The lack of resistance genes for root diseases means there's simply no selection pressure underground. A plant that seeds itself in the same soil every year ought to have root disease, says Cook. That's what happens in agriculture. I can't help but think that something else is going on out there that relieves the plant of selection pressure, so there's no need over evolutionary time to come up with a genetic strategy within plant populations. Something else is keeping these pathogens in a state of suppression, so they're there, but not raising havoc.
Some further comparison is in order here.
Natural plant communities grow year after year. Crop rotation, though considered good farming, is a peculiarity of agriculture. One purpose of rotation is to combat soil pathogens. So as Kennedy's work also shows, underground communities must follow a different logic than do above-ground communities. Plants may not develop genetic resistance, but Cook hypothesizes that they do have a strategy.