Need information on the new brown color gene (At) - Updated photos Post #36

[Daventry]

To all of the color gurus out there, I’m in need of some information on the brown gene. Has anyone come up with a name yet for a single dilute or double dilute brown yet?

We have a Section D Welsh Cob foal due in a few days out of a single dilute brown stallion. I would like to get the foal tested to see if it carries the At color gene, but when I went to the Pet DNA website, it had a notice that they are not currently accepting samples. Are they just back logged with samples…or is something wrong with the test and they are no longer doing it? http://www.petdnaservicesaz.com/equine-testing/understanding-equine-dna-and-agouti/

Are there any other labs testing for the brown gene? Last time I looked into it, the Pet DNA lab was the only one.

[epowers]

Brown with a copy of creme is generally called smoky brown or brown buckskin. As far as I know there is no universally recognized name for a brown-based double dilute- there is no test to determine the difference between that and a bay based double dilute, so you could only know based on parentage or offspring. The brown (“At”) test was unreliable (getting impossible results), so they pulled it. PetDNA has always been the only one doing the brown test, and, unfortunately, none of their research about their supposed “At” version of agouti is peer reviewed or published at all.

I think brown is an obvious phenotype, and certainly seems to breed true, but for now it’s not understood what exactly the genetic difference between brown and bay is. It’s very possible that there is another pigment-type switch working in conjunction with agouti that determines the amount of restriction of black pigment over the body.

[Daventry]

Thanks for the info. I was worried the test might have been pulled! I understand about the phenotype rather than genotype of the brown gene…what I’m not clear about is whether a smoky brown is actually a smokey brown or smutty buckskin. But then I guess, if it truly was a smutty buckskin, the black points would still be present, correct? As compared to the smoky brown horse who would have no black points whatsoever. Am I on the right track?

[epowers]

Brown horses have black points. Brown (seal brown) tests as E_A_, just like a bay would, but has less restriction of black pigment, so their black points tend to be less defined, and the body has a much greater expression of black pigment. Some seal browns are nearly black except for the soft points (muzzle, flank, etc). Because of this, and because one copy of creme has no dilution affect on black pigment, some smoky browns are virtually undistinguishable from “regular” browns. Because there is no genetic test, there is no hard and fast line that makes it easy to explain where dark/sooty bay ends and brown begins, except in classic seal brown cases.

[JB]

Smoky brown is the most commonly used term.

Pet DNA isn’t taking brown tests right now because they are working on sorting out a “glitch” in the test. Some horses who have tested as “a” elsewhere also tested as At with Pet DNA - doesn’t change what the horse is, but it does mess with the details and breeding outcomes. I don’t think it’s yet been determined what’s going on, just theories, including a possible combined gene that really looks like Ata (which would still be brown since the a is inactive).

Brown horses can have black or brown points. So, you can’t look at black legs and declare him bay or buckskin. But you would be safe, assuming there’s no possibility of Silver or any other dilute factor, in seeing brown legs and declaring him brown.

Daventry, it might be very apparent phenotypically that the foal is brown. Or not :lol: But yeah, if it’s not really, really obvious, you’re SOL on testing right now

[epowers]

A brown horse would not have “brown” or red points unless there was a dilution gene like silver at work. The legs on a brown horse will be black just like a bay, only more so (there tends not to be a sharp line of black-pigmented leg to red-pigmented rest of the horse by the knee). Unless you’re going to apply the same caveat to any other dark pointed (bay or black) horses, who can also have different “shades” of black. By definition, the dominant form of agouti pulls black pigment produced by an E_ horse to the points. Whether the horse is bay or brown, it definitely does not strip all black pigment from the horse.

[JB]

Some brown horses DO have brown points. Seal browns especially. I have one standing out there. He might look black, including his legs, but put him against my actual black horse and it’s clear his legs as well as his body are all a dark chocolate color. Not black.

I agree that the delineation between the legs/points and the body color tends to be a lot more blurred/undefined on browns, whereas some bays have a very clear line between them.

[stoicfish]

It seems that whatever causes the Brown is linked directly to the Agouti gene or is a dominate aspect of the E. Like a form of Black allele that is not susceptible to the Agouti.
It would be interesting to know if the Brown ever came through a chestnut.

[JB]

Do you mean, can At express in an ee horse?

Theoretically no, since Agouti acts on black pigment.

However, in reality there seems to be some evidence that in an ee horse there can be “bleed through”, some level of deactivation of e (so some level of activation of E) which might be what shows as sooty. Theory. If that’s the case, then if At is present, then again theoretically it could act on that.

[stoicfish]

[QUOTE=JB;8128545]
Do you mean, can At express in an ee horse?

Theoretically no, since Agouti acts on black pigment.

However, in reality there seems to be some evidence that in an ee horse there can be “bleed through”, some level of deactivation of e (so some level of activation of E) which might be what shows as sooty. Theory. If that’s the case, then if At is present, then again theoretically it could act on that.[/QUOTE]

No, I mean if you found Brown horses that had that trait passed to them through a chestnut parent (this is the horse with Brown in the family), you could assume it came from the Agouti as opposed to the E (Black). Using transmission to figure out the mechanics.

And e is a separate allele, correct? So there shouldn’t be a bleed through as it isn’t a suppression gene, right?

