First remember what everyone on newagtalk complains about the most, pick out a couple of those that you think are fixable and spend the money on those causes.

1.Weeds in the pigweed family

2.Diseases like SDS, southern rust, tar spot, ect.

3.Chemical drift from dicamba

4.Government subsidies. 1 billion is not enough to do anything about this one.

You could fund research to find a solution to these problems or offer a prize for the group that finds the solution.  My guess would be that if you were able to make the pigweed species go extent then number 3 would go away too.

Start a non for profit that has the goal of ending chemical spraying on crops, this would help get other people to donate to the cause and increase the good that could be accomplished.  Spend the money on getting rid of the reasons that farmers spray crops for, or finding other cost effective control methods.