I think it's just that certain families have more pure shinobi bloodlines, so their abilities to handle and manipulate chakra are more powerful, just through their genetics. Which means that this kind of breeding has made one particular, usually difficult, type of chakra manipulation easier for people in this family. So a while back one of these ancestors was just like, 'oh shit. Wow, I just figured out this really cool move that nobody else can do cuz they don't have my awesome chakra. I guss I'll teach it to my children and all the rest of my family.'
Why So Green And Lonely? We Are Accidents Waiting To Happen.