It starts with spit for soybean cyst nematode
Farmers stymied by soybean cyst nematode (SCN) that ravages once bulletproof SCN-resistant soybean varieties can look to one seemingly simple yet complex reason.
This isn’t the chewing tobacco-tarred spittle that some baseball players spew; it is secretions produced by newly hatched SCN. SCN injects its spit into a soybean root cell wall though a mouth spear called a stylet.
“Just like humans have salivary glands in their mouth to aid in digestion, the nematode produces proteins that are secreted through the stylet to modify plant tissue,” says Dick Hussey, a University of Georgia (UGA) nematologist. “It’s able to infect and penetrate the soybean root and suppress the immune response by establishing a feeding site.”
Because feeding sites interfere with plant water and nutrient flow, SCN feeding stealthily steals soybean yield. Farmers have dodged this scenario for nearly 30 years by planting SCN-resistant soybeans.
“SCN-resistant soybeans combat infection by preventing the nematodes from setting up feeding sites,” says Melissa Mitchum, a UGA nematologist.
There’s a hitch, though, as 95% of resistant varieties farmers plant share the same resistance source: PI 88788.
“When you repeatedly plant the same type of resistance, you select for resistance-breaking nematodes to grow and reproduce,” says Mitchum.
Initially, SCN damage is invisible.
“Farmers will wonder why soybeans aren’t growing well and shrug it off due to ‘sorry dirt,’ ” says Bob Kemerait, a UGA Extension plant pathologist. “Many times, sorry dirt is due to nematodes.”
Eventually, this underground marauder leaves visible symptoms of stunted plants and yellowed leaves. Even if a farmer plants SCN-resistant soybeans, yield losses up to 14 bushels per acre can result as SCN reproduction increases, according to Iowa State University (ISU) research. At a $14-per-bushel soybean price, this clips gross returns $196 per acre.
Nematologists use the term virulence to describe SCN’s ability to reproduce on a resistant soybean. They measure virulence through a metric called the female index.
“A fairly resistant plant is one that falls below a 10% female index,” says Mitchum.
The PI 88788 resistance source still has some effectiveness, she says. However, more SCN populations now exceed the 10% female index threshold. In Tennessee, for example, 93% of SCN populations had greater than 10% reproduction on soybean varieties with PI 88788 resistance.
The good news is alternative SCN-resistance sources with no yield drag exist, such as Peking-based resistance.
“A nematode population adapted toPI 88788 will not grow and reproduce well on soybeans with the Peking type of resistance,” says Mitchum.
“Some of our top-yielding varieties have Peking resistance,” adds Don Kyle, a Corteva Agriscience soybean breeder. The varieties may also lower SCN numbers, which nixes the likelihood of future infestations, says Kyle.
Had the farmer who hosted a 2019 ISU SCN-resistant variety trial planted a Peking variety in an adjacent field with SCN that resisted PI 88788 soybeans, he would have gleaned a 22 bushel-per-acre yield gain, says Greg Tylka, an ISU Extension nematologist. With soybeans priced at $14 per bushel, that’s a gross return of $308 per acre.
Still, farmers often don’t know resistance sources differ. “They [companies] will say varieties have soybean cyst nematode resistance, but farmers often don’t know what kind of resistance it is,” says Andrew Moore, a Resaca, Georgia, farmer. “If we are having yield losses in spite of
[PI 88788] resistance, we need to know there are other kinds of resistance.”
Farmers may find it difficult to access alternative resistance sources.
“I know I become frustrated when a grower sends me a [soil] sample and the nematode population has a 60% female index on PI 88788,” says Mitchum. “When they ask, ‘What can I do?’ and I tell them to plant soybeans with Peking resistance, they often tell me it’s not available in their maturity group. PI 88788 is still a good resistance source and we should preserve it. We want to partner with industry to develop new resistance sources that can be used in a crop rotation.”
It’s in the Genes
Unlocking new SCN-resistance sources lies in the discovery of novel (undiscovered) soybean and SCN genes.
“For decades, researchers knew soybeans had genes for resistance to the nematode, but we didn’t know what they were or how they functioned,” says Mitchum. “Soybean breeders just knew where these genes were located on the chromosome.” Scientists call this location the quantitative trait loci (QTL).
This changed in 2012, when researchers cloned two genes that spur most SCN resistance at two major QTL: Rhg1 and Rhg4. Rhg1 confers resistance in PI 88788, while Peking resistance is a combination of Rhg1 and Rhg4.
“It was a huge discovery, an aha moment,” says Mitchum. “We now know the proteins that enable soybeans to resist the nematode. We are starting to understand how these proteins function to confer resistance to SCN, and it’s allowed us to develop [molecular] markers from those genes.”
“In driving terms, the chromosome is the highway, and the molecular marker [that pinpoints the gene] is an exit sign telling the driver where to go,” says Zenglu Li, a UGA soybean breeder. “These molecular markers help us introgress (transfer) the genes into elite germplasm and cultivars and also improve the efficiency of breeding selections.”
The 2019 sequencing of the SCN genome also paved the way for new resistance resources by helping scientists identify SCN genes responsible for making proteins found in nematode spit, Hussey says. Ideally, soybean breeders could pyramid these new SCN resistance genes on top of genes like Rhg1 and Rhg4, he adds.
Determining what new genes do is a tough nut to crack, though.
