WASHINGTON — A freewheeling and almost entirely one-sided argument at the Supreme Court on Tuesday indicated that the justices would not allow Monsanto’s patents for genetically altered soybeans to be threatened by an Indiana farmer who used them without paying the company a fee.

The question in the case, Bowman v. Monsanto Company, No. 11-796, was whether patent rights to seeds and other things that can replicate themselves extend beyond the first generation. The justices appeared alert to the consequences of their eventual ruling not only for Monsanto’s very lucrative soybean patents but also for modern agriculture generally and for areas as varied as vaccines, cell lines and software.

A lawyer for Monsanto, Seth P. Waxman, a former United States solicitor general, was allowed to talk uninterrupted for long stretches, which is usually a sign of impending victory.

“Without the ability to limit reproduction of soybeans containing this patented trait,” he said, “Monsanto could not have commercialized its invention and never would have produced what is, by now, the most popular agricultural technology in America.”