1. Cross breed it with another bee species that have the desired flower trait, do this enough times and refine the result long enough till you got the desired bee. This is after all how it works in RL as well, although grossly simplified in MC.
2. Use the Extra Bees Tier 3 machines to break down bees with desired traits in order to get vial with the desired trait, then inoculate it unto a princess and drone of the species with the dragon egg dependecy.
3. Use gendustry(never played with this myself, so dont know the details, but apparently its a lot easier than the other 2 options. Some argue that it bypasses the whole mechanic of beekeeping, but I guess you should be the judge of that yourself. I think I will try it out, but I do think I will stick to the above methods.