Soybean cyst nematode plagues soybeans in at least 25 states, costing U.S. farmers more than $1 billion in lost yields each year.

For 50 years, the world’s soybean crop has depended on the use of cyst nematode resistant varieties of beans, but no one knew how these plants fought off the nematode pests. Now, the secrets of resistant soybean plants are finally coming to light.

First detected in North Carolina in 1954, it has been a growing problem ever since. Many farmers discover they have an infestation in their soil only when a soybean field that appears healthy yields low at harvest.

Surprisingly, one of the genes related to nematode resistance in soybeans also has been associated with human diseases including lymphocytic leukemia, spina bifida and cardiovascular disease, according to a team of University of Missouri researchers and their colleagues whose breakthrough was recently published in the journal Nature.

For years, natural resistance in some soybean varieties kept this pathogen in check when coupled with crop rotation. But now 90 percent of resistant soybeans originate from one source, and this monoculture has caused growing resistance in cyst nematode populations.

Researchers at the University of Missouri Bond Life Sciences Center are now trying to figure out how this natural defense works, with an eye toward creating future varieties that can beat cyst nematode.

Melissa Mitchum, a plant scientist and molecular nematologist at MU, has taken a major step forward by cloning the first gene linked to natural soybean cyst nematode resistance. This gene points to an entirely new, previously unknown cell process for nematode resistance.

Cyst nematodes hatch from eggs in the soil in the spring and quickly migrate to the roots of nearby soybean plants. Once inside the root, they use a needle-like stylet to inject a single host cell with nematode spit full of effector proteins and the nematode soon loses all its mobility to become dependent on the single soybean cell. These effector proteins change the cell, essentially reprogramming it to serve the nutritional needs of the parasite.

“We cloned a resistance gene for the most important pathogen on soybean. In the plant world, it’s like cloning the gene for Alzheimer’s or Parkinson’s disease,” said Mitchum. “You can’t come up with a new approach to combat the disease problem until you know what the gene is. This is why it’s such a major breakthrough, because it’s our first glimpse into the underlying mechanism of nematode resistance.”

The journal Nature published Mitchum’s research October 15 in its online edition.

“Nine years ago, when I began investigating the molecular basis of soybean resistance to nematodes in an effort to identify the genes involved, I never imagined it would be this complex,” said Melissa Mitchum, co-author of the paper and associate professor of plant sciences at the University of Missouri’s Bond Life Sciences Center.

“The gene responsible for nematode resistance was completely unexpected. The gene, called serine hydroxymethyltransferase (SHMT), is common in nature and found in different kingdoms including both animals and plants. In humans, mutations in the SHMT gene can lead to a deficiency of folate, a B vitamin that is essential to the production and maintenance of cells, and this has been linked to a variety of diseases.”

Mitchum and her team collaborated with Khalid Meksem’s group at Southern Illinois University to pinpoint the location of the gene in the soybean genome. They then identified soybean plants from a normally resistant variety, but with a mutated form of the SHMT gene.

They observed that these plants had lost resistance to nematodes. In another experiment, the SHMT gene was shut down using two different gene-silencing techniques. These soybeans also became susceptible. A third test put the resistant form of the SHMT gene into normally susceptible soybeans and found that these plants also became resistant.

“Plant breeders can put our results to use immediately,” Mitchum said. “We now know which genes to look for when breeding resistant varieties. Nematode resistance also can now be directly inserted into commercially important breeds of soybean. For farmers, developing new forms of resistance to SCN in soybeans can’t come soon enough. Nematodes are developing their own ways around natural defenses. “Hopefully, our discovery has paved the way to enhance the durability of resistant varieties of soybean”

Although plant breeders can use Mitchum’s discovery now, it may be another decade before she and her team discerns the technicalities of nematode resistance. So far, they know that two mutations in the SHMT gene alter the enzyme’s activity in such a way to provide resistance to the plant.

Together with Dmitry Korkin’s group, they found that the deformed enzyme malfunctions, particularly in regions of the enzyme known as the binding pockets, where the enzyme interacts with other molecules. Exactly how this affects the nematode is still unclear.

The journal Nature published Mitchum’s research October 15 in its online edition.