An Overview of Red Crown Rot of Soybean

Red crown rot of soybean is caused by the soilborne fungus Calonectria ilicicola (formerly known as Cylindrocladium parasiticum). In addition to soybean, the red crown rot pathogen is known to infect several additional plant species, including alfalfa and peanut.

Red crown rot was first observed on soybean in the U.S. in 1972 in North Carolina. Soon after, it was observed in additional states in the southeastern U.S. In 2018, nearly 50 years after the initial observation, red crown rot was found in Illinois. It has since been found in several states surrounding Illinois. Red crown rot remains an emerging disease in the soybean production region north of the initial observations from the early 1970s.

It is not known why red crown rot has recently been observed in new areas. It is certain, however, that changes in one or more of the three “sides” of the “plant disease triangle” account for the emergence of this disease in the northern U.S. The sides of the plant disease triangle consist of the pathogen, the host (soybean and/or alternative hosts), and the environment.

Symptoms and Signs

Symptomatic plants often occur in patches in fields infested with the pathogen (Figure 1). Over time, these patches become larger as the pathogen is distributed across the field following soil movement due to various means (farming equipment, erosion, etc.). Symptoms of red crown rot can be observed on different parts of affected soybean plants, including:

Reddish discoloration of roots and the lower stem just above the soil (Figure 2). These symptoms can be observed during the soybean vegetative stages (prior to flowering) and throughout the life of the plant. As plants get closer to maturity, the reddish discoloration may be more difficult to see, and a sharp knife may be used to scrape away the outermost stem/root tissue to observe the reddish discoloration underneath (Figure 3).

Interveinal chlorosis and necrosis of soybean leaves (Figure 4). These symptoms are typically observed during the soybean reproductive stages after flowering has begun (R1), and more often during seed and pod development stages (R3+). These symptoms begin as chlorotic (yellow) blotches that occur between the veins on soybean leaves. Over time, these chlorotic areas expand and eventually turn necrotic (dead), while the soybean leaf veins remain green. These symptoms are due to a toxin produced by the red crown rot fungus that is translocated through the plant and accumulated in the leaves.

Wilting and premature death (Figure 5). Affected plants may wilt and die prematurely, which can happen prior to and during soybean seed development stages. Under dry conditions, affected plants may wilt and die without the leaves exhibiting typical interveinal chlorosis/necrosis symptoms. The petioles and leaves often remain attached to the stem when plants die prematurely. In some cases, severely affected plants may not properly senesce at maturity, leaving patches of plants with green stems and foliage at harvest time (Figure 6).

Severe root rot (Figure 7). Roots infected with C. ilicicola can be severely rotted with black discoloration, which is especially noticeable at the end of the season. Affected plants can often be easily pulled out of the soil due to their lack of roots. The term “pencil roots” has been used to describe affected roots, as they resemble the shape of a pencil since lateral roots are often missing.

Red-orange perithecia on roots and lower stems (Figures 7-8). As plants near maturity or premature death, fungal structures known as perithecia may form on roots and lower stems. These small (0.01-0.02 inch; 0.25-0.5 mm) spherical-shaped structures are red-orange, often occur in bunches, and can be seen with the naked eye, although magnification is helpful in their observation. Perithecia are not always observed, and they may disappear over time; thus, the lack of perithecia does not eliminate red crown rot as the cause.

Conditions that Favor Disease

Root infection by C. ilicicola is favored by warm soil temperatures (77-86°F; 25-30°C) and wet conditions. Infection of soybean seedling roots generally results in the most severe symptoms compared to later infections of older plants. Infection may be favored in fields with poorly drained and heavy soils. The fungus survives as structures, known as microsclerotia, in the soil and in soybean roots. Research conducted in Japan has shown that microsclerotia can survive in the soil for at least 7 years. Symptoms of red crown rot in soybean roots may be more severe in fields infested with the soybean cyst nematode (Heterodera glycines) or southern root-knot nematode (Meloidogyne incognita).

Disease Cycle

Calonectria ilicicola survives as microsclerotia in the soil and soybean roots. Microsclerotia germinate and hyphae colonize soybean roots. Reddish discoloration occurs on roots and lower stems of vegetative soybean plants at approximately V5. During reproductive stages, at approximately R3, interveinal chlorosis, then necrosis may be seen on leaves. This is caused by a toxin produced by C. ilicicola that moves through the plant and accumulates in the leaves. Severely affected plants wilt and die prematurely, while perithecia form on lower stems and roots. Microsclerotia form inside infested soybean roots and return to the soil, ensuring survival of the pathogen.

Yield Losses and Impact

Red crown rot has been reported to reduce soybean yield by 25-70 percent in the U.S. Impacts on a field-scale may be minor at first when patches are small, but as patches get larger over time, red crown rot’s impact on field-scale yield averages can become greater.

