Erika Arnao, Ph.D., Ahmad Fakhoury, Ph.D., and Amanda Warner [center] at SIUC pre-screen fungal isolates in preparation for identification.
Erika Arnao, Ph.D., Ahmad Fakhoury, Ph.D., and Amanda Warner [center] at SIUC pre-screen fungal isolates in preparation for identification.

Growers and sales agronomists have recognized root rot and damping-off in seedling soybeans that even had a fungicide seed treatment. Is it caused by Pythium, Phytophthora, Fusarium, Rhizoctonia or combination of them? If so, which strains? Or is it something else entirely? Helping to answer those questions and more is the focus of the grower funded “Identification and Biology of Seedling Pathogens” research study.

“We have 14 investigators from 12 states working on the project,” said Jason Bond, associate professor, soybean pathology/nematology, Southern Illinois University. Bond is a participant as well as the coordinator for the project. “Some of the investigators are more Extension oriented, while others are more lab oriented, and some have overlapping duties.”

After decades of cutbacks in state and federal funding for basic research, growers have stepped up to the plate as never before, and the time has never been better. Recent additions to traditional analytical tools, such as molecular probing, expanding genomic databases and computerized search capabilities of those databases, make sample identification and classification faster and more complete than ever before. Taking advantage of classical research efforts and the new advances is the goal of the pathogen study. Funding is from the United Soybean Board and the North Central Soybean Research Program (NCSRP).

NCSRP is a coordinated research effort by state soybean checkoff organizations in Illinois, Indiana, Iowa, Kansas, Michigan, Minnesota, Missouri, Nebraska, North Dakota, Ohio, South Dakota and Wisconsin.

The goals are straightforward:

• Identify fungi responsible for causing seedling blights of soybeans

• Develop high throughput diagnostic tools for identifying fungal seeding pathogens

• Characterize the biology of seedling pathogens and develop assays for inoculation

• Identify the impact of environmental conditions on seedling pathogens.



The breadth of the effort and the rapid development in analytical tools in recent years are multiplying its potential impact. Examining seedling pathogens in their native environment means sampling can only take place once a year—at the seedling stage. The pathology project involves researchers across the 12 states who gather samples and submit them to researchers at Southern Illinois University and Michigan State University. There, isolates are evaluated under microscope as well as through molecular probing. Those samples are then compared via computer searches with known genetic databases, derived from domestic and international fungal collections.

“Using bioinformatics, the computer can match the identified sequence from the sample with an organism in the database,” explained Bond. “While not everything is in the database, we can find out a lot of what is going on in the soil that has been sampled.”

Although some of the tools being used, like genetic sequencing, have been available, they were limited and expensive. “If you would have said three or four years ago that you wanted to sequence everything found around these plants, you would have been laughed out of the room,” said Bond.

The tools themselves have expanded the horizons and accuracy of the evaluative process. Classical techniques like microscopic analysis required growing an isolate in a pure culture. That limited the technique to those organisms that can be cultured in the laboratory. Molecular probing is not limited that way.

Once sampled, examined and identified, the next step is to develop marker probes that will aid in rapid diagnostics in the lab, if not yet in the field itself. These probes could speed up and expand the results from a process that currently can take weeks.

“When you get a disease in the field, you don’t want to wait around,” noted Bond.



Knowing what is actually in the seedling complex of pathogens and other organisms found with them opens the door to refine appropriate disease management scenarios.

This involves identifying baseline sensitivity of the organism to seed treatments, a process that will identify those most effective to given pathogens and more.

“As we collect cultures and isolates, we can compare them to the isolates that have not been exposed to seed treatments. These samples exist in collections like those at Iowa State, the University of Illinois and the University of Minnesota,” said Bond. “Over time, we can evaluate if given Rhizoctonia or Fusarium isolates are becoming less sensitive or developing resistance to certain seed treatments.”

Another aspect being addressed is the impact of crop rotations on Pythium and Fusarium. “We do know that the simple fact of planting a crop can affect the biological life in the soil,” noted Bond. “While we don’t have a focus on cover crops as part of the study, we know they can have an impact from other research done.”

As an example, Bond cited a field trial with rapeseed and canola at Southern Illinois University. When those crops were turned under in the spring, less sudden death syndrome (SDS) was recorded in the soybean crop. “The SDS pathogen isn’t the most aggressive at causing seedling death in our area, not like Pythium or Rhizoctonia,” he said. “However, we were amazed at the impact these cover crops had.”


Bond suspects that with the increased interest and incidence of cover crops and the analytical technologies now available, such interactions will be better understood.

“We may get to the point where we will be able to identify fields based on pathogens and risk factors and whether fields will be at risk based on environmental factors,” said Bond.

“If there is a high risk factor, perhaps crop rotation or cover crops could be recommended. If we know that an area has a particular mix of pathogens, seed companies may be able to prescribe particular seed treatments. This study will help identify where there is severe disease pressure and those seed treatments with the greatest payback.”

Looking ahead, the study may have even greater benefit as a research base and data bank. As state, federal and grower funding is made available, other seed and soil researchers will be able to utilize these findings to better identify areas needing study and better focus those dollars.

With all the discussion of the need to feed an ever-growing population, the time to support such efforts has never been better.

“We have the technologies and the techniques, and these research efforts are addressing needs important to society,” said Bond.