DPIRD project harnesses the power of genome sequencing in WA crops

The Department of Primary Industries and Regional Development (DPIRD) study, which was granted $73,271 over two years from the Council of Grain Grower Organisations, is the first of its kind in Australian broadacre research and represents a new way of thinking by utilising technology which allows for the rapid obtaining of the RNA or DNA sequence of an organism.

That genetic information gives researchers the ability to precisely diagnose pests and diseases and provides a powerful capacity to understand them in a way that was not possible in the pre-genome sequencing era.

DPIRD research scientist Ben Congdon said genome sequencing had revolutionised science by giving researchers access to the code of life and had been evolving at a breathtaking pace over the past decade.

"The first human genome cost about $1 billion, but now it costs less than $1000 and continues to get cheaper - a human genome is millions of times larger than the average virus so the cost to sequence virus genomes is even faster and cheaper," Dr Congdon said.

"Now that genome sequencing is no longer cost-prohibitive to agricultural research, its extraordinary power can be leveraged to open up novel avenues for its use.

"The crop diagnostic and surveillance approach to be developed in this study will mark the first of its kind in Western Australia and act as a template for other pathogen groups."

Since the advent of serological and molecular techniques for detecting plant viruses, surveillance has involved taking a representative sample from the affected crop (usually 100 leaves), breaking the sample up in groups of two to 10 and testing them for a handful of known possible disease-causing viruses.

Depending on the crop and the viruses that are known to infect it, sometimes multiple different diagnostic platforms such as PCR (molecular) and ELISA (serological) are needed, each with their own unique leaf extraction, set of consumables and technical skill requirements.

Testing a single sub-sample with one of these tests is referred to as a 'reaction' hereafter.

As an example, Dr Congdon said pulse crops in WA were known to be affected by at least six different genetically diverse viruses that have a lot of overlapping symptoms.

"When 100 samples are sent in from a pulse crop, they are divided into sub-samples, usually 10 groups of 10 leaves, and tested for six different viruses which means a total of 60 reactions are needed to assess the presence and incidence of the six common viruses," he said.

"In many cases the crop is negative for all but one of these viruses and so significant resources - time and money on consumables - are expended in this process of elimination.

"Furthermore, due to their virus-specific, and sometimes strain-specific nature, these tests will miss genetic variants or unknown strains of the common viruses and unexpected or novel, sometimes biosecurity threats, disease-causing viruses."

Through its project, DPIRD aims to develop a completely new way of conducting crop diagnosis and surveillance using cutting edge genome sequencing technology - the Illumina MiSeq.

For this approach, using the previous example, all 100 samples from the single pulse crop are tested in one reaction which represents dramatic savings in time and money.

It also provides assumption-free detection of viruses and other micro-organisms in the crops so that genetic variants, new strains and new viruses are detected.

"Furthermore, beneficial viruses - potential candidates as biostimulant and biodefense agents - can be detected, whereas they would not even be looked for using the traditional method," Dr Congdon said.

"If samples are negative, no more money need be spent breaking the 100 leaves into sub-samples and testing for the specific viruses.

"If samples come up positive, follow-up sub-sampling and testing of the specific viruses detected to obtain a per cent incidence estimation can be achieved in a far more efficient manner."

Overall, the goal is to develop a new protocol utilising high-throughput genome sequencing technology for comprehensive and unbiased plant virus detection in a single bulk sample per crop.

Ultimately that level of detection provides many benefits to farmers in WA and around the world.

Firstly, it will lead to reduced costs and turnaround time to get a crop tested.

That will substantially reduce consumable costs and time associated with crop diagnostics and disease surveillance, especially given follow-up testing is targeted and efficient, meaning less money is wasted on testing for viruses that are absent.

It will also allow for more comprehensive testing power as it will provide an order of magnitude more information on the pathogenic microorganisms present.

For example, detection of unexpected viruses, virulent strains, resistance breaking strains and genetic variants not detected by specific PCR tests, providing a vital real-time update to the PCR test.

Dr Congdon said other benefits included identifying potential biosecurity incursions that begin at low incidences in a crop, as well as wide-scale applicability to other organism groups such as fungi, bacteria and arthropod pests.

"It will also provide capacity to find symbiotic virus species that offer potential as biostimulants or biocontrol agents for pests and diseases, such as endornaviruses, that increase plant vigour, immune system and subsequent yield," he said.

"Lastly, it will allow us to monitor the evolution of existing plant viruses within a system through surveillance and tracking of mutations and new strain development or incursion over time."

The initial project is for two-years with results expected to be extended to industry by the end of 2023.

Moving forward beyond the initial project, it's hoped the method could provide a proof-of-concept template for similar surveillance of beneficial and pathogenic species of bacteria, nematodes, phytoplasma and fungi, as well as beneficial and pest species of arthropods and the symbiotic or pathogenic microorganisms inside them.

Ultimately that would provide an opportunity to identify biocontrol agents for some of the most notorious arthropod pests which are developing pesticide resistance, or which will become difficult to control in the face of looming bans to certain pesticide groups.

Want weekly news highlights delivered to your inbox? Sign up to the Farm Weekly newsletter.