Obviously, there's plenty of references to Original Trilogy in Rogue One (duh!)
Are there any references to Prequel Trilogy specific content in Rogue One?
Indeed there are. These are all the prequel trilogy references to my knowledge.
Off the top of my head:
Bail Organa, and the actor who played him
(Possibly) the planet Mustafar (if that's where Vader's castle is)
Coruscant (though only see briefly, in the flashback to Jyn's childhood in their apartment there)