Board Thread:Naruto Discussions/@comment-4370692-20140515060658/@comment-1210805-20140515112429

Like Elvenora said, no one really knows. A lot of things have been said in recent chapters, but very little clarification has been given. Kaguya was said to have the Sharingan, Sasuke's new eye has consistently been called a Rinnegan, Sasuke and Madara were both born with Indra's chakra, Madara gained the Sage's chakra by implanting Hashirama's DNA, Sasuke got some power from the sage himself, Madara ate a tree and here we are.

There are multiple theories floating around, some seem reasonable, others insane, but we really just have to wait for Kishi to tell us.