Diagnosis

Symptoms caused by red crown rot can look similar to those caused by several other diseases. The presence of perithecia on lower stems and roots can improve the accuracy of a red crown rot diagnosis, but other fungi may produce structures that can look similar. In addition, the red crown rot pathogen may be present along with other soybean pathogens. Mixed infections may be possible and may complicate field diagnoses. For the most accurate diagnosis, send plant samples to a plant diagnostic laboratory, where additional techniques can be used to confirm the disease.

Diseases, Disorders, and Injury with Similar Symptoms

Red crown rot can be confused with other diseases and disorders. The most common of these are outlined below.

Diseases

Brown Stem Rot

Brown stem rot (caused by Cadophora gregata) causes interveinal chlorosis and necrosis symptoms in leaves after flowering (Figure 4), as well as occasional premature death.

How to distinguish red crown rot from brown stem rot: When stems are split lengthwise, browning of the pith and vascular tissue will be observed inside the stem with brown stem rot (Figure 9). Brown stem rot does not cause root rot.

Neocosmospora Stem Rot

Neocosmospora stem rot (caused by Fusarium neocosmosporiellum) causes mild interveinal chlorosis and necrosis symptoms in leaves, generally at growth stages beyond advanced seed fill (Figure 4). The fungus produces red-orange perithecia on the lower stems and roots below the soil line (Figure 10). This disease is not known to be widespread and has only been officially confirmed in a few states in the U.S.

How to distinguish red crown rot from Neocosmospora stem rot: In general, both Neocosmospora stem rot and red crown rot produce red-orange perithecia on the stems of affected plants. However, at present, Neocosmospora stem rot appears to be a disease of rare occurrence. The best method for a proper diagnosis is to submit plant samples to a diagnostic laboratory since microscopic observations would be required to observe the fungal structures.

Phytophthora Root and Stem Rot

Phytophthora root rot and stem rot (caused by Phytophthora sojae) can cause premature wilting and death of soybean plants, with leaves typically remaining attached to desiccated stems. 

How to distinguish red crown rot from Phytophthora root and stem rot: Phytophthora root and stem rot causes a dark-colored lesion (chocolate-brown to purple) that will extend up the stem from below the soil line (Figure 11). Roots are often soft to mushy, reddish-brown to black, with the bark easily peeling off and no external fruiting bodies. Foliage may turn prematurely yellow or wilt without pronounced interveinal chlorosis. Stem symptoms caused by red crown rot will remain near the soil line and will be reddish in color.

Rhizoctonia Root and Hypocotyl Rot

Rhizoctonia root and hypocotyl rot (caused by Rhizoctonia solani) can cause reddish-brown lesions on the roots and hypocotyl area of soybean plants, which can sometimes cause complete girdling and plant death (Figure 12).

How to distinguish red crown rot from Rhizoctonia root and hypocotyl rot: During the vegetative stages of soybean growth (prior to flowering), it may be difficult to distinguish between the reddish-brown lesions on the roots and hypocotyl caused by Rhizoctonia root and hypocotyl rot compared to the reddish discoloration caused by red crown rot. At this stage, the damage to the roots and hypocotyls may be more severe than what typically is observed with red crown rot. In general, post-flowering, interveinal chlorosis and necrosis leaf symptoms may be observed in plants affected by red crown rot, along with perithecia that may develop on affected roots and lower stems; these symptoms and perithecia will not be observed with Rhizoctonia root and hypocotyl rot.

Southern Blight

Southern blight (caused by Agroathelia rolfsii) can cause mild interveinal leaf chlorosis and necrosis of affected plants in small clumps during vegetative and reproductive growth stages (Figure 4). In addition, white to tan to maroon sclerotia may form at the crown of the plant and the soil line (Figure 13).

How to distinguish red crown rot from southern blight: When the environment is favorable, plants affected by southern blight produce a white mycelial mat growing from the soil line up onto the main stem. In addition, sclerotia form on top of the white fungus. Red crown rot does not produce the white mycelial mat nor the sclerotia on the stem.

Stem Canker

Stem canker (caused by different species of Diaporthe) causes interveinal chlorosis and necrosis symptoms in leaves sometime after flowering (Figure 4), and premature death. In general, symptoms are most regularly observed around R6.

How to distinguish red crown rot from stem canker: Stem canker causes reddish-brown to black lesions that develop on the outside of soybean stems, which often begin at a node on the stem (Figure 14). Red crown rot does not cause symptoms on nodes on the stems.

Sudden Death Syndrome

Sudden death syndrome (caused by Fusarium virguliforme) causes interveinal chlorosis and necrosis symptoms in leaves after flowering (Figure 4), as well as premature defoliation and death.

How to distinguish red crown rot from sudden death syndrome: With sudden death syndrome, blue spore masses are sometimes observed on the roots (Figure 15). In addition, plants affected by SDS may drop their leaves, leaving the petioles attached, whereas leaves often remain attached to plants affected by red crown rot. Root rot associated with red crown rot often is more severe than root damage associated with sudden death syndrome.

