Skip to main content
GrowersHelp your business growResearch reports, publications, fact sheets and more Improving plant industry access to new genetics through faster and more accurate diagnostics using next generation sequencing (MT18005)
Ongoing project

Improving plant industry access to new genetics through faster and more accurate diagnostics using next generation sequencing (MT18005)

Key research provider: Queensland University of Technology

What’s it all about?

This investment is tasked with supporting the adoption of ‘next generation sequencing’ in the screening of imported horticultural plant material in post-entry quarantine facilities. 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.

Currently, new plant material entering Australia can spend up to three years in post-entry quarantine facilities undergoing pathogen testing. Next generation sequencing offers a fast, reliable and cost-effective method to identify all known plant pathogens in a single test.

Previous research has demonstrated the approach’s success and efficiency in testing for viruses and viroids in imported plants, with next generation sequencing subsequently being adopted in the testing of imported ornamental grasses. This investment will provide the evidence and protocols needed for the technology to be adopted for further plant commodities, including horticulture crops.

Over the last six months, a large-scale quarantine screening of plant samples was completed using high throughput sequencing technology (HTS) yielding accurate and reproducible detections of plant viruses and viroids. A novel open-access tool, named VirReport, has been implemented to enable HTS testing using diverse compute resources. An IT infrastructure is underway to support the routine HTS testing at Post Entry Quarantine (PEQ) facilities. Additionally, progress has been made to advance the policy adoption of HTS by the end of 2022.

A novel approach that specifically detects signals from selected fastidious bacteria shows promise to use HTS as an accurate method for the identification of fastidious bacteria, particularly Candidatus Liberibacter and Xylella species. Lessons learned are informing strategies to continue to improve the design and use of HTS approaches for bacterial pathogen diagnosis.

Over the last reporting period, the team conducted large-scale side-by-side comparisons of nearly 200 plants using Post Entry Quarantine (PEQ) and small RNA-seq high throughput sequencing (HTS) methods. Results showed both approaches identified the same regulated and endemic viruses across several plant commodities.

Additionally, the HTS method flagged the presence of exotic viruses in commodities where these are not regulated, providing the opportunity extend the information available for decision making.

A policy framework and guidelines for using HTS technologies in diagnosing viruses and viroids is being developed, based on project outcomes.

The team also implemented a Next Generation Sequencing (NGS) protocol for fastidious and non-culturable bacteria, comparing this with existing diagnostic platforms.

A novel probe-based DNA enrichment strategy showed potential for bacterial pathogen detection. Engagement with PEQ will enable further validation and improvements for this approach.


This project is a multi-industry strategic levy investment in the Hort Innovation Citrus, Nursery, Potato - Fresh, Potato - Processing, Raspberry and Blackberry and Table Grape Funds