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Nucleic acids – a next-gen weed management tool

A rich weed genomic database is foundational to Associate Professor Todd Gaines’ work to identify nucleic acids as a new mode of action for weed control
Photo: Evan Collis

New solutions are being sought in the fight against weeds, can molecular based strategies developed in the medical industry play a role?

Across the globe different weed populations have evolved resistance to 21 of the 31 known herbicide sites of action and to 165 different herbicides.

As an industry we know we place selection pressure on weeds when herbicides are applied which drives these evolutionary changes. We need to cast the net wider to look for not only different modes of action for herbicides but innovative weed management solutions.

Associate Professor Todd Gaines has set his focus on this task. He is a molecular weed scientist from Colorado State University working to identify the molecular and genetic basis of complex herbicide resistance mechanisms utilising next generation sequencing and developing markers for rapid diagnostics. Professor Gaines, at present is spending a 12-month sabbatical at the Australian Herbicide Resistance Initiative (AHRI) at the University of Western Australia.

In fact, he is no stranger to Australia and its cropping systems having previously worked as a post-doctoral scientist with the founder of AHRI Professor Stephen Powles.

“Sabbaticals are valuable opportunities to reflect and take stock of scientific advances and to test these with world leading peers,” Professor Gaines says.

“Having grown up on a farm in Colorado, USA my fundamental science driver is to solve problems for growers to enable them to be more productive and sustainable.”

Australian growers are very efficient and resourceful, managing a range of herbicide resistance issues and leading the development of novel weed management practices like harvest weed seed control.

Director of AHRI, Professor Ken Flower says the core mission of AHRI is strategic and applied research, supported by GRDC investment, to minimise the adverse impact of herbicide resistance and crop weeds on Australian cropping.

Todd Gaines

A sabbatical at AHRI is giving Colorado State University Professor Todd Gaines (right) time to reflect on scientific advances and consolidate future collaborations, here photographed with AHRI director Professor Ken Flower. Photo: Evan Collis

“It has been great to have Todd spend a year immersed with our world-leading scientists. It is not only an opportunity to have an international weed scientist informally review AHR’s operations but an opportunity to build networks and formulate new research ideas. We are particularly focussed on reducing grower’s dependence on herbicides for weed control.”

Professor Gaines’ research interest is in-line with this agenda of AHRI’s; a new form of weed management, the deployment of next-generation RNA targeting technology.

About the technology

“RNA targeting is a cutting-edge technology that could revolutionise the way we manage weeds,” Professor Gaines says

“Instead of using traditional methods like herbicides or genetic modification of crops the approach involves spraying weeds with tiny nucleic acid molecules.”

“It presents a new mode of action for weed control.”

RNA is an important class of nucleic acids similar to DNA. Weed RNA can be targeted using small pieces of RNA or DNA that can shut down protein translation by binding to messenger RNAs in the coding process and inhibit gene function. The technology is being used in medicine for the highly specific therapeutic treatment of diseases with minor side effects.

“RNA targeting is a powerful gene-silencing tool used in functional genomics and expression studies, the process is known as spray-induced gene silencing or SIGS.”

“Weeds would be sprayed with these small nucleic acids reaching traditional chemical control gene targets or new targets within the weed.”

“This means we could either reverse herbicide resistance or completely disrupt weed growth and kill the weeds using a very targeted approach.”

It is a form of personalised weed control.

“The development of SIGS, however, has been slower in weed management than in pest or disease management due to the difficulty of obtaining stable molecules that easily enter plants.”

“Insects can ingest these molecules and nanoclay carriers have proved effective means of delivering the RNA targeting molecules to control fungal diseases such as late blight of potatoes.”

“The technology faces additional challenges for SIGS development for weed control as there is close relatedness between weed and crop species which creates challenges to identify weed-species specific regions of genes to target.”

“To address this, we need to know much more about weed genomes so we can accurately target regions of weed genomes to silence them.”

Producing SIGS at scale and economically is a further challenge,” Professor Gaines says.

Underpinning knowledge and resources

Foundational knowledge and resources are now being developed that can inform the development of SIGS. One such resource is the International Weed Genomics Consortium (IWGC).

The IWCC is a public-private collaboration with the vision to 1) develop genomics resources for major weed species, 2) make the data and analysis tools broadly available, and 3) to foster networking and training for weed scientists to use genomics tools.

“Through the IWGC and collaborating groups, 26 weed species now have high-quality annotated reference genomes,” Professor Gaines says.

“The Consortium provides reference genomes for important weed species and includes some Australian weeds of significance; ryegrass and wild oat.”

The IWGC also hosts a database with other Australian weeds completed by other groups such as downy brome completed by scientists in the USA and wild radish completed by CSIRO. AHRI researcher Associate Professor Qin Yu has also contributed to the IGWC by providing high quality reference genomes for goosegrass, and Johnson grass genome is being sequenced. This work has been done in collaboration with scientists from China and the USA.

“The availability of this genetic resource for weeds provides fundamental science understanding for future research such as the development of SIGS.”

We can also develop and improve rapid, in-field herbicide resistance diagnostics to assist on-farm decision-making and track the development and spread of herbicide resistant weeds.

“Furthermore, we can drive our understanding of herbicide resistance mechanisms to develop strategies to overcome or reverse resistance, whether through herbicide mixtures, RNA-targeting, or chemical inhibitors of herbicide metabolism.”

AHRI resistance gene discovery program led by Dr Yu has been leading pioneering work into novel non-target-site herbicide resistance gene discoveries. Major discoveries include cytochrome P450 endowing multiple herbicide resistance, aldo keto reductases and membrane transporters conferring glyphosate resistance,

Pathway to market

Bringing a new herbicide or pesticide to market is a long and expensive process, requiring rigorous testing and regulation. This process may take 10-12 years.

“Partnerships are key to the development of new products for growers to deploy to manage weeds,” Professor Gaines says.

The major international crop protection businesses Corteva, Syngenta, Bayer and BASF all partner with Colorado State University to underpin the operations of the International Weed Genomics Consortium, with additional support from Crop Life International and the US-based Foundation for Food and Agriculture Research.

“We have been seeking key industry collaborations as we progress from the genomic database work, testing the science and looking further down the pathway to market.”

More information: Todd Gaines, Ken Flower,

International Weed Genomics Consortium

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