Soybean Charcoal Rot versus Soybean Zone Lines

Soybean Charcoal Rot

In many parts of the nation, spring rains and poorly drained soils make for challenging planting conditions. Soybean seeds are often planted into wet soils, or soils that are soon wet due to spring rains. As the weeks pass after planting, the spring rains give way to a summer environment that is hot and dry. Unfortunately, this often provides the environment conducive for soybean charcoal rot. 

The fungus that causes charcoal rot is Macrophomina phaseolina, which persists in soils as hard, black structures called microsclerotia. Although Macrophomina can infect seedlings and young plants, charcoal rot does not typically manifest until late season, around R5 to R7. The symptoms of charcoal rot include yellow leaves, wilting, premature senescence, or premature plant death (Figure 1). After the plant matures or dies, microsclerotia can be observed. Management includes the planting of tolerant products and methods to help reduce drought and heat stress.

It is also important to note that Macrophominia is a great saprophyte, which means it can decay dead tissues. Due to the ubiquitous nature of this fungus, a high percentage of plants are infected, but disease does not develop unless conditions favor (stress) development. If disease does not occur in season, microsclerotia may be visible after maturity and the fungus can develop rapidly the longer the plants remain in the field, which can impact seed quality.

Soybean charcoal rot with distinctive charcoal appearance under the outer layer. Figure 1. Soybean charcoal rot with distinctive charcoal appearance under the outer layer.

Soybean Zone Lines

Soybean zone lines (Figure 2) have often been misdiagnosed as soybean charcoal rot. Publications and references have indicated a relationship between soybean zone lines and soybean charcoal rot. However, proper identification establishes the difference. 

North Dakota State University and multiple other collaborators, including Bayer, conducted a study to determine the cause of zone lines in soybean stems. After collecting data from many states and isolating from zone lines, the conclusion was that zone lines are not caused by Macrophomina phaseolina (Charcoal Rot), but by Diaporthe longicolla (a species of Diaporthe that also causes seed decay). A follow up study was performed where healthy soybean plants were inoculated with Diaporthe longicolla and zone lines were observed after the plants were killed. Therefore, zone lines in soybean stems do not indicate charcoal rot in soybean but, like charcoal rot, the lines are not visible until plant senescence or death.

Soybean zone lines. Figure 2. Soybean zone lines.

Continued research is being done on the yield response and management of soybean zone lines. Diaporthe longicolla and other fungi are being tested to identify which are associated with zone lines. The unpublished data indicates that stress and other diseases are the root cause of this symptomology. 


Giesele, L.J. Charcoal rot. CROPWATCH, University of Nebraska.

Smith, S., Chilvers, M., Dorrance, A., Hughes, T., Mueller, D., Niblack, T., and Wise, K.  2014 Charcoal rot management in the North Central Region. A4037. University of Wisconsin-Extension.

Melvick, D. 2018 Charcoal rot on soybean.  University of Minnesota Extension.

Herschman, D.E. 2011, Charcoal rot of soybean. Plant pathology Fact Sheet. PPFS-AG-S-02. University of Kentucky.

Olson, T. R., Gebreil, A., Micijevic, A.,Bradley, C. A., Wise, K. A.,Mueller, D. S., Chilvers, M. I., and Mathew, F. M. 2015. Association of Diaporthe longicolla with black zone lines on mature soybean plants. Plant Health Progress doi:10.1094/PHP-RS-15-0020.

Web sources verified 4/18/22.

Tracy Norcross

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