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Scientists using DNA to detect pathogens on seeds

By Sharon Omahen
University of Georgia

Using DNA technology, University of Georgia scientists are working to develop a quicker, easier way to detect pathogens on plant seeds.

"We started this project in light of our nation's concern over biosecurity in agriculture," said Ron Walcott, a plant pathologist with the UGA College of Agricultural and Environmental Sciences.

"Our goal is to develop a system that can detect pathogens in seeds," Walcott said, "whether they were put there intentionally or unintentionally during the seed production process."

Funded by USDA grant

Iowa State and Clemson scientists will work with Walcott on the four-year project. The U.S. Department of Agriculture National Research Initiative's Animal and Plant Biosecurity Program will fund it with a $900,000 grant.

"Seeds for our country's food crops are produced around the world in various countries, including Thailand and China," Walcott said. "Then they're shipped and sold in the United States. Hard labor is still heavily involved (in seed production), so there are always risks of introducing exotic pests."

The current methods used to screen seeds for fungi, bacteria and viruses can take weeks. The researchers' goal is to develop a quicker, more accurate and precise testing method.

New method will be quick, effective

"As an example, one of the currently employed tests requires that seeds be planted and grown out to determine if a pathogen is present," Walcott said. "This is time-consuming. And unfortunately, this test is expensive to conduct. And there's a risk of failure, depending on the level of seed infestation."

With current methods, he said, it could take weeks to develop a technique to detect a new pathogen suspected to be intentionally introduced into the nation's seed supply.

"If it were a case of bioterrorism, we'd need to know as soon as possible," he said. "We have a lot of techniques available now, but the methods are neither effective nor reliable."

Scientists now use up to five tests to detect different pathogens, he said. A goal of this project is to develop one test that would be used to detect all seed pathogens.

Uses DNA and RNA technology

The new detection method will rely on both DNA and RNA to find out whether pathogens are present.

"Plants have DNA just like we do, but some viruses have only RNA," Walcott said. "The plan is to use a technique called magnetic capture hybridization to capture and detect the presence of pathogen DNA/RNA in a seed sample."

DNA and RNA are the molecules that encode an organism's physiological characteristics. These codes include sequences unique to the organism.

"By relying on specific DNA or RNA sequences, highly specific and sensitive detection assays can be developed," Walcott said. "As such, this approach is highly applicable for the detection of low levels of pathogens in seeds."

To apply this technique, scientists crush a sample of seeds and mix crude nucleic acids from the seed extract with magnetic, polystyrene beads.

Just like fishing

The beads are coated with single-stranded DNA, which hybridizes or binds specifically to the pathogen's DNA. The scientists recover the beads with a magnet, then amplify the DNA by polymerase chain reaction.

"It's like fishing, but we use mirror-image DNA instead of night crawlers as bait," Walcott said. "This method is highly sensitive and efficient and can work for a wide range of seeds and pathogens. Most important, the turnaround time is just a day."

As a starting point, the research team is focusing on two watermelon diseases that Georgia growers fight: bacterial fruit blotch and gummy stem blight. The next phase will include detecting diseases of tomato, onion, wheat, corn and soybean.

"Once we have the system going, we will have the capability to detect more seedborne pathogens," Walcott said. "If a new one that's not in our database is introduced by terrorists or Mother Nature, it will just take a couple of days to add it to the system."

(Sharon Omahen is a news editor with the University of Georgia College of Agricultural and Environmental Sciences.)

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