If we assume gene X only controls one trait, but it turns out to control a lot of functions, we could introduce weird diseases or mutations by accident. When you selectively breed, you let evolved biological control mechanisms filter out potentially dangerous mututions

I don't trust profit-motivated corporations to tinker/optimize for bigger oranges and beefier cows without tolerating some possibly harmful tradeoffs. These are the ppl that brought us high fructose corn syrup. Given the means, they will ALWAYS want a "stickier" product..