The USDA has posted links to documents describing what would happen in the (likely?) event of a government shutdown. Most of the employees - 79% in fact  - of the Agricultural Marketing Service would continue to work, since their jobs are funded by fees for service.

From the USDA, on AMS activities after a shutdown:

The mission of the Agricultural Marketing Service (AMS) is to facilitate the competitive and efficient marketing of agricultural products. AMS programs support a strategic marketing perspective that adapts product and marketing decisions to consumer demands, changing domestic and international marketing practices, and new technologies.
Approximately 65% of AMS’s annual operating activities are conducted through fee-for-service or reimbursable activities which would continue during a funding hiatus. These activities include voluntary grading and inspection services, oversight of Research and Promotion Boards, laboratory testing, plant variety certification, and perishable agriculture licenses. For these activities, the Agency either bills in advance of services or maintains an adequate reserve on hand to bill in arrears for reimbursable grading and inspection activities.

Summary of AMS Activities Financed from Available Funds

These activities are conducted throughout the United States in both headquarters and 133 field office locations with 78% of AMS staff operating outside of the headquarters. As many of the Agency’s activities are seasonal in nature, peak employment occurs during the winter months due to the cotton, tobacco, and various fruit and vegetable grading and inspection activities.

In addition to AMS’ activities above, there are several appropriated activities that would be impacted by a funding hiatus where funding has been provided to States for auditing and testing activities who would continue to provide services for a limited period of time beyond the expiration of federal funding. Examples of these activities include Microbiological and Pesticide Data sampling and testing, Pesticide Recordkeeping and Country of Origin Labeling audits, and agriculture marketing grants.