Genetic Test Designed to Target Soybeans’ Silent Killer Soybean Cyst Nematode

In humans, high blood pressure is often called the silent killer. 

Its visible signs are not apparent until it’s too late. And likewise for soybeans – they have their own silent killer, the soybean cyst nematode (SCN). Growers think they’re protected from damage from this parasite because they plant SCN-resistant varieties, and see no apparent signs of a problem…until they realize their yields are only average, in years when they should be superior. 

“Producers think that because a variety is labelled resistant they’ve solved their problems,” says Prof. Terry Niblack, chair of the Department of Plant Pathology at The Ohio State University. “But that’s not true.”

Niblack and colleague Prof. Kris Lambert of the University of Illinois are leading a research consortium taking a genetic approach to halting the SCN’s march forward. Specifically, they’re creating a genetic map of SCN to help produce crucial management information, such as a field’s level and type of SCN infestation. The genetic map is a vital first step in the researchers’ drive towards a new, rapid genetic test – one that would take just a few hours to produce results, unlike the current costly and time-consuming lab test – that would tell them which kind of nematodes are present in a soybean field. 

Once the specific types of nematodes are identified, producers can choose the appropriate control methods. 

“Farmers need to have choices,” says Lambert. “Nematodes can be managed using natural host plant resistance and crop rotation. There’s a clear management strategy that works if you plant the right plants. The test we want to develop will help determine what nematodes are present so the right management plans can be developed for individual on-farm situations. It will help us deploy and preserve valuable soybean germplasm that is resistant to SCN.” 

SCN is an insidious pest. It gives other diseases an opportunity to take hold, making the likes of sudden death syndrome and brown stem rot worse. Eggs can persist in soil for six years. 

When the same source of resistance is used repeatedly, low-level reproduction on SCN-resistant roots leads to the buildup or selection of populations of SCN, with an increased ability to reproduce on the resistant varieties. The soybean resistance genes are present, but they’re overcome when SCN populations develop tolerance.

Virulence is central to their mission. Virulence is the ability of SCN to grow on a plant that is normally considered resistant or at least able to fight SCN. Some varieties are simply more resistant than others, says Lambert. 

But how do farmers choose which varieties to plant? That’s where the proposed rapid genetic test comes in. By understanding the gene sequence of the broad nematode family, and then analyzing and comparing them through a quick lab test, the researchers could determine which kind of infestation a particular field was laden with. Then, producers could make informed management decisions for control – it makes sense to choose a variety for which the specific nematode infestation is not resistant.

All this sounds logical, but the pursuit of genetic information is complicated. “It would be nice if there were only a couple of genetic sequence changes, but there are thousands,” says Lambert. That’s why the researchers are amassing a database of the sequence differences, and using them as markers to determine the differences between the various nematodes as they watch them evolve over a few generations. 

That’s where they are now, developing the SCN generations in the lab, looking for markers and honing their technique before moving the test into the field. In one sense, time is on their side – technology is moving ahead at such a pace that it’s making their sequencing lab work increasingly economical. For example, the cost of DNA sequencing used to be in the millions of dollars; now, it can be carried out for less than $1,000. 

That said, SCN is causing yield losses of an estimated $1.5 billion a year. Virulence is increasing all the time, and management has to keep pace. “Most SCN soybean varieties are yield competitive and yield very well in both SCN and non-SCN environments,” says Dr. David Wright, North Central Research Program director of research. “But managing SCN goes beyond competitive yields, and it’s necessary to take a long-term view if profitable soybean production is to remain sustainable.” 

This research is part of the U.S. Department of Energy Joint Genome Institute. It unites the expertise of five national laboratories to advance genomics in support of the department’s drive towards clean energy generation and environmental characterization and cleanup.