by Carolyn Bernhardt
October 8, 2024

In 2016, Minnesota recorded its first confirmed sighting of Palmer amaranth (Amaranthus palmeri), a notorious agricultural pest. Since then, the hardy weed has been reported several times in the fields of Minnesota, threatening crops and farmers' livelihoods. “While there have been introductions into Minnesota, the Minnesota Department of Agriculture (MDA) has been extremely successful at preventing Palmer from establishing,” says Anthony Brusa, PhD, a researcher in the Department of Agronomy and Plant Genetics in the College of Food, Agricultural and Natural Resource Sciences at the University of Minnesota.
Native to the southwestern United States and northern Mexico, Palmer amaranth produces up to a quarter million seeds per plant. This can decimate yields in agronomic landscapes, leading to losses of up to about 80 to 90% in soybean and corn respectively. “That's basically an entire loss of a year,” says Brusa. “Many growers may not be able to come back from that much of a catastrophic loss.”

Recognizing the need for more research, particularly for a reliable genetic test to detect tiny Palmer amaranth seeds that could contaminate seed mixes, the MDA called for action. Dr. Don Wyse, a long-time faculty member in the Department of Agronomy and Plant Genetics, and co-director of the Forever Green Initiative, immediately stepped up and proposed a research project. He enlisted Todd Gaines, an associate professor of molecular weed science at Colorado State University, and recruited Brusa as a postdoc, bringing in additional colleagues from Michigan State and USDA.
Together, the team developed a tool with over 99.7% accuracy for identifying Palmer amaranth, outperforming existing tests. Along the way, they also uncovered that some amaranth seed accessions in a national collection had been misidentified. Wyse saw this as further proof of the importance of their work. He engaged in spirited discussions about the future of Palmer amaranth research and efforts to keep the plant out of Minnesota. Wyse passed away in July of 2024. His boldness and leadership is greatly missed.
Sifting out solutions

Traditional visual identification methods for Palmer amaranth often fall short, leading observers to easily confuse multiple species with the invasive plant. Experts have found that it could hybridize with closely related pigweed species, complicating accurate identification. Clearly, the team needed a new, efficient solution.
Brusa explains, “The MDA saw the initial sighting and were extremely proactive; they wanted us to develop a test that could be conducted in-house. They were very rightly concerned about this sudden introduction of Palmer and wanted to address the situation quickly.”
The research team from the UMN joined forces with experts at Colorado State University (CSU) to focus research on two key objectives: developing a seed separation method and validating DNA markers for Palmer amaranth.
A significant aspect of the project involved assembling a comprehensive genetic panel of pigweed species. Brusa assembled samples from various regions, including South America and Africa, to ensure a representation of diverse genetic backgrounds.
But before molecular analysis, Brusa physically separated Palmer amaranth seeds from other seed types. Since the genetic material from Palmer amaranth is minuscule, researchers can struggle to detect it among larger seed varieties. So, Brusa began sieving the seed samples collected from the field. Brusa says, “By adding a few minutes of filtering, we can make the task much easier. It turns out that basic, low-tech stuff is still critically important to this work.”
Next, Brusa and team got to work identifying and validating DNA markers they could test to precisely detect Palmer amaranth. Using a low-cost genetic analysis technique—an idea Brusa got from colleagues at CSU—the team focused on distinguishing Palmer amaranth from related species like waterhemp.

Brusa used a technique called competitive fluorescence PCR. In this method, researchers use fluorescent dyes to detect specific genetic sequences unique to Palmer amaranth. These dyes glow when the samples are exposed to light, allowing experts to identify the weed. Brusa used special imaging equipment to capture the bright signals produced by the markers. This helped him analyze how strong the signals were and what patterns they made, which allows the user to tell Palmer amaranth apart from other similar pigweed species.
The biggest perk to this approach? It’s easy to teach a lab tech. Brusa wanted the method to be simple and reliable, reducing the chances of muddled results.
According to Brusa, “No test is perfect, but we wanted to make one that is going to catch as many of these things as possible.” This diligence resulted in a robust test with an impressive 99.9% accuracy rate for detecting Palmer amaranth in individual plants and seed pools. The team's research was published in 2021 in Pest Management Science (available to read for free from the University Digital Conservancy).
Future-proofing agriculture
Armed with this testing approach, experts can now focus on monitoring Palmer amaranth's seed dispersal and understanding its hybridization potential. The sneaky sprout’s rapid reproduction has already led to strong herbicide resistance in some populations, and researchers are keen to refine herbicide application strategies to improve management outcomes under varying conditions before that happens.
Brusa envisions the test being utilized by state-level agencies, allowing them to conduct their own in-house seed testing. Private testing laboratories are another possibility. “If a company wanted to come to us or Colorado and talk about licensing the test for their own use, this is definitely something that’s available,” he said (see licensing information). Moreover, there is a demand for this type of testing as specific state level regulations require seed producers to certify that their products are free from prohibited noxious weeds like Palmer amaranth.
As Palmer amaranth continues to pose a significant threat to Minnesota’s agricultural landscape, robust identification assays offer a glimmer of hope for farmers and regulators alike. The journey of this research underscores the importance of science in addressing agricultural challenges and highlights the critical role of collaborative efforts in managing invasive species.
The collaboration between researchers and the MDA, UMN, and CSU exemplifies the proactive measures necessary to combat this invasive species, according to Brusa. With continued monitoring and adaptation, Minnesota may be able to contain the spread of Palmer amaranth and protect its vital corn and soybean crops from devastating losses.
More information
Licensing: An assay for detecting Palmer amaranth DNA in individual and mixed samples
Palmer amaranth management, Minnesota Department of Agriculture
Preventing Palmer amaranth in Minnesota, University of Minnesota, Extension
Brusa, A., Patterson, E. L., Gaines, T. A., Dorn, K., Westra, P., Sparks, C. D., & Wyse, D. (2021). A needle in a seedstack: an improved method for detection of rare alleles in bulk seed testing through KASP. Pest Management Science, 77(5), 2477–2484. https://doi.org/10.1002/ps.6278 (available to read for free from the University Digital Conservancy)
Research from the Minnesota Invasive Terrestrial Plants and Pests Center is supported by the Environment and Natural Resources Trust Fund, as recommended by the Legislative-Citizen Commission on Minnesota Resources.
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