You can use the bait chooser to identify unknown seeds even if you don't know the bait for any fish. If you have both a fruit and a seed for that fruit in your inventory, only the seed will show up in the bait chooser. For example, if you have an apple and an apple seed, you should only see the apple seed on the list. So if you have both a lime and an unknown uncommon seed, and only the seed shows up in the bait chooser, that seed must be a lime seed.