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Rapid resistance testing and genomic herbicides

We keep hearing that the next new herbicide is ‘not a silver bullet’ to overcome herbicide resistance. The problem is that resistance is almost inevitable for each new product, and in some cases, weeds are already resistant to a new mode of action before it is released to the market!

Herbicide resistance testing is a critical component of the WeedSmart Big 6 strategy and has helped growers navigate resistance problems in the paddock; however, the lag time between collecting suspect plants and getting the test results suggesting effective options allows the weed seed bank to increase.

Fortunately, genomic researchers worldwide are making significant gains in identifying the genes involved in the various resistance mechanisms in different weeds and developing rapid tests for these genetic markers.

Dr. Todd Gaines is one of the world’s leading scientists in the genomics of herbicide resistance. Dr. Gaines is an Associate Professor based at Colorado State University in Fort Collins, USA and is currently on sabbatical at the Australian Herbicide Resistance Initiative (AHRI).

He says the first step to open the door to genomic solutions to herbicide resistance in the field is to map the genome. Weed scientists have been busy obtaining the genomes of 51 common weed species.

Once the weed’s genome is mapped, researchers look for the specific mechanism responsible for herbicide resistance. Some resistance mechanisms involve a particular target site mutation, and sometimes, the mechanism is related to the regulation of genes in metabolic resistance (e.g. P450s and GSTs).

Once the mechanism is identified, a lateral flow strip test – similar to the rapid antigen test (RAT) for Covid-19 – can detect if a particular protein (enzyme) is present in a plant tissue sample.

“Agronomists in the UK can already buy one of these tests for about £10 to determine if blackgrass has a particular resistance gene and then choose an appropriate herbicide,” says Todd.

This new research frontier is likely to supplement the current herbicide resistance testing process that generally takes several months to grow the seedlings and then observe the response to a range of herbicide options.

Rapid testing will certainly revolutionise current practice and is a stepping stone in genomics research that will likely lead to next-gen herbicides using RNAi technology. This technology uses tiny RNA (RNAi) strands to switch off the resistance mechanism in the weed.

“We first heard about RNAi technology ten years ago when Monsanto researchers developed a process to kill glyphosate-resistant Palmer amaranth weeds using an application of glyphosate plus RNAi,” says Todd. “The applied RNAi strands bound to the RNA in the plant, turning down the production of the EPSPS enzyme, effectively reversing herbicide resistance and making the resistant plant susceptible.”

The sticking point that researchers needed to overcome with RNAi technology is that RNA isn’t very stable in a drum, and uptake by the plant through the leaves is challenging.

The solution may lie in harnessing the power of antisense oligonucleotides, aka ASOs. ASOs are short, synthetic, single-stranded oligodeoxynucleotides that can alter RNA and reduce protein expression. ASOs can have the same effect as RNAi but are much more stable in water so they can be stored and transported in a drum. The plant can more readily take up ASOs, and ASOs are more stable within the plant.

If we know the specific gene or enzyme causing resistance, we can use an ASO to either turn off this resistance or target another enzyme in the weed critical to plant growth.

Genomics is a very promising field of weed control research that is also moving rapidly in managing diseases in plants and humans.

Researchers at the Centre for Crop and Disease Management are working on a project through the ARC Hub for Sustainable Crop Protection to find a novel strategy to help control the pathogen that causes Sclerotinia stem rot in canola and pulses. By using RNA interference (RNAi), the team are designing double-stranded RNA (dsRNA) constructs to target pathogenicity genes, in the hope of applying these dsRNA molecules encapsulated in nanoparticles called BioClay™ to silence these genes. This technique is called spray-induced gene silencing (SIGS) and has potential to be an alternative strategy to managing disease, in a time when fungicide resistance is a growing concern, and the cost of crop protection is increasing.

In medical research, over 20 years of research and clinical trials has resulted in 154 FDA-approved ASO drugs entering the market through to 2023.

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