Methane is a potent greenhouse gas, and one that has been linked to farming in several ways. Ruminants produce methane as part of the digestive process, rice paddies release methane through fermentation, and clearing land by burning forests or draining wetlands can all produce methane. But the amount of methane being released into the atmosphere is growing faster than any of these sources, and scientists are trying to find out where the excess methane is coming from.
Fracking has been identified as a possibility, but most industrial sources of methane are not increasing. Outgassing from the deep ocean is also a possibility but is difficult to observe, much less to measure. You can read more about this riddle at http://e360.yale.edu/feature/methane_riddle_what_is_causing_the_rise_in_emissions/3047/.