Board Thread:Naruto Discussions/@comment-24120130-20140607191120/@comment-28861328-20140701174756

Elveonora wrote: Genetics don't work in Narutoverse like IRL, chakra does though. We don't know how were Hagoromo and Hamura, Ashura and Indra conceived. For all we know, they might have been made the same way as Tailed Beasts were. Kaguya and Hagoromo each took a part of their chakra and did magic.

That is certainly true, but again, for that theory to be plausible, the Sharingan had to be part of Hagoromo's power for it to manifest in Indra.

I, like you, lean more towards a chakra-related birth, at the very least, to Hagoromo and Hamura, but we'll likely never know.