What are the roots of human cultural differences? Is it genetic, social and/or environmental?

Some of each. Naturally occurring flora and fauna in lands of origin tended to dictate what foods became traditional but social customs in most cases probably developed separate from that. Then of course things like language and religion often depended on a culture's ability to protect itself from encroaching cultures, Catholic/Spanish Speaking Latin America being one major example of that. 

Most of it is social and/or environmental

Some of it is genetic - there are entire tribes that lack the enzyme to digest milk

Primarily it was environmental. 

Groups of humans developed their cultures in isolation from one another.  So each culture was developed independently.   So the best answer of your choices would be environmental.