“We’ve discovered most of the nematode genes that produce the proteins in spit are what we call pioneer genes,” says Hussey. “They have not been identified in any other organism. This makes it more difficult for us to determine their function and what their products [like proteins in spit] do.”
Meanwhile, specific genes that grant SCN the ability to reproduce on resistant soybeans remain to be identified, says Mitchum. However, they are likely to produce proteins in SCN spit, she adds.
Not all plant resistance genes play well together. “It is critical to have the right combination of soybean resistance genes to produce a different type of mode of action,” Mitchum says.
All this takes money, which the UGA scientists credit the soybean checkoff for providing. Ditto for time.
“It took a decade to clone the soybean resistance genes Rhg1 and Rhg4,” she says.
Incorporating these genes into new varieties during breeding also may be a time-consuming and random process.
“When a plant breeder makes crosses and starts selecting these resistance genes, they also get some of the genes on either side of the chromosome,” says Wayne Parrott, a UGA plant geneticist. Many of these unwanted genes are benign, but some can slice yield potential if not removed.
“This is called linkage drag when you get those unwanted genes,” he adds. “Breeders have to keep making crosses until they eliminate them.”
Gene editing using tools like CRISPR/Cas9 can change this.
“It removes the randomness from the process,” Parrott says. “A gene can be added or deleted on the chromosome with no interference from neighboring genes.”
CRISPR/Cas9 also can shave the time it takes to make genetic changes in a soybean variety from years to months, he adds.
To Market, to Market
Cooperation with the seed industry also will be crucial in providing new sources of SCN resistance, says Parrott.
“The University of Georgia is not in the business of marketing,” he adds. “To get our varieties to market, we have to go through private industry.”
Still, it’s difficult for a company to redirect its breeding program to include a new SCN resistance source.
“A challenge is to find Peking varieties that are more broadly adapted than to a field with just SCN,” says Jim Schwartz, Beck’s director of research, agronomy, and PFR (Practical Farm Research).
For example, there are areas where a malady such as white mold can curtail yields akin to SCN. In these cases, an SCN-resistant variety would also have to include white mold tolerance, Schwartz points out.
Eventually, though, Mitchum believes their efforts will bear fruit. She expects more SCN-resistant varieties and novel types of SCN resistance sources will come to market in five to 10 years.
“This is why I get up every morning,” says Mitchum. “I love research. I want to know why that plant is resistant and another is not. I want to know why that nematode can overcome resistance and another nematode cannot. I want to use this knowledge to develop something beneficial for society, to help growers feed the world.
New Tech for Todes
Other new technologies that scientists are using to find new sources of soybean cyst nematode (SCN) resistance include:
- RNAi technology. This technology can reduce the expression of a plant gene or a nematode gene necessary for SCN survival. “There are some advantages to it because it allows you to just reduce expression, not completely knock out expression of a gene as CRISPR [a gene editing tool] does,” says Melissa Mitchum, a University of Georgia nematologist. This can give breeders additional options for designing genetic resistance to SCN, she adds.
- Synthetic biology. “This is where we actually tinker with [genetic] pathways, similar to an engineering circuit,” points out Mitchum. “For this to work, we need to know how plant SCN-resistance genes work and how they function to terminate or break down the feeding cell formed by the soybean cyst nematode.”
- Transgenic technology. BASF has obtained registration from the Environmental Protection Agency for an SCN transgenic trait. It expresses a novel Bt protein, Cry14Ab-1, that will be part of the GMB151 SCN trait bred into soybean varieties containing native SCN resistance, such as PI 88788 and Peking. BASF officials say the transgenic trait is expected to debut later this decade.
Tucked inside a greenhouse at the University of Georgia (UGA) is the Tode Farm — the nation’s largest active collection of experimentally adapted soybean cyst nematode (SCN) populations.
UGA nematologists grow these populations on soybeans that serve as sources of SCN resistance. This includes not only the widespread PI 88788 resistance source, but also Peking and less common ones, such as PI 90763 and the wild soybean Glycine soja.
Each SCN population is unique, with virulent populations sometimes overwhelming a resistance source while leaving others to grow uninhibited.
“By identifying the SCN virulence genes, we may be able to develop a molecular test to diagnose a grower’s field population and prescribe the most effective type of resistance to combat soybean cyst nematode,” says Melissa Mitchum, a UGA nematologist. “Prescriptive management will then become a reality for growers.”
Two soybean varieties sharing the PI 88788 source of soybean cyst nematode (SCN) resistance should both equally deter SCN, right?
“Not all resistance is created equal,” says Melissa Mitchum, a University of Georgia nematologist. “You may have two varieties with PI 88788 resistance, but they may not be the same genetically.”
Differences exist due to the number of genetic copies present at a resistance locus (location) on a chromosome that confers SCN resistance. For example, a variety that has nine copies of the Rhg1 gene on a chromosome will resist SCN more than one that has just five. Currently, there is no way for farmers to know copy differences. The good news is that varieties with low copy numbers will never make it through a company's product pipeline, she says.
“There can be slight differences between varieties with different copy numbers, but they aren’t wide,” says Don Kyle, a Corteva Agriscience soybean breeder. “We discard those that do not have acceptable levels of SCN resistance.”
Kyle advises checking resistance scores and SCN-resistance sources when selecting soybean varieties. In Corteva’s case, this information is listed on the soybean variety component of its website.