Complex sentence: Any animal that does not meet this level of improvement in the eye shape while maintaining the other qualities is culled from the breeding program; i.e., that animal is not used for breeding, but is instead spayed/neutered and placed in a pet home.
Split into simpler sentences: Any animal that does not meet this level of improvement in the eye shape while maintaining the other qualities is culled from the breeding program. Meaning, that animal is not used for breeding, but rather is spayed/neutered and placed in a pet home.