So, if I’m understanding all this color genetic thing-the base of every coat is red or black. Check. Now I understand dilutes and what coats are made when crossed with that gene. But I have recently read about a brown gene? Like the color we call seal bay or seal brown, is this different from a bay gene? And if it is, what a the ‘odds’ of a brown or black baby from breeding a brown mare to a brown stallion? How bout the odds on getting a chestnut from this cross?? Any insight? Tia!
Agouti is the gene that starts restricting black pigment to the points (lower legs, mane, tail). It’s one of several genes that have more than 2 forms (on/off).
A is bay
At is the now testable brown
A+ is the theorized wild bay
A is dominant over At. It’s unknown at this point where A+ falls in there.
So yes, genetically, bay and brown are different - same gene, different form of it.
The odds of a brown or black foal from 2 brown parents are fairly high. However, there’s more to it:
If both brown parents is heterozygous for black (meaning the are Ee), then there is a 25% chance the foal will be chestnut, and the Agouti status of the brown parents is irrelevant.
If at least 1 parent is homozygous for black (EE), then there will be no chestnut foal. There will be ONLY black or brown, since A is dominant over At, therefore any brown parent cannot have A (so cannot make bay), and a black parent is always aa (having neither bay nor brown).
The odds of black or brown depend on the Agouti status. If either brown parent is AtAt there will always be a brown foal produced if it’s black-based (see above regarding chestnut). But of both brown parents are Ata, there’s also a chance of a black foal
Another way to look at this in terms of chestnut are what the parents’ Extension status is, and it’s independent of the Agouti status.
Lol! I think I had to reread that response 3 times… Thank you for the details I know color genetics can be complicated!
It’s really not that complicated if you 1) break it down into the very basics, and 2) look at each genetic component for how it behaves on different colors and its dominance or recessiveness
You’ve already got the red and black base down - that’s the first step.
EVERYthing else is a modification of that. Sometimes it’s a simple dominance, where heterozygous makes its presence known. Sometimes it requires being homozygous.
Agouti modifies black pigment, and turns a black horse into a bay/brown/wild bay. It’s invisible on any red-based color because there’s no black to modify.
Cream modifies, period, though its modification can be very subtle on the darker colors, such as black and dark brown. Double cream is always obvious (on a non-gray), though other modifications can hide behind it. Dun is usually very obvious, and double dun doesn’t look any different from single.
So, when trying to figure out a potential outcome, start breaking down what you know - chestnuts are always ee, Agouti unknown unless 1 or both parents were black (or smoky black or perlino, etc). Anything black-based is at least Ee and may be EE, but if there’s a chestnut parent you KNOW it’s Ee.
Look at each component on its own to start, then figure out from there
You make it sound so simple!! I feel like I need to take class from you!
There are charts online that show the possible colors of foals from given colors of parents, and the likelihood, percentage-wise, of each color of foal. Keep in mind that color genetics are in its infancy, and there are a LOT of factors not understood and a few that may be MISunderstood.
Unfortunately those color calculators don’t include brown yet 
The only thing I don’t like about the color calculators is when it breaks down into, for example, 10% here and 5% there. For the color guru experts, we know to add a few of the percentages together so there is, say, a 33% chance, but I find many breeders don’t quite understand that part of it.
Hmmm - such as? Not doubting, I just can’t bring to mind an example I might have seen LOL
That’s why I asked, because the color calculators I have found only offer bay/black/chestnut… When I clearly have a brown! And a stallion that is tempting me-not because of his color fwiw- happens to be the same shade of brown! So I was just curious what they could produce if I bred them! 
I would love another brown!!