[JB]

Gotcha. Yes, an ee (red-base) horse can be homozygous for Agouti or whatever form - bay, brown, wild bay - and you’d never know it until s/he produces a bay or brown foal with a black parent (who is aa so couldn’t have been the cause).

e/E is the Extension gene - makes a horse black-based (EE or Ee) or red-based (ee). Technically an ee horse has no black pigment BUT, there are somatic mutation “things” that happen which can flip a given gene the other way in a specific location.

A non-gray horse can have the g flipped to a G in a specific location, like a leg.

A chestnut can have an e flip to E in a given location and cause/allow a big black or bay/brown splotch, often on the shoulder/lower neck area.

[stoicfish]

A non-gray horse can have the g flipped to a G in a specific location, like a leg.

A chestnut can have an e flip to E in a given location and cause/allow a big black or bay/brown splotch, often on the shoulder/lower neck area.

Didn’t know that, that is very interesting. Is it a flipped e or and dysfunctional E?

[JB]

Most likely flipped. For example, gray is dominant, with g being off and G being on. For the non-gray horse to have a gray leg, it has to be G there, flipped from g, since g can’t really be non-functional since it wasn’t doing anything in the first place. That logic would make it much more likely that a blood mark - which is a non-gray mark on an otherwise gray horse - would be the G having flipped to g

[epowers]

Yes, my chestnut mare had a brown filly with a black stallion. A chestnut just won’t express the genes that work with black pigment, they are still there.

[stoicfish]

[QUOTE=epowers;8128885]
Yes, my chestnut mare had a brown filly with a black stallion. A chestnut just won’t express the genes that work with black pigment, they are still there.[/QUOTE]

Right. That is a great example but you need to know the grandparents also.
If (my assumption) the E gene is the cause, then the parents of the black stallion should have the brown expression (assuming at least one was a bay) or great grandparents.
Or if it is carried by the Agouti gene then the chestnut would be the one to pass it on.
It is revealing because both parents, by phenotype contribute one or the other.

So do you know which side of the family it comes from?

[JB]

When chestnut x black = brown, the following are things you know:

1 - the black is Eeaa - Ee because he sent his e to make chestnut, and aa because otherwise he’d be bay or brown
2 - chestnut is ee, and then either Ata, or AAt, or AtAt (without knowing the colors of the chestnut’s parents). Why? ee is because she’s chestnut. For this result of brown, the chestnut had to have it, because that’s where the brown At came from since it couldn’t have come from a black parent. So that rules out the other combinations of AA or Aa.

Based on what we do know about brown, it is another form of Agouti, just like we know Bay is, just like we theorize wild bay is.

Brown is not caused by the E/extension gene. Extension is what makes a horse black-based or red-based. Agouti is what then restricts black pigment to some degree. In general, brown is the least restrictive, then bay, then wild bay being the most restrictive (which is why the leg points are low, and even the mane and tail tend to be diluted a bit). And the Ata brown horse is darker/less black restricted than the AtAt horse. Nearly all seal brown/black-bay horses are Ata by current testing. Nearly all the tested AtAt horses are lighter brown, often being difficult to distinguish from bay.

But the lighter end of Ata horses can be very similar to the darker end of AtAt horses.

When it comes to chestnuts, you do not know the Agouti status in most cases without testing or without seeing enough offspring. In some cases you can know it for certain:

• black x black = chestnut means the chestnut is eeaa
• brown x brown = chestnut means either Ata, AtAt, or aa - no bay A in the picture because brown horses do not have the Bay form, as that is dominant and the horse would be bay, not brown.

[RacetrackReject]

[QUOTE=epowers;8128332]
A brown horse would not have “brown” or red points unless there was a dilution gene like silver at work. The legs on a brown horse will be black just like a bay, only more so (there tends not to be a sharp line of black-pigmented leg to red-pigmented rest of the horse by the knee). Unless you’re going to apply the same caveat to any other dark pointed (bay or black) horses, who can also have different “shades” of black. By definition, the dominant form of agouti pulls black pigment produced by an E_ horse to the points. Whether the horse is bay or brown, it definitely does not strip all black pigment from the horse.[/QUOTE]

Not true. I have a brown gelding with brown points, which sometimes look black, as does he at times, but both are definitely brown when seen up close. He is a registered TB, no dilution genes at work.

[stoicfish]

Based on what we do know about brown, it is another form of Agouti, just like we know Bay is, just like we theorize wild bay is

Possibly but what if it is a difference in the E gene that allows it to be resistant to the Agouti?
Of course it will only show up along with the Agouti gene…

I know the rest of it and how it works. That is why a chestnut horse and a black horse producing a brown could revel if it is connected with the E.

[HiJumpGrrl]

How about brown x brown = Black? how would that work?
eeAta x eeAta = eeaa? is that right?
(my horse http://www.pedigreequery.com/whataboutfreud)

[stoicfish]

[QUOTE=HiJumpGrrl;8129086]
How about brown x brown = Black? how would that work?
eeAta x eeAta = eeaa? is that right?
(my horse http://www.pedigreequery.com/whataboutfreud)[/QUOTE]

That would just be a chestnut. Black is E and Agouti (bay)is A, chestnut is e.