User blog comment:Kaido King of the Beasts/Baseless Predictions Part 2: Baseless Boogaloo/@comment-5398287-20150430134527

Roger is still alive and was the previous Gomu Gomu no Mi user, but had it taken out and put into a fruit by the previous Yami Yami no Mi user - Luffy's mother - at his behest. Luffy's mom then died of an "unnamed disease" that caused 3 parallel slashes on her heart. A large black-haired man was seen inspecting a nearby fruit stall at the crime scene, but no other evidence surfaced, and the case was considered cold.

As for how Roger survived, the previous Ope Ope no Mi user - the unnamed famous doctor that Rosinante mentioned - created an enormous ROOM in Loguetown and "amputated" Roger's head right as the blades came down, Shambles-ing in some ketchup as well for "blood". Roger then went on to retire on Dawn Island, where he shaved and became known as the good-hearted but irritable mayor - Woop Slap.