Breeding will result in a male Bee unless you add Royal Jelly to the process. Royal Jelly can be acquired by collecting Royal Jelly shards. The rarity of Royal Jelly affects the stats of the resulting Queen Bee.
When you are ready to breed a Queen, visit your inventory to see how many shards you have and to redeem them for a Royal Jelly item.
There are three different rarities of Royal Jelly.