January 14, 2005

‘Omega Strain' of soybean cyst nematode Researchers take on new threat to crops

by K.C. Jaehnig

CARBONDALE, Ill. — When an evil, all-powerful Worm ravages the countryside, a small band of adventurers sets out to seek the Magic Sword that will undo the monster.

While it might sound like the plot for an epic film with great special effects, it is in fact the essence of an ongoing quest at Southern Illinois University Carbondale aimed at defeating the soybean cyst nematode, the chief cause of soybean crop loss not just in the Midwest but the world.

Supported by funds from the United Soybean Board, SIUC biotechnologist David A. Lightfoot and his research team — sometimes with scientists from other universities, sometimes alone — have been looking for the gene or genes that could make soybeans completely resistant to SCN, as the nematode is commonly known. That search has taken on new urgency in the face of what Lightfoot calls the "Omega Strain" of SCN.

"It's a biotype that can attack and defeat all our resistance sources," Lightfoot said.

"Natural variation has ceased to be able to deal with the worm. It's as if when we bred for resistance in soybean, we also bred for resistant worms."

It took roughly three years for the researchers to search through the forest of soybean DNA in which they thought the resistance gene or genes were hiding, but in 1998, that effort plus what Lightfoot termed "a lucky guess" struck gold.

"We found two genes — the most important one and its partner, the major and the minor," he said.

The major, dubbed Rhg1, is "absolutely necessary for resistance to every strain and biotype of the worm — without it, you are completely susceptible," Lightfoot said.

"With it, you have the potential to resist them all, if you have other genes to go with it. It's like the middle cog — it makes resistance work."

The minor, companion gene, Rhg4, transmits information to the major gene, which then acts on that information. Rhg4 also provides a certain amount of resistance on its own.

"We can prove in traditional ways that this one is a solid gene," Lightfoot said. "If we put it in a plant, it provides resistance. And the good news is that we are in a position to change it to make it even better."Rhg1 is more complicated — there's something strange about how it works. Resistance genes should be dominant — sort of like the gene for brown eyes in humans — but this one isn't. We're still trying to puzzle it out, but after we do that, we will have two genes that can be changed in ways to resist that ‘Omega strain.' Maybe this time we will be smart enough to design resistance the nematode can't overcome."

Knowing they were on the right path with the resistance genes, Lightfoot's team members began about four years ago trying to solve a related problem. Why, they wondered, did yields go down when resistance went up?

"We used every resource imaginable for the first two years to find out why resistant varieties can't produce as much, pushed our techniques to the limit, and every time, we came up with inconclusive answers," Lightfoot said.

Help came from a most unexpected source: SIUC's Department of Electrical and Computer Engineering.

"When we told them about our problems with the data set, they said it looked like a problem with pattern recognition (a computational method of categorizing meaningful patterns not readily apparent to the human eye)," Lightfoot said.

"When they reanalyzed the data, it turned out we'd been going at it all wrong for all these years. To get yield into a resistant type, it's not good to cross a resistant with a susceptible. You want to cross two high-yielding resistants. That's never been tried."

Lightfoot estimates the odds of success at 250,000 to one — odds about which he's remarkably cheerful.

"It's a lot better than 64 million to one, which is what it would have been with the old way," he said. "And it's doable. You take a couple of hundred breeders each doing 10 crosses a year — particularly if they can use markers to see what they're doing — and you could make fairly swift progress. High yield with durable resistance is our project goal."

Leading in research, scholarly and creative activities is among the goals of Southern at 150: Building Excellence Through Commitment, the blueprint for the development of the University by the time it celebrates its 150th anniversary in 2019.