Two different type of soybeans

(Photo: Crop Protection Network/Kristina Petrovic)

Big problems in little pathogens

February 5, 2024

By Carol Brown, Soybean Research & Information Network

Researchers continue to explore ways to improve the quality of soybeans through better genetics and management practices. One aspect of improvement is finding how to stave off diseases and pests that reduce soybean growth and can cause plant death.

Through projects funded by the North Central Soybean Research Program and the United Soybean Board, a team of researchers is looking at improving soybean disease management. One of the diseases they are studying is the Diaporthe/Phomopsis complex that leads to stem canker, or stem blight, and seed decay.

Febina Mathew, a crop pathologist at North Dakota State University, is working with Daren Mueller at Iowa State University and several other colleagues on combating Diaporthe diseases.

“One of the projects is identifying if Diaporthe isolates are sensitive to fungicides currently labeled for soybeans,” Mathew says. “Another project explores the impact of new fungicide chemistries and their efficacy against Diaporthe with different maturity groups, plant populations, application timing and more. A third project is looking at soybean seed quality after a delayed harvest, up to a month after soybeans typically should have been harvested.”

Diaporthe/Phomopsis 101

For many years, Phomopsi has been the name used to describe the pathogen that leads to soybean seed decay and stem canker. Scientists have studied Diaporthe/Phomopsis since the 1940s and discovered it is a complex of fungi, rather than just one fungus. The complex can cause multiple diseases, which are named accordingly based on where it infects the plant. If it infects the soybean stem, it is called stem canker or stem blight. Logically, seed decay infects soybean seeds.

Mathew says the fungus has an asexual stage, referred to as Phomopsis, and a sexual stage with the genus classification Diaporthe. In 2012, a scientific publication stated that Diaporthe would be used for this group of fungi going forward, but farmers, researchers and even taxonomists tend to use the names interchangeably.

Studying the complex

“We have already identified that Diaporthe/Phomopsis pathogens are capable of infecting any part of the plant,” Mathew says. “So far, my research team and I have identified 12 organisms that are part of the Diaporthe complex, and we continue to search for more,” she says.

These discoveries can help scientists who are looking to improve fungicide effectiveness in soybeans.

“Usually, a broad-spectrum fungicide is used to combat the pathogens and we assume it is broad enough to control any species belonging to the same genus or family,” Mathew explains. “But genes that confer resistance to one fungus may not work for another. Breeders stack genes that have resistance to several different fungi to ensure that soybean varieties will have broad disease resistance. Identifying these exact organisms will only help them develop varieties that have effective resistance against them.”

Part of the research compares the pathogens between geographical areas, as the team found a wide diversity of Diaporthe species infecting soybean plants. She says there is more diversity in the southern United States than in the north.

“We want to know why this diversity is occurring and what factors affect the prevalence of Diaporthe species,” Mathew says. “We want to conduct more surveys to identify if it’s a coincidence or if other factors, such as weeds, should be considered. Weeds are a great reservoir for Diaporthe and sometimes we find a lot of different species on the same weed. In North Dakota, we found a sunflower pathogen in soybeans and vice versa. We are studying to understand how this happens.”

Mueller is partnering with Mathew to monitor how Diaporthe moves between crops. Mueller built spore traps that capture airborne fungi and placed them in soybean research plots in several states. They are looking for multiple pathogens including Cercospora, which causes leaf blight, and Diaporthe species to identify which ones are present in and around fields in Iowa and North Dakota. They collect the fungi from traps weekly while soybeans are in the reproductive stages to identify microscopically what the traps have captured.

“While we understand a lot about Diaporthe fungi, we still have much to learn, including how different species of Diaporthe move across and within fields,” Mueller says. “Different fungi use different tactics to come in contact with the host plant and our research is looking at airborne fungi Diaporthe.”

Mueller and Mathew are also studying the effect of delayed soybean harvest on seed decay. If soybeans can’t be harvested when they are ready because of issues like rain or snow, the added moisture creates the opportunity for the fungus to develop and infect the seeds. The team is monitoring when seed decay symptoms and fungi develop beyond typical harvest times.

“We know timely harvest can reduce seed decay caused by Diaporthe, but with the weather uncertainties we have experienced over the past several decades, we want to understand how much delayed harvest can affect seed quality,” Mueller says.


Mathew continues to make strides in the Diaporthe research arena. Her team has published standardized inoculation methods in addition to identifying the individual species in the Diaporthe complex. She and her team also developed tools to screen soybean lines for resistance to the Diaporthe species and have breeders reaching out to her lab for information about screening new lines. Furthermore, her program has identified sources of resistance to these fungi that breeders can use for developing resistant commercial cultivars.

“There is much interest in this topic. In the last five months, I’ve given at least six presentations to industry and farmers to show how to diagnose the disease and what they can do to reduce its severity,” Mathew says. “There really are no in-season options at this point and we recommend crop rotation with non-hosts, such as small grains, and weed management.”

For more information on this project, go to