Unlocking Pigweed

Have plant geneticists found the key to Palmer amaranth’s glyphosate resistance?

palmer pigweed

Palmer amaranth, also known as Palmer pigweed, has become resistant to several herbicides – most notably glyphosate — photo courtesy Clemson University

Just hearing “pigweed” can cause fear in row-crop farmers, but Clemson University geneticist Chris Saski and other researchers believe they have discovered the armor this dreaded weed uses to protect itself against glyphosate herbicide.
According to researchers, a specific genetic feature — the extrachromosomal circular DNA (eccDNA) replicon — gives pigweed, or more specifically glyphosate-resistant Palmer amaranth, its resistance to the often-used herbicide, making this weed difficult to control.

The discovery could help refine herbicide treatment strategies and combat the rise of resistant weeds, says Saski.

“The DNA structure of the eccDNA replicon is sophisticated,” says Saski, who is an associate professor of systems genomics in Clemson’s Plant and Environmental Sciences Department. “This circular molecule contains functional genes intermixed among complicated repetitive DNA that seems to have originated from different chromosomes to form the circle.”

He says the difficult sequencing was only possible with advanced single-molecule technology provided by Pacific Biosciences, a biotechnology company based in Menlo Park, California.

This discovery provides an explanation of how weeds evolve and adjust to become resistant to herbicides.

A DNA Change In Pigweed

Glyphosate was introduced in the 1970s and became the most widely used herbicide on many food and non-food field crops as well as non-crop areas where total vegetation control is desired.

Then in 1996, Roundup Ready crops were introduced. Being able to plant a Roundup Ready crop and then spray the whole field to kill weeds but not the resistant crop worked well for about 10 years until weeds began to appear in sprayed fields. Older herbicides had to be reintroduced to control resistant weeds. Glyphosate-resistant pigweed is now found in 27 states.

Through this study, researchers found pigweed DNA in resistant plants had drastically changed to form a very large, self-replicating circular DNA in addition to its normal chromosomes that carried the gene for the protein that glyphosate attacked.

A Breakthrough Finding

“What this means is plants like pigweed that contain the eccDNA are able to survive and propagate where glyphosate is used frequently,” Saski says, adding that glyphosate stress might contribute and influence eccDNA formation and activity.

“Understanding the complete genomic structure and function of the eccDNA replicon will aid our knowledge of how plant genomes respond and evolve to stresses and help to further refine herbicide treatment strategies and combat the rise of resistant weeds,” he says.

Saski says future research will focus on how the eccDNA self-replicates in plant cells and on identifying the essential functional elements of the eccDNA.

An article about their research, “The eccDNA Replicon: A heritable, extra-nuclear vehicle that enables gene amplification and glyphosate resistance in Amaranthus palmeri,” appears in the current issue of The Plant Cell journal as a BreakThrough Report.

Clemson Extension Pigweed Expert

Clemson University Extension weed specialist Michael Marshall, who works at the Edisto Research and Education Center, says pigweed is an aggressive, invasive weed found throughout the United States. “Once it is introduced to an area, the weed rapidly adapts and produces many small seed. It can quickly become a major problem for producers.”

Pigweed plants can grow 2 to 3 inches per day and compete with crops for nutrients, water, sun and more. Pigweed’s emergence period extends well into the typical crop season and can produce viable seed after crop harvest in the fall.

Pigweed, annual morningglory and sicklepod are the three main weeds South Carolina growers must battle every year. Proper application of herbicides can help relieve some of the pressure.

Taking The Discovery Further

When the researchers discovered the mechanism that amplifies genes in pigweed, Saski applied for and was awarded funding from the Clemson University Research Foundation to advance this technology to the next level. The foundation helps explore the potential for moving research beyond Clemson laboratories and into commercial markets.

Research into pigweed’s glyphosate resistance mechanisms continues, but Marshall says this discovery could be a game changer for agriculture.

Article by Denise Attaway, College of Agriculture, Forestry and Life Sciences; Public Service and Agriculture.