Pod and Stem Blight and Phomopsis Seed Decay

Encyclopedia Article

Description Pod and Stem Blight & Phomopsis Seed Decay

Pod and stem blight is one of three diseases that make up the Diaporthe-Phomopsis complex. Other diseases in this complex include seed decay and stem canker (see page 31). Stems, petioles, pods and seeds are all susceptible to infection.

The most characteristic sign of pod and stem blight is linear rows of black specks on mature stems of soybeans. The specks, which are flask-shaped fruiting structures of the fungus known as pycnidia, can be seen during the season on prematurely killed petioles or stems.

Poor seed quality may result from infection. Seed infection occurs only if pods become infected. Pod infection can occur from flowering onwards, but extensive seed infection does not occur until plants have pods that are beginning to mature. Insect damage to pods favors development of seed infections. Phomopsis-infected seed are cracked and shriveled and are often covered with chalky, white mold. If infected seeds are planted, emergence may be low due to seed rot or seedling blight. Infected seedlings have reddish-brown, pinpoint lesions on the cotyledons or reddish-brown streaks on the stem near the soil line.

The fungi survive winter in infected seed and infested crop residue. Certain weeds may serve as hosts to some pathogenic Diaporthe and Phomopsis species. Infection can occur early in the growing season without causing symptoms. Disease is favored by warm, humid weather, when soybean plants are maturing. Also, disease is more severe if harvest is delayed.


This disease should be scouted R5 through R7, it is especially important to scout seed production fields because the fungus can be seed transmitted. 


Variety selection: Sources of resistance have been identified, and variation in seed infection has been reported among commercial soybean varieties. Unfortunately, there currently are no resistant varieties or lists of seed reactions of current varieties available. Varieties with an earlier relative maturity for a region are at greater risk of Phomopsis seed decay and pod and stem blight than fuller-season varieties.   

Seed selection: Do not plant seed with a high 
incidence of infection.  

Crop rotation and tillage: Crop rotation and tillage will reduce survival of Diaporthe and Phomopsis species. Non-host crops include corn. If tillage is considered to promote decay of pathogen-infested residue, be careful to minimize soil erosion and 
maintain soil quality.

Foliar fungicides: Application of foliar fungicides near R5 can protect seed quality, but may not affect yield.

Harvest: Harvest early maturity varieties first to lower the incidence of seed rot.  

Fungicide seed treatment: Most fungicide seed treatments, except metalaxyl/mefenoxam, are 
effective against Phomopsis species. Treating 
Phomopsis-infected seed lots may increase germination and improve plant establishment.

Photo by Daren Mueller