Board Thread:Naruto Discussions/@comment-945885-20140709082448/@comment-945885-20140714082558

We already know for a fact that Hagoromo was the one who gave chakra to mankind, using a technique to spread and disperse it to his followers while teaching the Ninshu creed. He did so because he thought that chakra would connect everyone and put an end to war and suffering; however, after he died, mankind eventually transformed ninshu into ninjutsu, severing their bonds and using chakra as a weapon.

It remains to be seen if other kekkei genkai originated with Kaguya; I'd be willing to bet that Jugo's does, but beyond that I am less certain. I wouldn't be surprised if she were the origin of all these mutations, similar to Apocalypse in the X-Men setting.

However, there are also several strong implications that these genetic mutations are preserved, if not cultivated, through selective breeding.