Soybean Diseases: How to Scout and Manage Threats to Plant Health

Soybean growers are a resilient lot, relying on their skills, experience and sheer hard work to see them through the many difficulties involved in doing their jobs. One of the highest-priority challenges facing every farmer is protecting their crops throughout the growing season — an ongoing struggle considering the number of threats to soybean plant health.

📸: BASF internal photograph/Featuring a productive soybean farm.

Each year U.S. soybean growers lose millions of bushels of yield due to the effects of soybean plant diseases. The toll differs from year to year as growing conditions change. In 2023, those losses were estimated at about 4.8%.¹ Going back a bit further, in one study of 29 soybean-producing states in the U.S., losses from soybean disease over five years (2015–2019) ranged from around 6% to more than 10%.² From 1996 and 2016, average annual losses to soybean disease in the U.S. totaled nearly $4.55 billion.³

Preventing yield loss starts with knowing how to identify and manage soybean diseases that could plague your crop. In this article, we look at diseases that have been particularly troublesome to soybean growers in recent years and consider their causes and effects, how to scout for and identify them, and strategies for managing and minimizing their impact on crop yield.  

CONTENTS

1. Soybean cyst nematode (SCN) 
2. Soybean sudden death syndrome (SDS)
3. Soybean White mold
4. Frogeye leaf spot
5. Soybean mosaic virus
6. Cercospora leaf blight and purple seed stain 
7. Soybean seedling diseases 

Soybean cyst nematode

Soybean cyst nematode (Heterodera glycines), often referred to as SCN, is the single most destructive pathogen affecting soybean crops in North America, responsible for more than a billion dollars in U.S. losses every year. Initially identified in North Carolina in 1954, SCN has continued to spread throughout North America, wreaking considerable damage: By 2021, the hit to U.S. soybeans from SCN was 100 million bushels lost.⁴ The 2022 figure was in the same ballpark, with 95.6 million bushels lost.⁵

The soybean cyst nematode is a microscopic parasitic roundworm whose life cycle consists of egg, juvenile (larvae) and adult. It does its damage by interrupting soybean’s normal uptake of water and nutrients, which results in stunting, yellowing and early plant maturation. The nematode also weakens the plant’s defenses to other root-damaging diseases. Under optimal conditions, one life cycle of the disease can be completed in three or four weeks, and fields might host three or four generations of the nematodes within one growing season.  

📸: Beeman and Tylka/Iowa State University//Featuring each stage of the SCN Lifecycle.  

An SCN infection begins when hatched nematode juveniles (larvae) penetrate a soybean root and feed on it. When the larvae mature, adult females emerge and cling to the root’s surface, where they are visible as small white or yellow lemon-shaped nodules not much larger than a coarse grain of sugar. Those nodules may each contain up to 400 eggs. 

📸: BASF internal photograph/ SCN cysts visible on soybean roots

📸: BASF internal photograph/ SCN cysts visible on soybean roots

When the female dies, the nodules become hardened cysts that can break away from the root and easily be spread by farm machinery, animals, wind and water. The eggs inside the cysts can remain viable for many years.

📸: Iowa State University/Featuring the SCN lifecycle infection in soybean roots.  

What conditions help soybean cyst nematode thrive? 

Soybean cyst nematodes can do their disruptive work in all kinds of soil and weather, but they are particularly at home in drier conditions and lighter, sandier soils. By contrast, no-till fields or fields with high clay content tend to have fewer SCNs. The nematodes also prefer high-pH soils and are more prolific, and create greater corresponding yield loss in soils with a pH higher than 6.5.  

Identifying and scouting for soybean cyst nematode 

Dense infestations of SCN often show visible signs of damage above ground, such as yellowing or stunted soy growth. But since SCN is a root parasite, the presence and extent of the disease can often be hard to spot. This is a worrisome reality for growers because nematodes can cause a yield loss of up to a 30% before symptoms become visible above ground. 

Scouting is the best way for growers to confirm the presence of SCN in their field. BASF recommends two specific approaches to scouting, depending on when you plan to scout: 

1. Six weeks after planting: Dig (don’t pull) roots and look for female nodules.  
2. After fall harvest: Collect soil samples and have them tested for SCN.  

