When breeding his/her animals, the farmer can intentionally chose animals that do not have characteristics leading to stereotypic behaviors (e.g. no brain pathology, low stress etc.) (Mason et al., 2007)

Above is an example of a chicken building a nest. Chickens with higher tendencies  of building their nests tend to have a higher frequency of locomotion stereotypies (i.e. pacing) , so the farmer can chose chickens that do not have that trait (Mason et al., 2007).

Downside: 

By selecting animals that secrete less cortisol, indicator of stress, there is a risk of long term health consequences for the animal. So overall there will be a decrease of welfare instead of an increase (Mason et al., 2007).