Novel discovery could fortify soybean cyst nematode resistance

Researchers have discovered a new and unexpected way to prevent soybean cyst nematode (SCN) from attacking soybeans. The loss of function of the GmSNAP02 gene in resistant soybean varieties like PI 90763 and PI 437654 thwarts SCN’s ability to attack the soybean plant.

″Think of it like a lock-and-key model, where SCN is the key and GmSNAP02 is the lock,″ explains Melissa Mitchum, professor in the College of Agricultural & Environmental Sciences at the University of Georgia and a member of the research team that made the discovery. ″If you get rid of that lock, the nematode can’t access the plant. You make the parasite ineffective.″

The SCN Coalition is excited about the discovery and encourages farmers and industry stakeholders to continue to advocate for new tools like this.

Adding to Peking’s defenses

Nematodes that can reproduce on Peking genetic resistance appear to be exploiting GmSNAP02. ″We think PI 90763 resistance works by losing this GmSNAP02 protein, circumventing the nematodes and making the plant more resistant,″ Mitchum explains.

″This gene could have a relatively immediate impact for farmers,″ she continues. ″It will help bring down SCN populations for farmers who have planted PI 88788 repeatedly and have high and aggressive SCN populations.″

After decades of heavy and near exclusive use of PI 88788 genetic resistance, SCN has developed resistance to what had been a powerful means of control. Consequently, there’s an urgency for alternative modes of resistance to be rotated with PI 88788 to control populations. One such alternative farmers are increasingly using is Peking-based resistance, a three-gene model. 

″Those three genes are what farmers need today to battle nematodes,″ says Andrew Scaboo, assistant professor in the Division of Plant Science and Technology at the University of Missouri who spearheaded the project with Mitchum. But if farmers use Peking exclusively, he warns nematodes will develop resistance.

Nematode development on Peking, PI 90763 and PI 437654 soybean lines at five days post-inoculation (dpi). A good copy of the SNAP02 gene is present in the Peking line. White arrowheads denote swollen parasitic juvenile nematodes in Peking, indicative of successful feeding site establishment and development. A bad copy of the SNAP02 gene in PI 90763 and PI 437654 prevents these nematodes from feeding and reproducing.

″This is where this fourth gene comes into play. Adding a nonfunctioning copy of GmSNAP02 enhances the nematode resistance of Peking,″ Scaboo says. ″If we can come up with a strategy now for using this and other genes in rotation, we could avoid a repeat of the situation we now have with PI 88788.″

A quadruple stack would enhance the genetic diversity on the market, which is critical to long-term management of SCN. ″As we bring different modes of action into the rotation, we enhance the durability of all the tools in our toolbox,″ Mitchum explains.

Next steps

Scaboo is a year into a roughly three-year process developing the plant material needed to test whether the GmSNAP02 omission impacts yield. That question must be answered before the new resistance tool can be moved toward commercialization.

Meanwhile, interest from private breeders is already high. ″Nearly every major company and some of the smaller ones have reached out and set up meetings since the report on the discovery was published,″ Scaboo says. ″That signals they know SCN is a big problem for farmers.″

Private breeders account for over 90% of U.S. soybean varieties on the market today. Their buy-in is critical to getting this new tool in farmers’ hands. Whether they commit will hinge on how much they prioritize the quadruple stack and whether it fits their return-on-investment strategy.

Scaboo is optimistic. The fact CRISPR gene editing can be used to ″knock out″ GmSNAP02 is an advantage – especially for breeders working with a Peking background. He explains, ″CRISPR technology facilitates and speeds along the breeding process for forging this stack.″

Scaboo’s optimism is also grounded in the fact that companies are invested in the longevity of their soybean varieties. ″One way to give products longevity is with better control of pathogens,″ Scaboo says. ″With GmSNAP02, the private sector can pursue prescriptive management strategies for pathogens like SCN. The resistance this gene provides has the potential not only to protect soybeans and raise yield, but also to manage SCN long term.

Discovery paves the way for more progress

The knowledge gained with this discovery is of equal, if not more, importance. ″The fact you could knock out a gene in a resistant background and gain more resistance was unexpected,″ Mitchum says.

″Looking ahead, we want to understand how the nematode may be targeting SNAP02,″ Mitchum says. ″Hopefully, that understanding will give insight into how we can further enhance durability of the tools in our toolbox and add to it.″

Advances in technology are also shifting the conversation on SCN management. ″We are starting to understand the genetic architecture on a level that the resistance source is becoming irrelevant,″ Scaboo says. ″It would be great for seed companies, farmers and the industry to start talking about these resistance genes rather than sources like Peking or PI 88788.″

The value of public/private collaboration

The GmSNAP02 project started with a plant breeder (Scaboo) and a nematologist (Mitchum) who set out to map the genetic architecture of known sources of SCN resistance. Four years of interdisciplinary research involved professors, research staff and students. It was funded by farmer-supplied checkoff dollars by way of the Missouri Soybean Merchandising Council, the North Central Soybean Research Program and the United Soybean Board. The National Science Foundation–National Institute of Food and Agriculture provided additional grant funding. The next steps – getting this new mode of resistance to farmers – will require investment from the private sector and an all-hands-on-deck approach to drum up awareness.

″All those people, industries and perspectives are what made this happen,″ Scaboo says. ″That public/private collaboration is so important when it comes to delivering new tools like GmSNAP02 that better equip farmers to manage SCN.″