Since the latest edition of Game Informer Magazine is focused is on the WiiU, with New Super Mario Bros. U as the front cover, Miyamoto did an interview where he talked about the Koopalings (the main enemies on NSMBU). He has said that the Koopalings are not related to Bowser; that Bowser Jr. is his only child who's mother has yet to be revealed.

Here's the quote where he talked about it:

“Our current story is that the seven Koopalings are not Bowser’s children. Bower’s only child is Bowser Jr. and we don’t know who the the mother is.”