URBANA, Ill. (U.S.A.) — Few pests eat away at farm profitability as much as soybean cyst nematode (SCN). Causing at least $1.5 billion in yield losses annually, it’s soybean’s single biggest threat. Unfortunately, soybean’s most effective tool, genetic resistance, is starting to fail.
That’s why a multi-institution research team led by the University of Illinois Urbana-Champaign — with sustained funding from the North Central Soybean Research Program and the Illinois Soybean Association — has developed the first pangenome for SCN.
“The SCN pangenome allows us to do population genetic analysis of nematodes to understand how they’re overcoming resistance,” said senior study author Matt Hudson, professor in the Department of Crop Sciences, part of the College of Agricultural, Consumer and Environmental Sciences at Illinois.
Hudson added that the pangenome could also help develop technology to easily test which soybean resistance type to plant in a given area, and may one day help design new tools to eliminate the most virulent SCN types before they cause damage.
But first, exactly what is a pangenome?
“It’s a modern approach scientists use to catalog the genetic diversity of a species. For decades, the standard practice was to choose a single individual and treat it as the reference. Imagine choosing a single person to represent all of the genetic diversity of the human species; that’d be impossible,” said Lucas Borges dos Santos, doctoral student in the Informatics Program at Illinois.
Hudson and his colleagues are leading a related soybean pangenome project, representing over 400 individual plants and resulting in multiple publications describing the crop’s genomic diversity. But pulling together an SCN pangenome — or even a high-quality genome from a single SCN individual — was a tougher nut to crack.
“One problem with SCN is that they’re either living in soybean roots, swimming around in the soil, or they’re eggs. It’s hard to extract DNA from adults, so we typically try eggs,” Hudson said. “But with their hard exterior, they’re like little cans of beans in the soil. That lets them survive for decades, but makes it really hard to extract DNA.”
In the past, researchers had to freeze-dry and then pound the eggs into powder, but that extreme mechanical force broke the DNA into fragments too tiny to use for high-quality genome assembly. Several years ago, co-author Kim Walden* of the Roy J. Carver Biotechnology Center at Illinois concocted a mix of enzymes to gently dissolve the shells while keeping the DNA intact, the literal breakthrough that made the pangenome possible.
The classic test of SCN virulence, the HG Type test, involves infecting seven soybean varieties with nematodes and measuring how well they reproduce. If SCN can develop females on soybean types 2, 5, and 7, its HG Type is 2.5.7. To develop a comprehensive pangenome, Borges dos Santos assembled and combined genomes from nine SCN populations, each comprising several thousand individuals and representing the full gamut of HG Types.
The key finding from the SCN pangenome is its sheer diversity.
“If you looked at the differences in DNA between humans and chimps, some of these worms would be humans and some of them would be chimps,” Hudson said. “The HG Types are very different from each other, and a lot of the genes are specific to each population. They're very, very diverse.”
This diversity is what makes it hard to pin down durable resistance in soybean. When an SCN population meets a resistant soybean, early generations may suffer, but later generations can mine their extensive genome to deploy virulence genes that still work. But all is not lost for soybeans. Borges dos Santos says the pangenome enables a deeper understanding of SCN virulence genes and proteins, setting the stage for potential control mechanisms.
“We're looking at ways to alter the nematode populations themselves,” Hudson said. “For malaria mosquitoes, scientists can engineer and release male-sterile mosquitoes that reduce reproduction and spread of the disease. We have an Illinois Soybean Association grant along similar lines for SCN.”
Although the pangenome won’t translate into changes on the farm just yet, the advancement is welcome news for soybean commodity groups.
“Soybean cyst nematode remains the most damaging soybean pest in the U.S., costing farmers more than a billion dollars every year. This new pangenome finally gives researchers and breeders a full picture of SCN's genetic diversity and adaptability that can deliver the deeper understanding we need to stay ahead of this pest,” said Stephanie Porter, outreach agronomist at the Illinois Soybean Association. “This research strengthens the foundation for developing more durable resistance and aligns directly with ISA’s commitment to protecting Illinois soybean yields."
The study, “Pangenome analysis of nine Soybean Cyst Nematode genomes reveals hidden variation contributing to diversity and adaptation,” is published in BMC Genomics [DOI: 10.1186/s12864-025-12493-x]. *Study co-author Kim Walden passed away in 2024.
Hudson is also affiliated with the Department of Bioengineering in the Grainger College of Engineering, the Center for Advanced Bioenergy and Bioproducts Innovation, the Center for Digital Agriculture, the National Center for Supercomputing Applications, and the Carl R. Woese Institute for Genomic Biology at U. of I.
Research in the College of ACES is made possible in part by Hatch funding from USDA’s National Institute of Food and Agriculture. This study was also supported by the North Central Soybean Research Program and the Illinois Soybean Association. Hudson's work with SCN is also supported by the United Soybean Board.