Developing new soybean cultivars resistant to disease and pests is not an easy endeavor. It often entails years of careful work to tease out the function of genes in the soybean plant, of which there are over 60,000.

By crossing susceptible soybeans to resistant ones and then testing the resulting progeny, researchers can slowly determine which parts of the genome are important for resistance. At this stage, scientists are often faced with a long list of candidate genes that need to be analyzed one by one to verify their functions.

A conventional method for determining gene function in plants is to simply delete the gene from the genome. This is more easily said than done, as the process can take months to even years to complete because the first attempt often needs to be repeated.

Since this timeframe is not practical when so many genes need testing, researchers have turned to a relatively rapid technique involving viruses for short-term gene inactivation. While the results can’t be passed on to the next generation of soybeans like the traditional deletion method can, the Virus-Induced Gene Silencing system (VIGS) can be used to quickly prove or disprove a soybean gene’s importance for resistance.

Feng Qu, a virologist at The Ohio State University, is the go-to person for soybean researchers who want to utilize VIGS once they have a list of candidate genes that might be responsible for resistance.

“Our research is not just to silence the gene. Specifically, we don’t just see if the plant looks different. We also want to see if the plant becomes more or less susceptible to pathogens like Phytophthora sojae or aphids,” Qu says.

Sometimes, the process is successful at silencing the target genes, but there’s no change in soybean resistance, indicating the gene has an unrelated function. The process of developing the modified virus, infecting the plant and confirming gene silencing can take two and a half to three months.

“A lot of times, we know the gene we want to silence is silenced, but we don’t see any change in susceptibility,” Qu states. “That’s the most common problem.”

But persistence pays off. Qu recently collaborated with entomologist Andy Michel on a checkoff-funded project to find resistance genes against soybean aphids. Using the DNA sequences from the seven candidate genes Michel identified, Dr. Qu made each into unique virus vectors to infect an aphid-resistant soybean cultivar.

The next step was to test how the plants responded to aphids.

“It was a lot of work,” Dr. Qu explains, detailing how they had to synchronize aphids to be the same age before applying them to the gene-silenced plants. Out of the seven genes they silenced, one paid off. “The plants that were originally resistant to aphids became more susceptible so we know we hit the right gene.”

Now, Qu has to confirm this result using the more stable method of deleting the gene from the soybean’s DNA. If the genetically modified plants show the same increase in susceptibility to aphids, the identified gene can be placed on the high priority list for developing new aphid-resistant soybeans.

 

Here’s a closer look at how VIGS works:

  • Several plant viruses, such as bean pod mottle virus or apple latent spherical virus, can be used for virus-induced gene silencing.
  • Researchers modify the viruses by adding the plant gene of interest.
  • When plants are infected with the modified virus, the plant starts targeting the virus genome to disable it. Since this virus also contains soybean gene sequence, the plant ends up inactivating all copies of that gene including the ones in its own cells.
  • Ultimately, the soybean’s defense system against viruses does an effective job at silencing specific plant genes, making research on gene function substantially more time efficient.
  • Once genes are silenced, the researcher can monitor the soybean’s response to a disease or pest. If the soybean becomes more susceptible, then the silenced gene is needed for resistance. Conversely, if the plant has increased resistance once the gene is silenced, then researchers know to avoid integrating that gene into new cultivars.
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