Genetics colour people - DNA test results!

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Charmin

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Okay so I'm feeling a little dumb...

We are breeding from my mare next year and we were interested to see what colours we would get from potential sires.

I have been told on here that my mare is seal brown as she has a brown muzzle. Here are the DNA results:

[TABLE="width: 100%"]
[TR="bgcolor: #cce6ff"]
[TD]
Horse Name​
[/TD]
[TD]
Breed​
[/TD]
[TD]
RFactor​
[/TD]
[TD]
Agouti​
[/TD]
[/TR]
[TR]
[TD]
Ruby​
[/TD]
[TD]
Connemara Cross​
[/TD]
[TD]
Ee​
[/TD]
[TD]
AA​
[/TD]
[/TR]
[/TABLE]

Result Guide:
[TABLE="width: 100%"]
[TR]
[TD="colspan: 2"]Red/Black Factor[/TD]
[/TR]
[TR="bgcolor: #e2e2e2"]
[TD="width: 8%"]
EE​
[/TD]
[TD="width: 92%"]Homozygous for Black Factor. Horse carries two copies of the Black gene. Horse is Black based.[/TD]
[/TR]
[TR="bgcolor: #e2e2e2"]
[TD="width: 8%"]
Ee​
[/TD]
[TD="width: 92%"]Heterozygous. Horse is Black based but carries a recessive copy of the Red gene.[/TD]
[/TR]
[TR="bgcolor: #e2e2e2"]
[TD="width: 8%"]
ee​
[/TD]
[TD="width: 92%"]Homozygous Red. Horse carries two copies of the Red gene. Horse has a red base pigment.[/TD]
[/TR]
[TR]
[TD="colspan: 2"]Agouti[/TD]
[/TR]
[TR="bgcolor: #e2e2e2"]
[TD="width: 8%"] AA
[/TD]
[TD="width: 92%"]Homozygous for Agouti. Horse carries two copies of the Agouti gene.[/TD]
[/TR]
[TR="bgcolor: #e2e2e2"]
[TD="width: 8%"]
Aa​
[/TD]
[TD="width: 92%"]Heterozygous. Horse carries one copy of the Agouti gene.[/TD]
[/TR]
[TR="bgcolor: #e2e2e2"]
[TD="width: 8%"]
aa​
[/TD]
[TD="width: 92%"]Non-Agouti. If horse is black based (E), black pigment will be evenly distributed.[/TD]
[/TR]
[/TABLE]

So I'm a bit confused. Can a horse carrying the black base be brown, or is she bay?

And am I right in thinking Agouti gene is the distribution of black points? So is she actually a bay?

So confusing!

Am I also right in thinking she doesn't carry the cream gene and so if put with a cremello would produce a palomino or buckskin?

Here are some pictures of her:

545071_10150733782421421_1565942510_n.jpg


527432_10151263080441421_1413427538_n.jpg


x3wdxu.jpg
 
They don't seem to differentiate between Wild bay, bay and seal brown which are all versions of the Agouti allele.

She is seal brown.

ETA - as she has a 50% chance of passing on chestnut to her foal and if the sire passes on chestnut too (so you have a chestnut base coloured foal), agouti becomes irrelevant as it doesn't change chestnut based coats.
 
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Okay, is chestnut one of the main base colours? As 50% does that mean 50% the foal will be orange chesnut, or do other genes affect it as she holds the chesnut gene but isn't chestnut herself? Or does her homozygous agouti mean that chestnut orange foals aren't possible, as they'll have some form of black?

Gosh this is so interesting yet mind boggling. Thank you so much for your time!
 
At the basic level there are only two colours - black and chestnut. Every other colour is other genes diluting or modifying the base colour.

Your mare has one black gene (E) and one chestnut (e). For a horse to *look* chestnut (or be a chestnut based colour eg palomino, red dun), they need two chestnut genes (ee). So a foal needs to inherit one from the sire and one from the dam.

If you want a chestnut/chestnut based foal, then a chestnut sire would give you a 50/50 chance. If you want a black/black based foal then you need a sire that is homozygous for black (EE), or luck on your side so Ruby passes on the E to her foal.

Of course, if you chose a homozygous grey sire. it wouldn't matter what base colour the foal is as it will grey out due to having a grey gene.


I firmly believe that colour should be lower on the list than conformation, temperament, movement and talent when choosing a stallion.
 
