Board Thread:Naruto Discussions/@comment-945885-20140709082448/@comment-24531362-20140720003554

Man of Sin wrote:

My point was that the powers of the Sage family had divided over the generation.

I agree with you, and have made that point on several previous discussions. However, that fact is explainable under the rules of normal biology. Each son of Hagoromo inherited a different trait, with the mother presumably having neither. Therefore, what we can guess is that the Rinnegan-traits display a form of incomplete dominance, and also likely multiple alleles. We can theorize that the Rinnegan manifests with an allele pattern similar to rrr (R being recessive alleles for the Rinnegan) and that non-Rinnegan-esque eyes manifest with an allele pattern of RR (R being dominant alleles for normal eyes). The cross between an rrr and an RR (Hagoromo and wife) occurs. Possible combinations include an RrR or rRr (since the tri-allele trait only exists once, but the trait requires three alleles, one parent will donate two alleles). These two combinations will exist as a Sharingan or the super-chakra of Asura (with RrR being a bit more likely, in this example, to be a Sharingan because only one dojutsu allele is required for manifestation, allowing it to become more common over many generations, as evidenced by modern times). Only a complete reintegration of the two sides' genes (or tampering through the mutagenic effects of chakra, which is the only way we have seen thus far) could possibly create a new Rinnegan naturally.