It was previously believed that Brown was a shade of Bay. However research by scientists has now revealed that Brown is a base colour. It is now believed that the difference between the two is in the Agouti gene (‘A’), which creates both bay and brown. The Agouti gene is a modifier which restricts the black pigment on a base coloured Black horse. Chestnut and other red-based colours are not visibly affected by this gene, as there is no black pigment to affect. They can however have Agouti genes which they may pass on to their foals.

It seems now that the Agouti gene has two forms, and the reason we see both Brown & Bay is that the Agouti gene which causes Bay has more effect than the Agouti gene which causes Brown. So when the Agouti for Bay takes effect, it restricts the black colouring more effectively on the horses body, while the Agouti for Brown has less effect, so only restricts the black on more limited areas, such as the muzzle/nose, flanks, elbow area, and occasionally the insides of the upper legs. It does seem that the Bay and Brown forms of the Agouti gene do inherit separately from each other, so they are not the exact same gene expressing at random & differently in individual black based horses.