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Forget shades & modifyers like cream & grey for now -she is bay carrying chestnut so she will pass on a bay gene and it is 50:50 of her her passing on chestnut. This means she cannot produce a black foal but will produce a bay or, if the sire has red, a chestnut foal.

I don't see seal brown - I see bay with a mealy muzzle.
 
The newrider forum has a very informative colour section, the stickied threads are a great read if you are interested.

The two base colours are chestnut and black, these are the E/e variants, called the RFactor on the test you had done. E is black, e is chestnut - and black is dominant over chestnut. So if a horse is ee, it will be chestnut, if it is EE it will be black, and if it is Ee, it will be black.

The agouti gene (A) only acts on black (E), restricting the black colour to the points of the horse. It doesnt matter if the horse has one or two copies of the agouti gene (AA or Aa), it still acts the same way on that horse. If a horse is aa, then it will be black, not bay. If a horse is chestnut, then the presence of the agouti gene is irrelevant - the horse has no black pigment for it to affect. Your mare is very much capable of having a chestnut foal if bred to a chestnut (50% chance) or to a heterozygous black/bay (25% chance of chestnut). Because your mare is AA, she will always pass on the agouti gene, so you will never get a black foal from her.

You are correct in thinking she doesnt carry the cream gene (a single copy of the cream gene on a bay horse gives a buckskin, two copies gives a perlino) so if you bred her to a cremello you would get a palomino or a buckskin depending on whether she passed on E or e.
 
Oh colour's not a factor in deciding the stallion, we were interested in what colours the different matches would throw. Basically getting a bit excited and ahead of ourselves!

The website is very useful. A little confusing that people have bays with mealy muzzles called bays when I'd just about got my head around the suggestion she was in fact brown. Is brown just simply a version of the bay, or genetically are they different?

I'll go have a look at those stickied threads now - thank you so much for your help! It's so interesting. I don't really care what colour it is as long as it's healthy and well but it's nice to look at the possibilities (the tests main purpose was to see if she had the cream gene, as a cremello stallion is on the list and mum didn't really want a cremello, sorry to cremello lovers!)
 
If you look at the bay thread in the picture gallery, you will see that many people don't differentiate between bay, wild bay and seal brown. They are slightly different genetically (different versions of agouti) and you can see the difference when looking at them, if you know what to look for.

You can't get a double dilute foal (cremello, perlino, smoky cream) if one of the parents doesn't have a cream gene. So your Mum can breathe a sigh of relief on that one if you go for the cremello stallion.
 
The only times cream doesn't show are on greys & some blacks so you didn't really need to test.
Actually my mare is wild bay plus she has pangare and produced a bright orange foal with pangare to a palomino sire.
 
s4sugar said:
The only times cream doesn't show are on greys & some blacks so you didn't really need to test.
Click to expand...

Looking and understanding the genes now I do feel a bit foolish - but it was relatively inexpensive and given us an educational (and dare I say it - fun?!) evening so I won't feel too bad!
 
As I understand it, brown and bay are slightly different versions of the same gene. The wikipedia page (scroll down to the section on agouti phenotypes) http://en.wikipedia.org/wiki/Equine_coat_color_genetics#Agouti suggests that 'normal' bay (A) is dominant over brown (At), but that brown is dominant over non-bay (a). So for your mare to be seal brown, her AA genes are actually AtAt (as you know she doesnt have a recessive agouti gene), meaning she could have a bay or a brown foal depending on the genetics of the stallion. I'm not sure how the A+ bay allele fits in here
 
Do the different varieties of bay result in different varieties of buckskin if diluted by cream? Having owned three buckskins that all looked totally different I just wonder why.
 
I would expect a wild bay buckskin to have less black on it's legs, unless the horse has Sooty which adds black and often causes dapples.

Brown and bay based buckskins look very similar, again it's the presence, or not of Sooty that makes a big difference.
 
Oh I see. Sorry.

I don't know, but it's certainly the form of agouti that I've seen the least. It would be interesting to know whether that's because it's less common or recessive, or both.
 
Charmin, please can you tell me what you need to do for a test, and were you recommended a company or did you pick one at random from the internet. I would like to know for sure what colour my horse is. Thanks.
 
caseycat said:
Charmin, please can you tell me what you need to do for a test, and were you recommended a company or did you pick one at random from the internet. I would like to know for sure what colour my horse is. Thanks.
Click to expand...

Hi - I will check with mum where she used and what she had to do. Think it was a few strands of tail hair. The one faracat posted seems to be more comprehensive than the one I used though, I'm sure there's some better ones out there :)
 
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