(Adds warning to airlines in paragraphs 3-4) By David Shepardson WASHINGTON, Oct 6 (Reuters) – The Trump administration said on Monday that funds from a U.S. government program that subsidizes commercial air service to rural airports are set to expire Sunday because of an ongoing partial government shutdown. The U.S. Transportation Department said the subsidies in the Essential Air Service program will end Sunday after the department transferred unrelated funding from the Federal Aviation Administration as an advance unless a government funding standoff is resolved. USDOT will stop reimbursing carriers on Sunday under the program and told them they can stop flights they had signed contracts to fly, according to a notice seen by Reuters. The government told airlines if they fly Essential Ai

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