New Advancements in the Nematode War

By Mace Thornton

The insidious Soybean Cyst Nematode (SCN) lurks beneath the soil across the state of Illinois and in many other U.S. soybean-growing states. Microscopic in size, SCN populations hide like stealthy predators, silently sucking the productivity out of a soybean plant’s roots, laying eggs that form cysts that then hatch into juvenile nematodes. If left unchecked, it’s a destructive cycle of infection that leads to yield loss. Even when a massive infestation invades a field, the pathogen can go undetected until it’s too late to ward off the havoc of its destructive appetite for soybean roots.

The Illinois Soybean Association (ISA) Soybean Production Team is working in conjunction with numerous researchers on several projects aimed at keeping the SCN scourge at bay. Dr. Nathan Schroeder is one of the many crop scientists collaborating with ISA. An Associate Professor of Crop Science and Director of Graduate Programs at the University of Illinois (U of I) of Agricultural, Consumer and Environmental Sciences, Schroeder leads an ongoing effort to team up ISA and Illinois soybean farmers to gather field samples for SCN evaluation.

Through the free-to-farmers SCN testing initiative, farmers can email researchers at freeSCNtesting@illinois.edu to receive a free sampling kit, complete with instructions and return postage. Samples are collected six inches below the soil line. A gallon ziptop bag is filled halfway with soil collected from various parts of the field. Samples should be kept cool, ideally in a refrigerator, double-bagged and shipped early in the week with an ice pack to the U of I Extension Plant Clinic.

"We provide farmers with all the necessary information they need to send in samples, and we even throw in free shipping labels," Schroeder explains. "It's about arming our farmers with the tools they need to tackle SCN head-on.”

At the clinic, the samples are evaluated for infestations. Eggs are counted, and the farmer is advised whether to consider treatment.

“With that sort of assessment, we can tell the farmer the likelihood of expected loss. Illinois farmers have heard about SCN for decades now. It’s easy for it to fall off the radar, but SCN remains the No. 1 source of yield loss for soybean growers in the U.S.,” Schroeder said. “But with the right knowledge and resources, we can turn the tide in our favor."

SCN remains a stealthy opponent, though. The pest is developing resistance to evade the most common genetic control method that has been bred into the plants. “The vast majority of soybean varieties Illinois, as well as throughout the Midwest, get their resistance to SCN basically from one genetic source – PI88788 – so over the decades, SCN has started to adapt, as is nature’s way,” Schroeder says.

To further study this situation, researchers who discover SCN eggs in relatively high numbers in their samples subject those samples to an additional greenhouse test to assess their resistance level. It’s all part of the effort to unravel the genetic puzzle that allows the pervasive pest to persevere. In doing so, researchers can advise farmers to consider planting varieties with other resistance code.

“The SCN populations present now are different than five or 10 years ago,” Schroeder says. “We have to keep an eye on the shifts in the populations.”

The testing program has been welcomed by farmers, with samples coming in from more than half of Illinois counties. But gaps remain, according to Schroeder. "We have a fairly decent gap in southern Illinois, especially the counties bordering the Ohio, and we also have a gap right on the Wisconsin border, where we haven’t received many samples at all,” Schroeder says. “Filling those gaps would be useful. Every sample we receive helps us gain a clearer understanding of the nematode's behavior and empowers farmers to make informed decisions. It feels like we're making a real difference. Every sample, every test—it's a step forward, and it’s useful for the grower.”

Meanwhile, Dr. Matthew Hudson and Dr. Andrew Scaboo, who were featured in an ISA Agronomy Webinar on March 14, are both using advanced genomic tools to find new soybean defenses against SCN.

Hudson, Professor of Crop Science at the U of I, is using the power of supercomputing and digital technology and genomic and molecular biology in his checkoff-funded research to thwart SCN. He says the pest, “loses a lot of money for a lot of people.”

“We don’t have good chemical controls,” he says. “We’re reliant on resistant soybeans, but they don’t always work for everyone, and they seem to be getting a little less effective.”

He says artificial intelligence is one of the tools researchers are using to greater effect. In the crop science world, an effort has been funded by USDA to develop an AI tool, the Crop Wizard, that only uses trusted data originating from state Cooperative Extension programs. Although the tool is still under development, farmers who want to check out this resource can visit the website at https:// www.uiuc.chat/cropwizard/chat.

“It will answer questions, for example, about SCN, and it will give you references that link you out to the original Extension publications,” Hudson says. “You don’t have to trust what it tells you, but you can go straight to the source and figure out where it came from. It’ll format this information in a nice way and give you a narrative around it.”