With your SCN numbers in hand, you’ll be better prepared for the following year. You can learn more about where and how to have your soil evaluated for SCN at The SCN Coalition.  

Managing soybean cyst nematode 

Soybean cyst nematode cannot be completely eradicated, but there are effective strategies to help manage the spread of the pathogen and its impact on yield. Good management begins with maintaining a healthy crop. Be aware of factors that weaken plant health, such as inadequate moisture, poor soil, other diseases, pests, etc., which will only increase the threat to soybeans in an SCN-infested field. 

Strategies for managing SCN include the following:  

Crop rotation

The range of SCN hosts is limited, so rotating to a non-host crop (such as corn) will help suppress the SCN population in the soil. BASF Seeds Agronomist David Pazdernik advises, “If your cyst levels are low to medium, you can simply do a corn-soybean-corn-soybean rotation. That will help to significantly reduce the number of cysts in your soil.”

If levels are high, Pazdernik recommends growing two years of corn before returning to soybeans. “That can reduce your soybean cysts by somewhere around 80%,” he says.   

Choosing seed varieties for their genetic resistance

The primary native resistant genes still in use today originated in China and have been bred into current soybean varieties, which researchers continue to refine. Consult with your seed advisor, who can help you choose a resistant variety that matches your needs.

BASF recently announced the Nemasphere nematode resistance trait, the result of a years-long partnership with Corteva Agriscience and M.S. Technologies. Nemasphere is the first and only biotechnology trait for SCN and is anticipated to hit the market in 2028, pending regulatory approval.  

Applying seed treatments

BASF Technical Field Representative Nick Tinsley says seed treatments are a good complement to other SCN management strategies:

“Because this pathogen is feeding below ground on that root system, a seed treatment is a nice approach to provide some extra protection. At BASF, we have ILEVO® seed treatment to help provide protection against soybean cyst nematode.”   

Find more information about Soybean Cyst Nematode at Grow Smart™ Live:

1. Game-Changing Soybean Cyst Nematode Trait to Combat Silent Yield Killer
2. Soybean Cyst Nematode: Part 1 - Behind the Headlines
3. Soybean Cyst Nematode: Part 2 - Management Options
4. Soybean Cyst Nematode (SCN): Part 3 - Tools against a Silent Robber
5. Take Action Against Soybean Yield Loss – Join SCN Action Month

Soybean sudden death syndrome

First found in Arkansas in the early 1970s, sudden death syndrome, or SDS, has since spread into most soybean-producing states in the U.S. and developed into one of the most destructive soybean diseases in North America.

The pathogen causing SDS is a soilborne fungus (Fusarium virguliforme) that rots the plant at its roots and mottles and burns the leaves, which eventually drop off. In recent years, the negative impact of SDS on U.S. soybean yields has been substantial, with nearly 19 million bushels lost in 2022.⁶

The fungus that causes SDS can live for several years in the soil or in corn or soy crop residue. The pathogen takes hold on soybean roots early — shortly after germination — and stays in place as the plant grows. In the soybean’s late vegetative or early reproductive stages, that infection in the root releases a toxin that compromises the root system and courses upward in the plant, where its toxic effects are easily seen on the leaves via yellow mottling between the veins, eventual leaf necrosis, leaf drop and aborted pods. 

What conditions help soybean sudden death syndrome thrive? 

SDS develops in compacted soil when the weather is cool and wet, and infection can occur within days of planting. Wet soil helps the fungus penetrate the root system more easily, and substantial rainfall in the early reproductive stages can lead to the development of the foliar symptoms. The severity of the infection can worsen if soybean cyst nematode (SCN) is present in the soil. SCN causes wounds on soybean roots that serve as entry points for fungal infections.

Identifying and scouting for soybean sudden death syndrome 

📸: Duane Rathmann/Featuring soybean leaves infected by sudden death syndrome (SDS).  

The foliar symptoms of SDS don’t typically show up until after flowering (R1–R2), often in late July or early August.

