The first horse I ever bred is now just over three years old and she has started to develop lumps under her jaw. What could be causing this?

It sounds like the tooth bumps young horses develop on their lower jaws. The adult teeth are forming in the jawbone but haven't yet erupted into the mouth. Young horses from the ages of three to five can get these bumps, which do not look particularly attractive, but they do disappear as the horse grows up.