Well if you ask me to be the idea guy ! :p
I would have done cross-breeding by surroundings one pepper with different colors, as it is (kinda) done in Nier Replicant.
Player would for example plant one blue pepper, surrond it with 2 yellow peppers or more and the next day the blue pepper would become a green one.
So a day in the game would be "plant seed and try combination" and then the player click next day with all the new pepper already grown out.