RAT testing weeds for resistance and spraying them with next generation herbicides

Written by: Peter Newman

Let’s face it, COVID sucked!

But it wasn’t all bad, we did learn a few things from the experience, such as:

How to do a RAT test,

How to use a QR code,

How to maintain good personal hygiene in the absence of toilet paper,

And the names of the state premiers of Australia.

What if we could use something like a RAT test in the field to test for herbicide resistance?

We already can! Just crush up some leaves, stick in the RAT test and voila. Resistance results in 10 minutes.

Then imagine if, by knowing the exact enzymes that exist, we then spray the weeds with next-generation herbicides that are actually tiny strands of RNA that bind to RNA in the plant and switch off the production of the enzyme, reversing the resistance and enabling the herbicide to work again.

One day, these strands of RNA may even be herbicides in their own right, that don’t reverse the resistance, but actually wipe out specific enzymes in the plant, and kill the plant outright.

Now that COVID has settled down, we’re back to having visiting scientists at AHRI, such as Associate Professor, Dr. Todd Gaines who is currently spending a year with us. Todd is an old friend of AHRI, and is famous for creating the dimmer switch analogy that helps luddites like me attempt to understand the complex world of genomics in which he works. Todd recently gave a seminar at AHRI that summarised this crazy world of genomics and the use of new technology such as RNAi or ASO’s.

Will the global effort into understanding herbicide resistance at a genetic level one day lead to the next generation of herbicides, the possibilities of which are endless?

AHRI Insight regularly features research from the team on the genes involved in herbicide resistance. Sometimes it’s hard to know if this is merely defining the problem, or if this research will ultimately lead to the development of new solutions to controlling herbicide-resistant weeds.

This edition of AHRI Insight will show you that this basic research will soon be critical in developing new solutions for crop protection.

Dr. Todd Gaines is one of the world leading scientists in the field of the genomics of herbicide resistance. Todd is based at Colorado State University in Fort Collins, USA. Todd gave us a mind-bending presentation in April this year that summarised both his work, and the work of many colleagues around the world.

I’m going to share with you a few highlights.

1. Describing the Genome

You’ve heard of scientists describing the human genome.

Well, the weed scientists of the world have been busy describing the genome of our common weed species. 51 species in fact!

2. Finding the markers for resistance

As you’ve read in many AHRI insights in the past, our researchers and many other researchers around the world have been finding the specific mutations that are responsible for herbicide resistance. Sometimes this is describing a particular target site mutation, and more recently there has been a global effort to understand the genes, and regulation of genes in metabolic resistance (e.g., P450’s and GST’s).

3. The weed RAT test

A Rapid Antigen Test (RAT)

I know calling it a RAT test is saying that it’s a “test test”, but you know what I mean.

A RAT test is actually a lateral flow strip test. They can detect if a particular protein (enzyme) is present.

Agros in the UK can already buy one of these for 10 quid to determine if blackgrass has a particular resistance gene and then choose an appropriate herbicide.


This is where this basic research that has been going on for years now is going to pay off. We will ultimately be able to quickly test our weeds in the field, and within 10 minutes get an answer as to the resistance genes present and therefore which herbicides will still work.

For more info on how the lateral flow assay for resistance testing in blackgrass works, click here.

4. Next gen herbicides – RNAi

This is where the story gets really crazy.

We first heard about RNAi technology 10 years ago. Monsanto researchers worked out how to make glyphosate resistant palmer amaranth susceptible to glyphosate by switching off the resistance by spraying tiny strands of RNA. This RNA bound to the RNA in the plant, turning down the production of the EPSPS enzyme. Spraying glyphosate plus RNAi killed the resistant weeds.

But, the problem with RNAi technology is that RNA isn’t very stable in a drum and uptake by the plant through the leaves is challenging.

RNAi is a great idea, but it hasn’t quite made the big time yet.


5. Enter the ASO’s

Here’s a big word for you, bigger than wheelbarrow even!

antisense oligonucleotides, aka ASO’s.

ASO’s are kind of like the next generation of RNAi. They work in a similar way, but ASO’s are much more stable in water, so they can be stored and transported in a drum.

And, they have improved uptake by the plant, and are more stable within the plant.

If we know the specific gene or enzyme that is causing resistance, we can either use an ASO to turn off this resistance,


We can target another enzyme in the plant altogether that is critical to plant growth, and create an ASO that is a herbicide itself.

There are already four FDA approved drugs in the USA using this technology. It’s not just about weeds!


Picture this

This may sound a bit sci fi, but can you imagine a day in the future where our agronomists RAT test our weeds, then choose an ASO herbicide that is specifically designed to control that weed because we not only know the genome of the weed, we know the specific herbicide resistance mutations it contains.


There you have it. When we start out in basic research, sometimes we don’t know where it’s going to end up. We’re not there yet, but this is an amazing story of how the weeds researchers and molecular biologists of the world are working together to take the world of herbicide development to a whole new level.

Thanks for explaining these complicated ideas to us, Todd. We’re lucky to have people like you and many colleagues around the world working to solve the problems of tomorrow.


Check out Dr. Todd Gaines’ recent research paper, titled The International Weed Genomics Consortium: Community Resources for Weed Genomics Research.

More information

Want to learn more about Associate Professor Todd Gaines’ research?

Watch his seminar below, titled “Harnessing genomics to improve weed management”, or listen to our podcast interview with Todd.

Posted in: AHRI Insight, Gene discovery for herbicide resistance

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