Field Assay for Identification of Palmer Amaranth from Single Seeds, Seed Mixtures, and Leaves

Extremely Accurate Contamination Detection

At a Glance

Researchers at CSU and University of Minnesota have developed a DNA genotyping assay that identifies the presence of Palmer amaranth seeds in a mixture of seeds, for the purpose of detecting noxious weed seed contamination. The test can be used by seed producers to determine if their seed may be sold in locations were Palmer amaranth (Ameranthus palmeri) is a prohibited noxious weed, and they must certify their clean seed.


Amaranthus is a genus of between 60-70 annual or short-lived perennial plants and include many classifications. Some amaranth species are cultivated as leaf vegetables, pseudocereals, and ornamental plants. Unfortunately, some amaranth species are extremely invasive and are classified as noxious weeds, such as Palmer amaranth. This weed poses a serious economic threat to crops such as corn and soybeans and is classified as a prohibited noxious weed in multiple Midwestern states.

Thus, several states that are experiencing large crop loss due to Palmer amaranth require certified Palmer amaranth-free seed to be able to grow any amaranth type. Seed producers and sellers must test their seeds and seed mixtures to prove there is no threat of such an invasive weed in them, as all of the Amaranthus genus have very similar, small black seeds and it is impossible to visually distinguish the species. Typical testing involves growing a sample of seeds to show plant identification, which is slow and unreliable. Other testing offered includes testing individual seeds using DNA sequencing, which is expensive and burdensome. There is a need for a highly sensitive, specific field assay for the detection of Palmer amaranth seeds in a mixture of other Amaranthus seeds and debris.


Researchers have identified several single nucleotide polymorphisms (SNPs) that can be used to identify Palmer amaranth from a mixed pool of Amaranthus species DNA. This assay is more accurate and robust than any commercially available test. By using these SNPs, this assay is capable of detecting Amaranthus species from multiple geographic locations, including regional US populations as well as South American and African populations. Furthermore, the test is easy to perform and more efficient that other molecular diagnostic tests available for Palmer amaranth detection.


  • Capable of detecting a simple palmer Amaranth seed in a pool of at least 200 Amaranthus species.
  • Sensitivity greater than 99.8%.
  • Specificity greater than 99.6%.
  • Accuracy is greater than 99.7%.
  • Easy to use and interpret results.
  • Inexpensive cost per test.


  • Detection of Palmer Amaranth seed contamination in Amaranthus species mixtures.


A. Brusa, et al.(2021) A needle in a seedstack: an improved method for detection of rare alleles in bulk seed testing through KASP. Pest Manag Sci. 2021 May;77(5):2477-2484. doi: 10.1002/ps.6278.



(1) Brusa A, Patterson EL, Gaines TA, Dorn K, Westra P, Sparks CD, Wyse D. A needle in a seedstack: an improved method for detection of rare alleles in bulk seed testing through KASP. Pest Manag Sci. 2021 May;77(5):2477-2484. doi: 10.1002/ps.6278. Epub 2021 Feb 2. PMID: 33442897.

(2) Hensleigh, Patick, and Pokorny, Monica (2017) Agronomy Technical Note Palmer Amaranth. Agronomy Technical Note MT-92, United States Department of Agriculture, Natural Resources Conservation Service (March 2017).

(3) Petruzzello, Melissa. “Amaranth.” Encyclopædia Britannica, Encyclopædia Britannica, Inc.,

Last Updated: February 2024
Seed mixture

Available for Licensing
TRL: 6


Todd Gaines
Eric Patterson
Crystal Sparks
Anthony Brusa
Kevin Dorn

Reference Number
2020-091 and 17-051
Licensing Manager

Jessy McGowan