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sector_ico_Agrifood_trans Agrifood

Validation of a next generation-based method for virus/viroid detection in propagative tree fruit material

  • Project Leaders: Michael Rott, Nick Ibuki, Travis Banks
  • Institutions: Canadian Food Inspection Agency (CFIA)
  • Budget: $397023
  • Program/Competition: User Partnership Program
  • Genome Centre(s): Genome British Columbia
  • Fiscal Year: 2016
  • Status: Closed

High quality tree fruit production requires plants free of harmful pests and diseases. A statistical overview of the Canadian fruit industry by Agriculture and Agri-Food Canada, estimated that tree fruits in Canada generated $240 M in revenues in 2011, with over 30% ($75M) from British Columbia, second behind Ontario at $108M. Damage caused by viruses and virus-like pathogens can be very serious. Plum pox virus (PPV) is the most economically important disease of stone fruits worldwide. Since 2000, Canada has spent $160M to eradicate PPV. The Canadian Food Inspection Agency (CFIA) Centre for Plant Health (CPH) is responsible for developing and enforcing regulations on the import of propagative plants into the country and requires that this material be free from regulated pests and pathogens. Propagative tree fruit material from unapproved sources takes three years. Though vital, the long time frames can put Canadian growers at a competitive disadvantage with respect to testing new variety imports.

The CFIA Sidney Laboratory has developed a metagenomic approach using next generation sequencing (NGS) and advanced bioinformatics to rapidly identify viruses and viroids from tree fruit samples. This will be a disruptive technology with the potential to reduce testing from years to weeks, speeding up the release process for new, high-value crops. This technology would also enable growers to effectively monitor that 2nd, 3rd and 4th generation propagation material is maintained virus-free through independent fee-for-service laboratories certified by CFIA. This is a critical step for an industry proposed national clean plant program (NCPP).

The main research objectives were 1) to validate the NGS method as an alternative for the detection of viruses infecting tree fruit propagative material; 2) To create a national clean plant repository of virus free tree fruit propagative material based on NGS testing and 3) to demonstrate the effectiveness of NGS testing to improve tree fruit import and audit testing. Objectives 1 and 3 were achieved and objective 2 is well underway. As a result of this project, NGS will be used for the first time in 2022 for the audit testing of Prunus and Malus plants entering Canada by CFIA. The viruses testing program, once validated by end users will shorten the testing timeframe from 3 years to 1 year. To hasten the adoption of the platform, Summerland Varieties Corporation (SVC), the British Columbia Cherry Association (BCCA), CFIA, and Vineland Research Innovation Centre (VRIC), are partnering to propose research into validating the NGS platform.