My impression is that you just grow a lot of plants, pick the two stongest parents with the qualities that you want, breed those, grow a lot of the new seeds, pick the best parents again, then breed those, and continue to do so each crop. This would be the method that a farmer uses to maintain a healthy crop with desired characteristics. The key to this method is to always breed the parent plants in a highly controlled setting so that you get zero undesired pollination from other plants. Then of course you can just use clones of the chosen parents to continually make seeds.