John C. Rupe research focuses on the epidemiology and control of soybean diseases with an emphasis on sudden death syndrome (SDS), seedling diseases, and charcoal rot. His current SDS research investigates the interaction of the SDS pathogen,
Fusarium solani f. sp.
glycines, with the soybean cyst nematode (SCN),
Heterodera glycines, and how cultivar resistance effects SDS development.