Signs to watch for in soybeans include: 

1. Yellow spots scattered on the leaf tissue between leaf veins. The spots will grow to larger brown blotches that may fall out, leaving large holes in the leaves. Eventually, dead leaves will fall from the plant, but petioles remain, attached to the stem.
2. Aborted pods (most commonly in stages R3–R5) 
3. Plants that can be easily pulled from the soil
4. Roots with a blue tinge (fungal growth)
5. Symptoms often appear first at field entry points where soil compaction is present.
6. The internal tissue of the main root will appear gray to reddish brown (in contrast to the white tissue of a healthy root). In SDS, the pith of the stem will remain white. If you see brown pith, even though the leaf symptoms may appear as described above, the problem may be brown stem rot, not SDS.

📸: Duane Rathmann/Featuring soybean roots with blue tinge fungal growth infected by sudden death syndrome (SDS)

Managing soybean sudden death syndrome 

Managing SDS and protecting yields requires an integrated approach, usually involving some combination of the following elements: 

Soil drainage improvements. Since SDS thrives in wet conditions, improving drainage on problem fields can help hinder the spread of infection. Minimizing soil compaction can also help.  

Choosing resistant seed varieties. Ask your seed retailer to recommend soybean varieties with at least some resistance to SDS. And since SDS can be worsened by SCN, the selected variety should also include resistance to SCN.  

Applying a seed treatment. BASF Seeds Agronomist David Pazdernik says:

“Since sudden death syndrome is a soilborne disease, foliar fungicides will not work. But you can use good seed treatments. ILEVO is a very good seed treatment that you can use for sudden death syndrome.” 

Timing. Pazdernik says the planting date can make a difference:

“The earlier you plant, the more likely you are to get sudden death. So, if you have severe sudden-death issues in certain fields, plant those last.” 

Find more information about Sudden Death Syndrome of Soybeans at Grow Smart™ Live: 

1. Sudden Death Syndrome in Soybeans: What to Know 
2. What Is Sudden Death Syndrome in Soybeans, and How Can I Manage It? 

📸: BASF internal photograph/Featuring a grower field checking soybean crops.

Soybean White mold

Soybean White mold was first discovered in central Illinois in 1948, and has since become an annual threat. Caused by the pathogen Sclerotinia sclerotiorum, soybean White mold is responsible for causing an estimated 29.9 million bushels of lost yield in 2023 alone.⁷ This was nearly triple the losses experienced in 2022.⁸ These figures point to soybean White mold’s unpredictability — under the right conditions, it can cause extensive damage to soybean fields. The pathogen is monocyclic, meaning it can infect crops only once each season, but it can survive for up to five years in the soil and has a large variety of hosts.

What conditions help soybean White mold thrive?

White mold in soybean prefers cooler temperatures, surviving and spreading best in temperatures between 60 and 70 F. Cooler temps combined with saturated soil provide ideal conditions for soybean White mold to thrive. Additionally, planting soybeans less than 30" apart can increase the risk of White mold.

Identifying and scouting for soybean White mold

White mold typically infects soybeans at the R1–R3 growth stages. It spreads upward from the stem base, coating the plant in telltale fuzzy white fungal growth and decimating the plant beneath. Upon reaching its mature stage, soybean White mold then forms new sclerotia, a blackened protective coating that contains the next wave of White mold infection. 

📸:Duane Rathmann/ Featuring an image of White mold stem infection symptoms

📸:Duane Rathmann/ Featuring an image of sclerotia in the stem due to White mold

Start scouting for soybean White mold before plants reach the R2 growth stage, so you have a chance to actually control the infection. If you’re already seeing obvious signs of White mold infection, such as wilting leaves at the top of the plant, you’ve likely passed the point where management strategies will be effective. Check your field for saturated soil and areas with particularly thick canopies, and look for water-stained lesions of the main stem. 

Managing soybean White mold

Controlling soybean White mold involves a mix of strategies, from applying foliar fungicide at the right time to considering factors such as row spacing and the field’s history with this pathogen. 

1. If your field has a history of White mold, consider rotating to a non-host crop like corn or a small grain for two to three years to reduce the presence of sclerotia in the soil. Don’t rotate to fellow host crops like canola, tomato, beans, potato, peas, sunflowers or cole crops. 
2. White mold also harbors in many broadleaf weeds, so controlling weeds with herbicides and other management practices can also control White mold.
3. The optimal time to apply foliar fungicide to treat soybean White mold is during the R2 growth stage. Research has shown that applying during this time maximizes your chances of protecting overall yield. Endura® fungicide from BASF is proven to control White mold, with a long-lasting residual effect.   
4. Avoid spreading White mold to uninfected fields by harvesting the infected field last.

