quite frankly, I consider the breeders to be nothing more than glorified backyard breeders who only breed their horses for a rare "pattern".