Let me respond from an Indian perspective. It is keeping agriculture as an occupation for the farmer viable. While there is a large population needing food & agri produce and their ability & willingness to pay is increasing, small farmers are unable to make enough income for a decent living.
That is a highly regional question. If you are asking from a global perspective, I think the general consensus that the largest overall problem facing agriculture today is how are we going to continue to feed a growing population on a fixed to declining base of ag land.
In the grain belt of the United States, this is largely an ag econ question. How do we continue to produce corn and soybeans cost and still make a profit with tighter commodity markets?
In California, the biggest issue currently is access to water.
In many developing countries, the two largest problems are fighting crop spoilage, and having access to a wider (export) market.
Others can give you better and more in-depth answers regarding their own regions.
Climate change and global warming faced our globe with real challenge to support us with enough foods!,
these conditions along with high evaporation and cropping activities deteriorate soil salinity in many regions in developing countries, so all lead to a higher food prices and more poverty in future!, as we see some