Find more information about soybean White mold at Grow Smart™ Live: 

1. Soybean White Mold: Effective Strategies for Fungicide Application
2. White Mold Control with Endura® Fungicide

Frogeye leaf spot

A common threat to soybean yield each season, frogeye leaf spot (FLS) in soybeans was first found in the U.S. in 1924. The disease, caused by the fungal pathogen Cercospora sojina K. hara, has historically been a larger threat to soybean operations in southern states, but more recently has become an annual problem regardless of the region for most U.S. soybean growers.

What conditions help frogeye leaf spot thrive?

Frogeye leaf spot prefers hot and humid conditions, thriving when temperatures reach 75–85 F and it’s rainy. Wet leaves make the ideal hotbed for frogeye leaf spot infection. When temperatures rise above 77 F and the air is humid, Cercospora sojina K. hara starts producing spores and splashing onto the plant, increasing the risk of infection.

Identifying and scouting for frogeye leaf spot

As a foliar soybean disease, frogeye leaf spot primarily affects the leaves of soybean plants during the reproductive growth stages. Start scouting during R1, especially if the summer has been hot and humid, and scout at least a few plants every 10 acres to make sure you have a full picture of the presence and severity of disease in your fields.

While scouting, inspect leaves for eye-like lesions that have a gray center and a red, brown or purple border. You may see a black dot resembling a pupil in an eye at the center of each lesion.

📸: BASF employee, Albre Brown, Ph.D. Technical Marketing Manager, Soybean Fungicides and Insecticides/Featuring Frogeye leaf spot lesions on soybean plants that have started to darken to brown.

Managing frogeye leaf spot

Frogeye leaf spot management starts with carefully selecting the right seed. You can also manage and prevent infection through cultural practices and fungicide application. 

1. Seed selection: Talk with your BASF representative to determine which FLS-resistant seed varieties are right for your region and operation.
2. Crop rotation: To disrupt the FLS life cycle, consider rotating to a non-host crop such as corn, sorghum or small grains.
3. Fungicide application: If frogeye leaf spot is present in your crop, applying a fungicide such as Revytek® fungicide or Revylok® fungicide during the R2–R4 growth stages can safeguard against yield loss. 

Find more information about frogeye leaf spot at Grow Smart™ Live: 

1. Identifying and Managing Frogeye Leaf Spot in Soybeans

Soybean mosaic virus

Responsible for reducing seed quality and lowering oil content, soybean mosaic virus (SMV) is one of the most prevalent viral diseases in soybeans worldwide and can reduce yield from 8–35%, or more if working in concert with other viruses such as bean pod mottle virus.

What conditions help soybean mosaic virus thrive?

Soybean mosaic virus is most often introduced to a field through infected seed, though it can also be transmitted via aphids. Thus, the conditions that favor aphid reproduction — 72–77 F, relative humidity below 78% — can increase the likelihood of SMV infection. SMV symptoms are most noticeable in cool weather but symptoms can all but disappear as temperatures rise, making it difficult to get an accurate assessment of the infection.

Identifying and scouting for soybean mosaic virus

The effects of SMV on soybean can vary based on the seed variety, the strain of the virus, the plant’s growth stage, and the environmental conditions.

Most commonly you may see these SMV symptoms in the field: 

1. Stunted growth
2. Fewer pods
3. Light- and dark-green mosaic patterning on trifoliate leaves, which may become blistered over time
4. Leaf curling, wrinkling or distortion 

📸:@Craig Grau and the University of Wisconsin-Madison Teaching Images, bugwood.org/Featuring a soybean plant showing foliar symptoms of soybean mosaic virus.

Symptoms will appear more severe in younger plants and when temperatures are cooler. 

Managing soybean mosaic virus

While SMV cannot be controlled chemically, growers can adopt several strategies to manage the virus.

1. Plant SMV-free seed. One of the most effective ways to control soybean mosaic virus is to make sure you’re starting with virus-free seed. To plant with confidence, submit a seed sample to a plant pathology lab to have it tested for SMV.
2. Choose a disease-resistant soybean variety. Ask your seed retailer, a nearby extension office agent or a seed company professional like your regional BASF representative which soybean varieties provide the best SMV-resistant genetics. 
3. Control aphids. Thirty different aphid species are vectors for SMV. Controlling these populations can reduce the risk of soybean mosaic virus infection.

