Identification of Herbicide Resistance Genes in the Invasive Weed, Palmer Amaranth

At a Glance

Researchers at Colorado State University in collaboration with the University of Illinois have identified a candidate gene that may contribute to metabolic resistance to the herbicide 4‐hydroxyphenylpyruvate dioxygenase including tembotrione and mesotrione in the dicot weed, Palmer amaranth (Amaranthus palmeri). This candidate gene was found to have substantially increased gene expression in HPPD-resistant Palmer amaranth suggesting it enhances the weed’s ability to metabolize these herbicides.


Palmer amaranth is a dioecious invasive weed that is extremely competitive in cropping systems across North America. According to the latest survey conducted by Weed Science Society of America, it ranks as the hardest weed to control in grass crops, and the most troublesome weed for large crops like corn and sorghum (4). Palmer amaranth is a prolific and noxious weed, due to its large size (6-10 feet tall), aggressive growth rate (two to three inches per day in optimum conditions), prolonged emergence during growing season, large seed production (up to 1 million seeds per plant), and its propensity to develop resistance quickly (3). Scientists have been working to better understand the mechanisms of herbicide resistance in aggressive weed species. By discovering the underlying mechanisms of herbicide resistance, we gain insights into plant evolution. This includes genetic factors and mechanisms for herbicide resistance, and how these genes are upregulated or downregulated when herbicides are applied (1) and (2). Further, advances can be made to inform management strategies to reduce crop losses and costly inputs, diagnosing resistant populations and even crop improvement to develop new herbicide resistance traits towards enhanced food security.

Thus, the identification of mechanisms of action and the gene expression of resistant Palmer amaranth plants is critical for crop production and yield. Current methods are time-consuming and expensive HPLC tests that use a sample and must be taken to a lab for processing.


Using RNAseq to study resistant and susceptible populations of Palmer amaranth, this team of scientists have identified a key gene and regulatory mechanisms involved in herbicide resistance to HPPDs. Previous work has shown that resistant plants are able to rapidly detoxify HPPD quickly. This important scientific advance can be further developed into a diagnostic assay to rapidly identify herbicide resistant populations of Palmer amaranth, preventing the spread of the weed in crops and fields.

Methods and genetic sequences are available upon request


  • Improved Palmer amaranth management
  • Improved food security and sustainable crop production


  • Diagnostic marker development to identify HPPD-resistant populations of Palmer amaranth
  • Enable safener discovery for dicot crops
  • Predict the potential for metabolic cross‐resistance to other herbicides
  • Crop improvement to develop new herbicide resistance traits for HPPD‐inhibiting herbicide resistance, in crops such as cotton, canola, and soybean
Last Updated: September 2022
A farmer holding a weed in a field


IP Status

US Provisional Patent


Anita Küpper

Todd Gaines

Roland Beffa

Darci Giacomini

Patrick Tranel

Carlos Rigon

Franck Dayan

Reference Number