Jim Burton of North Carolina State University’s Horticultural Science Department is studying the genome of herbicide-resistant Palmer amaranth in hopes of learning more about the genetic adaptation that has allowed the plant to resist herbicides like glyphosate.

Burton, who specializes in weed science and herbicide behavior in plants, believes that learning more about Palmer’s resistance could lead to the creation of crops that can adapt to other hardships, including drought, and could ultimately help farmers better deal with resistant weeds.

For years, farmers have relied on the convenience of genetically modified crops to easily manage the problem of weeds in their fields. Roundup Ready crops like cotton, soybeans and corn allowed growers to manage weeds by spraying entire fields with the herbicide glyphosate without damaging crops. But heavy reliance on Roundup Ready crops has led to the emergence of weeds that are resistant to Roundup and other herbicides.

“Roundup has proven to be a very effective weed management tool. But if you use only one tool in your toolbox, when it comes to weeds, you’re going to shoot yourself in the foot,” Burton said.

Roundup-resistant weeds, like the voracious Palmer amaranth, have left growers with few tools to keep weeds out of their fields. In some cases, these resistant weeds are so invasive they even cut into crop yields. North Carolina State weed scientist Alan York estimates that about half of all Palmer amaranth populations in eastern North Carolina are resistant to glysophate, and about half show resistance to another class of herbicides, ALS (acetolactate sythase) inhibitors. A quarter of all Palmer is believed to be resistant to both types of herbicides.

Currently, better management strategies show the most promise for controlling this resistant weed, and North Carolina State weed scientists are working to educate growers. “In my opinion, the overall level of control growers are achieving is better now than it was three or four years ago,” York said. “The problem is not going away; it is just something growers will have to deal with from now on.”

When Roundup Ready crops first became available, scientists believed it would be difficult for weeds to develop resistance to glyphosate, so they were surprised when resistant strains of Palmer began showing up in fields of the Southeast.

“In 1980, people said, ‘Herbicide resistance is never going to be a problem.’ But with resistance, if you don’t manage for it, you’re lost.”

Recent discoveries

Scientists at the University of Georgia and the University of Colorado recently discovered that gene amplification in resistant Palmer has led to this unexpected resistance to glyphosate. Most plants have one gene that produces an enzyme that binds with glyphosate. But this single gene cannot produce enough enzyme, known as EPSPS, so glyphosate normally overwhelms and kills the plant.

Glyphosate kills by blocking the production of specific amino acids that are made in plants, but not animals, making it a relatively safe herbicide. Plants try to fight back by producing EPSPS, but non-resistant plants don’t produce enough enzyme to protect themselves.

Resistant Palmer amaranth has a new defense: Amplifying the gene for EPSPS to create multiple copies on different strands of the plant’s DNA. These plants with multiple EPSPS genes can produce enough of the enzyme to bind with and overcome glyphosate, making it ineffective in killing the weed.

“This is something brand new that’s never shown up before in plants,” Burton said. “This plant has so many of these enzymes that they swamp Roundup.”

Burton and his research colleagues are looking at the transcriptome, or RNA, of both resistant and non-resistant Palmer, in hopes of understanding how the plant developed this gene amplification. Jenn Schaff at the North Carolina State Genomic Sciences Laboratory performed the transcriptome sequencing, and Elizabeth Scholl in Plant Pathology performed the initial bioinformatic analysis.

Role of different genes

The researchers are also looking at the role of the different genes: Are there differences in how they control specific biological processes or molecular functions? Are there differences in genes that could be involved in herbicide resistance? The researchers have discovered the resistant and non-resistant Palmer are genetically similar, and 97 to 98 percent of genes in Palmer have been identified in other biological organisms.

Learning more about the mechanism of resistance in Palmer amaranth could help farmers in several ways. One benefit would be developing precise — and, it is hoped, simple — in-field tests that would help growers identify resistant Palmer in their fields.

“What we could do with this information pretty easily would be to develop markers where we could go into a population and determine where there is resistance to different herbicides. One of the reasons why farmers don’t manage their resistance issues, or they haven’t in the past, is they’re not really sure they have a resistance problem. They believe, ‘If it comes to my field, I’ll deal with it.’”

But Burton believes that an in-field test could confirm a grower has herbicide-resistant Palmer. He hopes the information would encourage farmers to respond more quickly in dealing with resistant weeds, potentially slowing the spread of the resistance problem.

Palmer amaranth is native to the Sonoran Desert in the southwestern United States and northwestern Mexico. As a result, it is capable of withstanding drought and temperatures of 95 to 105 degrees F. If genes controlling for drought heat tolerance could be identified and better understood, the genetic material could be incorporated into crops to make them more tolerant of hot, dry conditions that Southeast growers face.

Discovering the keys to Palmer’s relentless adaptability could help scientists use traits to growers’ advantage. Could cotton ever be as productive or as stress tolerant as Palmer amaranth? Burton believes it’s a question worth asking.
The fact that genetic research has become more affordable makes it possible for researchers to take a closer look at genetic composition, like that of Palmer amaranth, and to discover new information that could be used to the advantage of agriculture. “We can learn from this,” Burton said. “It is the start of a more detailed understanding of this rather amazing plant.”