Board Thread:Theories and Speculation/@comment-1512913-20160709202754/@comment-1872728-20160712155147

Elveonora wrote: Meaning that Six Paths Senjutsu isn't an original, innate trait of Hagoromo's chakra, but something he developed later in his life. I think I get what you mean now, but I still think that it's genetically related somehow. So Kaguya ate the Chakra Fruit right? The fruit bears most (if not all) of the Physical Energy and Spiritual Energy of the people on Earth. It also bears most of the Natural Energy on Earth, so the Chakra Fruit is basically the Sage Chakra Fruit, and the God Tree is basically the first Sage Mode user.

When Kaguya ate the fruit, she changed physically, which gives the impression that her genetics are changed as well. This means that her chakra is now permanently composed of Sage Chakra. Also, after Hagoromo manifested his Rinnegan, his Sage Mode manifested a Rinnegan-like marking on his forehead, which looks as if his Sage Mode is being mutated by genetics, so I think that Six Paths Sage Mode is an innate trait, but it's just inactive until the person learns Sage Mode.