One of the down sides to modern agriculture is after long periods of selective breeding we have plants and animals that have little genetic diversity. This makes it less likely that they have the genetic resources to respond to a new disease or shift in climate.
For example a small population of humans who have a mutation that confers an immunity to the HIV virus. So, over time that mutation would end up becoming more common in our population as they get to live longer and have more kids than those being killed off by AIDS.
Unfortunately if all the members of the population are nearly clones of each other, they either all have resistance or none of them do.
So I'd predict that if we continue business-as-usual we will have to deal with an increasing number of plagues attacking our food supply.
I suppose that if people were planting small diverse gardens, even if our plants have lost their genetic diversity, at least diseases have further to travel than wandering through vast monoculture farms.
Though since genetic material can be shared among species, (weird idea, but true), so just being planted around other species might be able to restore genetic diversity.