We farmers like to make decisions for our plants and animals. We generally choose when and whether they breed; when and what they eat, and where they stay.
I tend toward a lassiz faire, libertarian lifestyle anyway; and we have a farm where animals have the life (for a while) liberty (till they hit the fence) and the pursuit of happiness (no limitations).
Kidding aside, we've developed a system that is the antithesis of domestication breeding. This system does mimic the breeding programs nature conducts without permission or privacy all around us. We'll use our pig herd as an example.
First, nobody is castrated. We've done our homework and have tens of thousands of dollars of sales saying that castrating is not necessarily necessary. This means we don't know who the fathers of our piglets our.
Second, we give nearly all our gilts one chance at a litter. In this area too, we have not found a quality decrease in older animals. Gilts grow significantly during their pregnancy, and if we like the result we can keep her. Otherwise we can have our pig and eat her too.
So do we have any say in the direction of our pig herd's genetics? Normally farmers micromanage breeding in focused pursuit of specific traits. We are definitely interested in improving our pigs but we do this with selection pressure rather than trait or line breeding.
Our primary breeding pressure is culling females. Any females that don't raise a decent size litter are culled before they get a second chance. While culling sows who have just weaned their first litter, we also consider other traits such as body shape.
The second tool is culling any pig big enough to go for behavior. Any pig that makes me nervous is culled at the next available opportunity.
Finally, since older sows require a bigger boar to breed them, we get to choose the paternity of the offspring from our older sows. We pick one lucky boar and don't take him to market. Thus we know the parentage of a good portion of our piglets.
The downside of this kind of management is less control. The upsides are less work, and less inbreeding side-effects.
In the practice of breeding its common to pursue one trait and unwittingly achieve and number of other undesirable ones. A good example would be dog fanciers breeding collies with longer and longer noses until their skull was too small for their brain. That would never happen in nature.
So we macromanage. We don't tell our animals which plants to eat, where they may sleep, or even who they procreate with. Telling everything what to do takes a lot of energy and time anyway.
As a bonus, we insulate ourselves against even small versions of these problems described by Temple Grandin.