Humans such as Dr. Hudson still have to do all the hard work to feed scientific results into the system. Right now, he’s focused on the genetic code of SCN.

“What we're trying to do with soybean cyst nematode is create what we call a pan-genome,” he explains. “That's a picture not of one nematode or not of a mixture of nematodes, but a picture of all of the variations, all of the genes within soybean cyst nematode. It turns out that this is a bigger undertaking than we thought it would be when we started, but there are still some clues coming out of this analysis that allow us to narrow this down.”

Hudson says Dr. Melissa Mitchum, Professor of Plant Nematology at the University of Georgia, has grown isolated nematode types to see how they respond on different types of soybeans.

“One of the things that she in particular found is that you can put almost any nematodes on almost any soybean, and if you give them long enough, they will come to be virulent on that soybean even if they're not virulent to begin with,” he says. “After a few generations, you are going to end up with a lot more nematodes than you started with.”

To combat the constantly moving target presented by SCN, new testing has been developed that allows researchers to sequence a whole genome from a single worm. When offspring from that genome are introduced to two different types of resistant soybeans, each of the identical SCN types eventually develops a specific resistance to the type of resistant soybean that served as its host.

“So you think about how much diversity there is in these nematodes here, and then expand that to a field, even a single field, you're talking about a whole lot of nematodes, most of which are different from each other, and which are constantly creating new opportunities to parasitize resistant soybeans,” he says.

“There are differences all the way through the genome, even between supposedly inbred populations growing in a pot. That's very different from what we see in soybeans, which are a little limited in diversity. That makes the nematode very, very powerful in the amount of different genotypes that it's able to bring to bear in overcoming resistance.”

Soybean breeders originally used genetic information to produce consistently SCN-resistant soybeans, but now that the resulting PI88788 soybean type is common, SCN is developing virulence to even that type. So, to boost soybean resistance to SCN in an enduring manner, researchers are studying the soybean genome through its own USDA-funded pan-genome project in hopes of producing hundreds of different soybean lines resistant to the quickly evolving SCN menace.

“Hopefully, that’s going to allow us to narrow down both the location and the function of more and more resistance genes that we can incorporate into the (soybean) population,” Hudson says.

The University of Missouri’s Dr. Scaboo says one of the reasons SCN is so good at adapting is its lifecycle is less than 30 days. “You can have multiple life cycles throughout a growing season,” Scaboo explains. “And as our winters are warmer and as farmers are planting earlier and earlier, this can become much more of an issue with the number of actual life cycles that nematodes go through in a growing season.”

It’s best to manage SCN in a few different ways, but crop rotation is one of the most effective management strategies, he says. Seed treatments and resistant cultivars can also be used, but each one has an issue. The problem is that the resistant cultivar has been overused and is starting to break down. This “underscores the pressing need for updated strategies to combat SCN infestation effectively.”

“Farmers and stakeholders must prioritize research and development of novel resistance mechanisms to counter the evolving threat posed by virulent strains of SCN,” Scaboo says. “Additionally, collaborative efforts between researchers, breeders and agricultural Extension services are essential to disseminate updated information and implement effective management practices across soybean-growing regions. By staying proactive and adaptive in our approach to nematode management, we can safeguard soybean yields and ensure the sustainability of this crucial agricultural crop.”

Furthermore, Scaboo emphasizes the importance of ongoing monitoring and surveillance, such as the ISA-supported SCN testing initiative at the U of I.

“This data is crucial for guiding breeding programs and developing resistant cultivars tailored to specific regional challenges,” he says. “The challenges posed by soybean cyst nematode require a multifaceted approach that integrates scientific research, breeding advancements, proactive monitoring and farmer education. By leveraging these strategies collaboratively, we can enhance resilience against nematode infestation and safeguard the productivity and profitability of soybean farming operations for years to come.”

Dr. Hudson equates the situation to the famous “Red Queen” narrative from “Alice in Wonderland.”

“The Red Queen, who's like a card with arms and legs, says you have to keep running just to stand still,” he says. “So the battle probably cannot be won, in the sense that we will not exterminate soybean cyst nematodes. They're not going to go away. They're here forever. If we keep running, which in this case means we keep developing new soybean varieties with new resistance sources, new genetics, and we keep improving our agronomy practices in terms of rotation and adding things like seed treatments where they help, then we might be able to stand still. We may be able to keep SCN at the level of problem it is, but we have to keep running.”