A needle in a seedstack: Minnesota, Colorado research team presents a new way to detect Palmer amaranth

The University of Minnesota’s Invasive Terrestrial Plants and Pests Center and Colorado State University have developed a new test using a chemistry called KASP for identifying Palmer amaranth that has shown 99.9% accuracy.

Palmer amaranth is an aggressive weed. It can grow up to 3 inches a day, will get to more than 6 feet tall and produces thousands of seeds. Minnesota Department of Agriculture
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ST. PAUL ― An inexpensive and reliable genetic test developed in Minnesota will soon be available to detect an aggressive and prolific weed species that can have a major impact on agricultural yield.

The University of Minnesota’s Invasive Terrestrial Plants and Pests Center and Colorado State University have developed a new test for identifying Palmer amaranth that has shown 99.9% accuracy, according to the two universities.

Palmer amaranth is a weed that's native to the American Southwest that has caused a lot of problems in row crops like corn, soybean and cotton in the southern U.S. in the last 20 years. It's illegal to sell any kind of seed in Minnesota that contains Palmer amaranth, which has shown potential to wipe out up to 91% of corn yields and 68% of soybean yields.

In the last decade, Palmer amaranth has spread into the Midwest; it was introduced in Minnesota in 2016. The study's lead author, Anthony Brusa, a postdoctoral associate in the College of Food, Agricultural and Natural Resource Sciences, said their project got started in Colorado and stretched to include the University of Minnesota in 2018.

"The main challenge when you're trying to identify it is that there's a number of related pigweed species, and Palmer amaranth, which is a much larger threat than some of the other species, looks very similar when you see it growing out in the field," Brusa said. "And it's even more difficult to identify the differences in seed."


How the test was made

2537042+Hay Palmer amaranth.jpg
Palmer amaranth (Agweek file photo)

Researchers collected samples of Palmer amaranth and related species from across the U.S. as well as Mexico, South America and Africa, and performed genomic sequencing on them, searching for specific genetic differences between species.

The targets identified were then used to design a set of three genetic markers for the identification of Palmer DNA against the DNA of related pigweed species, and the tests were validated for performance against "the most robust testing panel assembled to date," according to a UMN press release.

“We believe this has the potential to help prevent Palmer seed from being introduced as a contaminant in pollinator seed mixes, bird seed, and other seed lots sold from areas where Palmer is currently a problem, into areas like Minnesota,” said co-author Todd Gaines, an associate professor of molecular weed science at Colorado State University. “We also see great potential for this to be used to help protect corn and soybean exports by verifying the absence of Palmer in grain sold to countries that won’t accept Palmer-contaminated products.”

The research was funded through the Minnesota Environment and Natural Resources Trust Fund, and collaborators included University of Minnesota Extension, Colorado State University, Michigan State University and the Minnesota Department of Agriculture.

How it will work

Palmer seed on lined paper for scale.jpg
Palmer amaranth seeds are shown on lined paper to indicate their tiny size. Though the seeds are small, the weed can grow to be massive and reproduce quickly to overtake crops. Photo courtesy of the University of Minnesota

Brusa said the test is able to identify the individual plants a grower finds in their field and thinks might be a polymer, which is then sent into the lab for testing. The test will also work on batches of seed, he said.

"In that case, you would be looking at seed manufacturing companies that need to comply with regulatory guidelines to be able to sell their seed within certain states," Brusa said.


He said that researchers decided they wanted to make the test "as standardized as possible," by using common techniques that most labs will be able to do.

"The samples get sent into lab, they extract DNA, they're running a simple reaction that they should be able to do on most hardware, and then the output as long as their machine is able to read fluorescent dyes, they can tell you whether or not you have Palmer present in your sample," Brusa said.

The prevention of Palmer amaranth is a team effort between researchers and growers, said Brusa, as control efforts wouldn't be possible without farmers sending in their samples.

Coming soon

The research team, which includes members of the University of Minnesota and Colorado State University, is working on the last few details of getting the licensing agreement in place, Brusa said. Once that is done, he said they're going to start licensing the test out to private labs.

Researchers hope to make the new test technology commercially available to agronomic professionals across the country by the end of 2021, which can be applied to both individual samples and bulk seed mixes.

Denise Thiede, section manager for seed, noxious weed, hemp and biotechnology at the Minnesota Department of Agriculture, said the commercialization of the test "will provide new options to seed companies labeling seed for sale in Minnesota as well as other industries that may be at risk for introducing Palmer amaranth."

Why it's unique

Brusa said that compared to other similar tests currently being used to test for Palmer amaranth, their test uses a different type of chemistry called KASP. He said KASP allows them to get a "very low threshold when doing bulk seed testing," and can find if a batch of hundreds of seeds contains even one seed that's contaminated.


"The other benefit for KASP is that it's a lot less sensitive to issues with DNA concentration and DNA quality," Brusa said. "I've run it with some samples that were in very bad shape from out in the field, and we were still able to get really solid results out of it."

For Brusa, being a part of the team that developed the test is a high point in his career as a researcher. He said it was the first project this size that he's led, and he was grateful to work with a "really strong" team.

"There were a bunch of people with very specialized skills that I was able to reach out to, and they were able to help me develop this very well," he said.

Competitiveness between other states and universities developing their own tests wasn't something Brusa said he was ever concerned about. In a professional career based around fighting invasive species, it's always about helping farmers stay on top.

"It's a neverending fight, but you can develop some really important tools that can save farmers' livelihoods," he said.

2537042+Hay Palmer amaranth.jpg
Palmer amaranth (Agweek file photo)

2537042+Hay Palmer amaranth.jpg
Palmer amaranth (Agweek file photo)

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