Bad Genes?

I've read some posts here and there and some people say they try to wean out the bad genes(undesired genes) they don't want in their horse's blood line. Are they referring to their horse's color? Can someone elaborate this for me please and thank you.

Usually yes that's what they're referring to, however bad can mean different things to different people. Most people view Gray and White as "bad" because they cover the original color completely. In Clydesdales Sabino is often considered undesirable. For a while in Gypsy Vanners Tobanio was considered undesirable(I've no idea if it still is or not!). For me I try to breed only for Black TBs so "A" genes are undesirable for me.