What do I do now?

Okay, so I'm growing an appel, apple boom from the verystart, which is using the seed. So far it's going great: the sprout is growing and new leaves are coming in. But I started to notice that the root is starting to brown. What should I do? Should I cut the brown part off of wait and see if it's normal? And how long does it take for the sprout to start becoming a tree?