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The USDA will send your file back to your lender's underwriter. They'll prep the file for clear to close and you'll be off and running.
Your lender could come back with more conditions, but I doubt it. Most lenders try to send complete files to USDA so that there's not anything that would cause USDA to reject the file. When my file came back from USDA my lender didn't have any more conditions for me.