USDA stipulates that you must be at least 30 days behind on your payments before they will start the short sale process. This is different from most other loan programs. haven't heard of another loan program where they specifically stipulate that you must be behind on the payments before they will consider a short sale.
The good news is that their short sale guidelines state that you won't have a deficiency after completion of a short sale. Here is the text from their short sale guidelines:
A borrower who successfully sells the property securing the loan using the Pre-Foreclosure Sale Option is relieved of the mortgage obligation. The borrower shall not be pursued for deficiency judgments by either the Servicer or the Agency.
This is good news for anyone that has an USDA and wants to get out from under their upside down mortgage.