Fungus that causes stem rot are in the Rhizoctonia, Fusarium or Pythium genera.
Stem rot can readily infect crops that are in their vegetative or flowering stages.
Also leaving previous dead roots in soil can increase the risk of stem rot.
Producers of soybeans tend to not manage for the disease because it is not normally yield limiting in a large area.
Fungicides can be used to manage the disease as well as burning the crop after harvest or letting it decompose.