Taproot Decline

Taproot decline (caused by Xylaria necrophora) causes interveinal chlorosis and necrosis symptoms in leaves beginning at early vegetative stages, but especially during flowering and pod fill (Figure 4), and may cause premature death.

How to distinguish red crown rot from taproot decline: Taproot decline causes roots to degrade and become brittle, in some cases snapping easily when plants are removed from the soil. At reproductive growth stages (generally, seed fill and beyond), interveinal chlorosis is most commonly observed in the uppermost canopy; however, symptoms can be observed at any soybean growth stage from early vegetative stages (~V3) through beginning maturity. Black stroma produced by the fungus are generally present on the taproot or lateral roots and sometimes on the nodules (Figure 16). Red crown rot produces perithecia on the lower stem and roots of affected plants, taproot decline does not produce perithecia.

Injury

Triazole Fungicide Injury

Foliar fungicide products that contain triazole (demethylation inhibitor; FRAC Group Code 3) active ingredients may cause interveinal chlorosis and necrosis symptoms on leaves when applied during hot weather (Figure 17). Some triazoles (e.g., prothioconazole and tebuconazole) are more prone to causing injury than others.

How to distinguish red crown rot from triazole fungicide injury: Symptoms of triazole fungicide injury will only occur on leaves that came in contact with the fungicide, and nearly all plants in a field will be affected uniformly. However, symptoms can become more severe 21-28 days post-application and may be most severe in stressed areas of fields. No other symptoms will occur. Red crown rot will not generally occur consistently across a field.

Disease Management

Host Resistance

No commercial soybean varieties are currently marketed as resistant to red crown rot, although differences in susceptibility among varieties have been observed. Check with your local seed company representative for information about specific varieties.

Cultural Practices

Rotating to non-host crops for at least two years may help reduce inoculum, although the red crown rot pathogen can survive in the soil for multiple years. Avoid rotations with alfalfa and peanut, as they are also hosts of the pathogen.

Planting date may have an effect on red crown rot severity, as maximum root infection is known to occur between 77 and 86°F (25 and 30°C). This means that late-planted soybean fields (i.e. double crop soybean planted after winter wheat or winter canola harvest) may be at greater risk than those planted earlier in the spring; however, severe red crown rot can still occur in fields planted in early spring.

Chemical Control 

Currently, only a few fungicide seed treatment products include red crown rot on their label. These seed treatments have varied in their efficacy for red crown rot management in university field trials. Some of these seed treatments have delayed red crown rot symptom development, resulting in positive yield responses. For more information about specific fungicide seed treatment products, see Fungicide Efficacy for Control of Soybean Seedling Diseases. Foliar-applied fungicides, regardless of application timing, are not likely to affect red crown rot.

Management of Plant-Parasitic Nematodes

Managing soybean cyst nematode and southern root-knot nematode may help reduce the severity of symptoms caused by red crown rot.

Clean Equipment to Reduce Pathogen Spread

Pressure washing field equipment to remove soil before moving to another field may help slow down the spread of the red crown rot pathogen to new fields.

Acknowledgements

Authors

Carl A. Bradley, University of Kentucky; Tom Allen, Mississippi State University; Alyssa Betts, University of Delaware; Mandy Bish, University of Missouri; Boris X. Camiletti, University of Illinois at Urbana-Champaign; Martin Chilvers, Michigan State University; David Langston, Virginia Tech University; Horacio Lopez-Nicora, The Ohio State University; LeAnn Lux, North Carolina State University; Dean Malvick, University of Minnesota; Boyd Padgett, LSU AgCenter, Trey Price, LSU AgCenter; Damon Smith, University of Wisconsin-Madison; and Darcy Telenko, Purdue University.

Reviewers

Travis Faske, University of Arkansas; Daren Mueller, Iowa State University; Madalyn Shires, South Dakota State University; Terry Spurlock, University of Arkansas; and Richard Wade Webster, North Dakota State University.

Sponsors

The authors thank the United States Department of Agriculture - National Institute of Food and Agriculture, Foundation for Food & Agriculture Research, United Soybean Board, Illinois Soybean Association, Indiana Soybean Alliance, Kentucky Soybean Promotion Board, Louisiana Soybean and Grain Research and Promotion Board, Mississippi Soybean Promotion Board, and Missouri Soybean Merchandising Council for their support.

How to cite: Bradley, C., Allen, T., Betts, A., Bish, M., Camiletti, B. X., Chilvers, M., Langston, D., Lopez-Nicora, H., Lux, L., Malvick, D., Padgett, B., Price, T., Smith, D., Telenko, D. 2026. An Overview of Red Crown Rot of Soybean. Crop Protection Network. CPN-1032. https://cropprotectionnetwork.org/publications/an-overview-of-red-crown-rot-of-soybean.