Next gen sequencing fast tracking imported greenlife
A cross-industry horticulture project that has the potential to reduce plant quarantine testing lag times is underway. Faster plant quarantine testing will provide several benefits for plant industries (including nursery stock), such as reduced costs to import plant material from overseas; ability to import more plant varieties to adapt to local environmental conditions; and a rapid and safe release of pest-free plants.
Strengthening Australia’s plant biosecurity system at the border
Having strict biosecurity measures is paramount to stopping exotic pests and diseases from crossing Australia’s borders. A robust biosecurity system is vital for protecting our eight-billion-dollar horticulture industry.
However, Australian growers need access to new plant material for ornamental, landscape, forestry, vegetables, berries, vines and fruit tree producers allowing their crops to remain globally competitive and to keep their businesses profitable. But one of the challenges they face is the time it takes for this material to become available. Currently, new plant material entering Australia can spend up to three years in post-entry quarantine facilities undergoing pathogen testing.
To address this challenge, new technology is being introduced through a project titled MT18005 Improving plant industry access to new genetics through faster and more accurate diagnostics using next generation sequencing. A multi-industry strategic levy investment under the Hort Innovation Citrus, Nursery, Potato – Fresh, Potato – Processing, Raspberry and Blackberry and Table Grape Funds, this project is supporting the adoption of ‘next generation sequencing’ in the screening of imported horticultural plant material in post-entry quarantine facilities. The project team is working closely with industry representatives and the Australian Government to address their needs and lead to policy adoption of the new methodology to accelerate quarantine testing at the border.
Finding genetic information
Leading this project is Associate Professor Roberto Barrero from the Queensland University of Technology (QUT). He explained how next generation sequencing can provide researchers and post-quarantine inspectors with the information they require, particularly in nursery stock.
“In horticultural nursery crops, including ornamental and landscape nursery stock, we are keen to bring new varieties of plants to Australia that can provide benefits to our growers,” Professor Barrero said.
“The new next generation sequencing technology allows us to get information about the genetics of imported greenlife rapidly. Importantly it also allows us to screen for the presence of potential viruses that might be in these plants.
“The technology has the potential to allow plants to move through the quarantine process much more quickly – allowing industry speedier access to new genetic stocks.”
Previous research by the research team has demonstrated the approach’s success and efficiency in testing for viruses, as well as genetic sequences that are related to viruses called viroids, in imported plants. The new Hort Innovation initiative is allowing the research team, in partnership with the Australian Quarantine agency, to conduct large scale trials to optimise a single assay to detect regulated and endemic viruses and viroids of interest to plant industries.
“We learned at the beginning of this collaboration that most of the virus surveillance work was already done by the plants themselves. Plants have immune systems and although they are not as sophisticated as humans’ immune systems, they have the capacity to recognise viruses inside the plant cells and respond to them by chopping their genetic information into small pieces,” he said.
“Next generation sequencing instruments can allow us to look at the information contained in these small pieces.”
The research teams have worked together to develop a strategy where they use computers to reconstruct viruses that might be present in the plants that are being tested.
“Having the opportunity to provide more comprehensive information to importers – and the growers building their businesses around these commodities – can reassure them that they can receive a return on their investment,” Professor Barrero said.
In collaboration with a research team at Agriculture Victoria, next generation sequencing approaches are being actively developed and optimised for the diagnosis of key culturable, fastidious and non-culturable bacteria. Significant progress is being made by a team led by Fiona Constable at AgriBio, La Trobe University. The availability of bacterial next generation sequencing assays will increase the resilience of genetic tests employed to detect exotic bacteria at the border.
Professor Barrero said that establishing next generation sequencing technology will result in tangible benefits for potato growers, including cost-efficiencies and varietal access.
“Next generation sequencing technologies are becoming more and more affordable over time and one direct benefit to growers will be significant import cost savings,” he said.
“Alternatively, imports savings can allow growers to import more plant varieties increasing the possibilities of one or more of these to adapt to Australian conditions.”
Perhaps the most important benefit is that potato growers will have access to new potato plant material at least a year earlier than what they currently do.
“Accelerated access to new genetics will facilitate reaching the market with improved varieties more quickly, and should also increase the industry profitability,” Professor Barrero said.
It is hoped that post-entry quarantine facilities are adopting this technology for routine testing in 2-3 years’ time, according to Professor Barrero.
“It’s a very ambitions timeline to be able to offer this technology for a range of industries. Increasing the plant biosecurity system at the border is critical to prevent entry of a COVID-19-like organism for plant crops.”