Find more information about soybean mosaic virus at Grow Smart™ Live: 

1. What Is Soybean Mosaic Virus?

Cercospora leaf blight and purple seed stain in soybean    

The seedborne disease Cercospora leaf blight (CLB) was responsible for 3.5 million soybean bushels of yield loss in 2023.⁹ CLB and its counterpart manifestation, purple seed stain, are both caused by the same soybean fungal disease, Cercospora kikuchii and Cercospora spp.¹⁰ 

What conditions help Cercospora leaf blight thrive?

The presence of infection in seed, plus environmental conditions that favor the disease or cause crop stress, can increase the severity of a Cercospora infection.

1. Infected seed: Purple seed stain indicates that seed is infected but doesn’t guarantee leaf blight.
2. Crop stress: Drought and heat stress can increase the severity of a Cercospora infection.
3. Presence of initial inoculum: Cercospora is more likely to cause problems if it has overwintered in infected crop residue or seed
4. Environmental conditions that favor the disease: Cercospora prefers high moisture from rain, dew or humidity and temperatures above 73 F.

Identifying and scouting for Cercospora leaf blight

CLB is most noticeable during R5–R6, when foliar symptoms are prominent. Look for these symptoms throughout the plant: 

1. Foliar symptoms: Upper leaves can take on a reddish-purple bronzing that resembles sunburn. 
2. Petiole and pod symptoms: Petioles and pods can develop black ovate lesions and lose leaves.
3. Defoliation: Plants with severe infection, in conditions highly favorable to disease development, can experience severe defoliation.

📸: BASF employee, Albre Brown, Ph.D. Technical Marketing Manager, Soybean Fungicides and Insecticides/Featuring an image of a soybean plant displaying foliar symptoms of Cercospora leaf blight.

Managing Cercospora leaf blight

Controlling CLB infection in your field starts with choosing high-quality seed. Healthy, uninfected seeds are round, smooth and creamy yellow, and have a better rate of germination and emergence than smaller, discolored seeds. Seeds affected by purple seed stain have reduced germination rates due to the fungi taking up residence in the seed and degrading the plant’s early-stage food supply.

If your field has a history of CLB infection, consider widening the space between rows, as narrow row spacing and high canopy density can increase moisture and humidity, conditions that are conducive to the growth and spread of CLB.

Finally, take a proactive approach by applying a preventive application of fungicide, such as Revylok® fungicide. 

Find more information about Cercospora leaf blight on Grow Smart™ Live: 

1. Cercospora Leaf Blight and Purple Seed Stain in Soybeans

Soybean seedling diseases 

Seedling diseases are caused by soilborne fungi and by fungus-like organisms called oomycetes. They typically overwinter in the soil and thrive in wet, poorly drained fields. They are a significant danger to newly planted crops but can also infect plants later in the season.

Each year, seedling diseases claim millions of bushels in soybean yield. 

Following are brief introductions to four significant seedling disease threats to soybeans: Fusarium root rot, Pythium disease, Rhizoctonia root rot and Phytophthora root and stem rot.

Fusarium root rot in soybeans

While hundreds of species of Fusarium exist, the two species most commonly linked to Fusarium root rot in soybeans are Fusarium solani and Fusarium oxysporum. As with other seedling diseases discussed here, the effects of early infection with Fusarium root rot can include: 

1. Damping-off (both pre- and post-emergence) 
2. Poor and/or late emergence 
3. Weak stands 
4. Stunted growth  

📸: BASF employee/Featuring untreated soybean crops with Fusarium root rot (Left) and healthy roots (Right) treated with Relenya® fungicidal seed treatment.

Fusarium spp. thrive in cool temperatures and wet soil. Management tactics include crop rotation and fungicide seed treatments that include Obvius Plus® fungicide seed treatment and Relenya® seed treatment.

Talk to your seed advisor for more advice about managing Fusarium root rot.

