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

A mixture of seeds and leaves of the Amaranthus plant

Available for Licensing
TRL: 5

IP Status

US Provisional Patent


Todd Gaines
Eric Patterson
Crystal Sparks

At A Glance

Researchers at CSU 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 (A. palmeri) is a prohibited noxious weed, and they must certify their clean seed.

Licensing Director

Jillian Lang

Reference No.:  2020-091


Amaranthus is a genus of between 60-70 annual or short-lived perennial plants and include many classifications (1,3). Some amaranth species are cultivated as leaf vegetables, pseudocereals, and ornamental plants (3).Unfortunately, some amaranth species are extremely invasive and 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 (1).

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 (2). 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 (1). 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.

Technology Overview

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 robust and capable of detecting Amaranthus species from multiple geographic locations, including regional US populations and 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 single Palmer amaranth seed in a pool of at least 200 Amaranthus species seeds or leaves
  • Sensitivity greater than 99.8%
  • Specificity greater than 99.6%
  • Accuracy is greater than 99.7%
  • Validation of genes across 20 populations of Palmer amaranth to ensure no Palmer amaranth is in a seed mixture
  • Easy to use and interpret results
  • Decreased cost per test
  • Detection of Palmer amaranth seed contamination in Amaranthus species mixtures

(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: June 2022

Add keywords or various names of inventors here (text is hidden)

Palmer amaranth, Amaranthus palmeri, noxious weed, invasive weeds, crop certification, diagnostic assay, molecular diagnostics, seed contamination, weed seeds, seed certification,

The MCIA Seed Laboratory, Minnesota Dept of Agriculture, USDA ISU Seed Lab, Eurofins Diagnostic, National Plant Diagnostic Network