WASHINGTON — An Indiana farmer who clashed with Monsanto Co. over his replanting of its patented soybean seeds ran into steady skeptical questions Tuesday from the Supreme Court.

The justices strongly suggested that they would rule for Monsanto and decide that the company’s patent protection for its genetically modified seeds covers not just the first planting, but also seeds that are generated later.

“Why in the world” would any company invest millions of dollars in creating a new seed if a farmer could buy one and freely reproduce it, asked Chief Justice John G. Roberts Jr.