User blog comment:Omega natsu2/Chapter 372: Breach, Predictions./@comment-2214433-20140219093238/@comment-7418318-20140219102821

@Naruto: To cut it short. All the chakra was in a tree. A woman ate a fruit of the tree (which was forbidden, though it was never explained by whom or why) and later gave birth to the Sage of the Six Paths. Apart from having two sons who founded the Uchia and Senju bloodlines, as we jsut learned he also bestowed chakra on other people.

And it was never explained how much of his oh-so-great power came from being born as his mother's son and how much came from the jubi, which he later locked into himself.