Soybean Pythium seedling blight 

Pythium usually begins its assault just a few weeks after planting, particularly if it’s been planted in very wet, poorly drained fields. Like other seedling diseases, it causes damping-off and can lead to substantial stand reductions. The Pythium pathogen can live underground for years and springs into action when temperatures and moisture are optimal.

📸: BASF employee/Featuring a closeup shot of a soybean crop with Pythium seedling blight.

Your chances against Pythium disease can be improved with good drainage, good seed, and a good fungicide. Talk to your seed advisor about Obvius Plus® fungicide seed treatment, which offers protection against Pythium infection.

Find more information about Pythium infections on Grow Smart™ Live: 

1. Pythium Prevention in Corn and Soy

Rhizoctonia root rot in soybeans 

Rhizoctonia root rot, caused by Rhizoctonia solani, is one of the most common soybean diseases in the U.S. It can cause damping-off, both pre- and post-emergence. As with other seedling disease pathogens, Rhizoctonia solani can survive for years in fields. It thrives during wet, cool springs that are followed by dry, hot days.

📸: BASF internal photograph/Featuring Rhizoctonia root rot in soybeans.

Managing Rhizoctonia root rot involves using sound cultural practices and making good choices in seed variety and fungicide seed treatments. Talk to your seed advisor about Obvius Plus® fungicide seed treatment and Relenya® seed treatment, both of which can help protect against Rhizoctonia.

Phytophthora root and stem rot of soybeans

Phytophthora root and stem rot can infect soybean plants throughout the growing season, causing a variety of symptoms, including yellowing leaves, seed and root rot and eventual death. The spores that cause the disease can overwinter in crop residue and live for years in the soil. Like other root-rot diseases, Phytophthora prefers wet conditions and poorly drained fields.

📸: BASF employee/Featuring Phytophthora stem rot in a soybean field.  

Dealing successfully with Phytophthora root and stem rot can involve making careful seed choices, applying fungicide seed treatments, and using sound cultural practices such as improving drainage.

Talk to your seed advisor about BASF’s Obvius Plus® fungicide seed treatment to learn how it can help protect against Phytophthora. 

📸: BASF internal photograph/Featuring a soybean grower field checking crops for common disease threats to soybeans.

Revylok is a trademark of BASF. Revytek, Endura, ILEVO, Obvius Plus and Relenya are registered trademarks of BASF.

________________________________________________

Endnotes

1. Crop Protection Network, “Soybean Disease Loss Estimates from the United States and Ontario, Canada — 2023.” March 14, 2024. https://cropprotectionnetwork.org/publications/soybean-disease-loss-estimates-from-the-united-states-and-ontario-canada-2023
2. Bradley, C. A., Allen, T. W., Sisson, A. J., Bergstrom, G. C., Bissonnette, K. M., Bond, J., ... & Wise, K. A. (2021). Soybean yield loss estimates due to diseases in the United States and Ontario, Canada, from 2015 to 2019. Plant Health Progress, 22(4), 483-495.
3. Bandara, A. Y., Weerasooriya, D. K., Bradley, C. A., Allen, T. W., & Esker, P. D. (2020). Dissecting the economic impact of soybean diseases in the United States over two decades. PloS one, 15(4), e0231141.
4. Crop Protection Network, “Soybean Disease Loss Estimates From the United States and Ontario, Canada — 2021." April 12, 2022. https://cropprotectionnetwork.org/publications/soybean-disease-loss-estimates-from-the-united-states-and-ontario-canada-2021
5. Crop Protection Network. “Soybean Disease Loss Estimates From the United States and Ontario, Canada — 2022." April 19, 2023. https://cropprotectionnetwork.org/publications/soybean-disease-loss-estimates-from-the-united-states-and-ontario-canada-2022
6. Crop Protection Network, “Soybean Disease Loss Estimates From the United States and Ontario, Canada — 2021.” 
7. Bradley, et al. “Soybean yield loss estimates due to diseases…”
8. Crop Protection Network. “Soybean Disease Loss Estimates From the United States and Ontario, Canada — 2022.”
9. Bradley, et al. “Soybean yield loss estimates due to diseases…”
10. Albu, S., et al (2016). Cercospora cf. flagellaris and Cercospora cf. sigesbeckiae Are Associated with Cercospora Leaf Blight and Purple Seed Stain on Soybean in North America. Phytopathology, 106(11), 1376-1385.