New technology to detect and identify plant diseases

January 2023 | Canadian Food Inspection Agency | by Dr. Sean Li, Khanh Duong and Nathan Buchanan

As international trade increases, a growing number of plant diseases are threatening global agriculture and food security. The Canadian Food Inspection Agency (CFIA) is constantly seeking ways to improve plant health while supporting Canada’s economy.

Early detection and identification of these diseases help the CFIA protect Canada’s crops and the environment while facilitating trade. At the CFIA’s Charlottetown Laboratory, a new online tool called Clasnip combines genetic data and computer science to quickly and accurately identify diseases.

New tools needed to identify potato diseases

Potatoes can be subject to several diseases that cause serious economic harm to farmers by reducing yield. Some of these diseases can be hard to test for. For example:

Bacterial ring rot (Brr) threatens the potato industry across the globe, particularly seed potato production. Canada, the United States and many European countries have zero tolerance for this disease.
Potato blackleg and soft rot are other common bacterial diseases that result in heavy losses for the potato industry.
Similarly, zebra chip disease, caused by Candidatus Liberibactersolanacearum (CLso), has led to major losses in the United States, Mexico, Central America and New Zealand.
Potato virus Y (PVY) is yet another disease of worldwide concern for potato producers that can significantly reduce potato yields. Even a low incidence of PVY can mean that seed lots can’t be certified.

Studying genetic patterns in the DNA of these plant pathogens can help scientists better understand how diseases can impact some plant hosts, but not others. Next-generation sequencing (NGS) – or high-throughput sequencing – has become a fast and cost-effective technique to decode and analyze a large number of DNA sequences. Approaches for identifying microorganisms have evolved rapidly, but many methods are time-consuming, complicated and expensive. This is especially true for bacteria that grow very slowly or cannot be grown in a lab.

Clasnip (www.clasnip.com)

To help solve these issues, scientists at the CFIA’s Charlottetown Laboratory have developed Clasnip, a free, easy-to-use web-based platform for the classification and identification of closely related microorganisms.

Clasnip (or “classification based on snips”) looks at tiny variations in genetic code called single nucleotide polymorphisms (SNPs), also known as snips. There are two main modules:

new sample classification of a sequence by referencing an existing database and
database building

For new sample classifications, users can compare snips with curated, high-quality reference databases. This helps scientists accurately identify pathogens much faster than traditional methods — often within a few seconds! The tool has been used to quickly identify specific genetic signatures and to differentiate species from close relatives for pathogens of concern, including CLso, Brr, potato blackleg, soft rot and PVY.

Users can also build custom databases and evaluate the accuracy of classification using snips, fragments or whole genome sequences. To build a database, users provide folders and subfolders organized by classification groups. Each reference sample is provided in FASTA format, a text-based representation of nucleotide sequences, and added to the appropriate subfolder. Sequences of one gene, multiple genes, or even whole genomes can be added to a database and indexed. Users can then browse database details and statistics on classification performance including snip similarity among groups, probabilities, classification accuracy and reports on misclassified samples.

The importance of Clasnip

Emerging and re-emerging plant diseases pose a significant concern to agriculture and global food security. Using next-generation sequencing technology and bioinformatics tools to detect and identify plant diseases is an important part of the CFIA’s cooperative strategy to protect plant health and support growing global trade. CFIA scientists need tools to quickly and cost-effectively screen samples of high-risk pathogens and closely related microorganisms at the species and subspecies levels.

Thanks to innovators at the CFIA’s Charlottetown Laboratory, Clasnip helps scientists to rapidly detect and identify regulated plant diseases and other pathogens of concern. This helps the CFIA protect Canada’s plant resources and the environment, while supporting economic growth.

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