Developing disease-resistant oysters to meet an imminent threat to Eastern Canada’s industry

A deadly disease-causing parasite threatens Atlantic oysters. A genomics-based breeding program will develop MSX-resistant oysters—protecting coastal jobs, food security and a multimillion-dollar industry.

Cultured and wild oysters are a significant contributor to the economies of Eastern Canada and a potent tourist symbol of the region. Yet this natural wealth is threatened by a pathogen for which there is no treatment, that is spreading through the region, and is expected to cause 95 per cent mortality within the next two–three years.  

Multinucleate sphere unknown (MSX) is a disease of American and Pacific cupped oysters caused by the parasite Haplosporidium nelsoni. First detected in Canada in Cape Breton, NS in 2002, MSX was found last summer in oysters in Bedeque Bay, PEI and has spread throughout that province. Now, the Canadian Food Inspection Agency has declared all of PEI an infected area for MSX, and experts anticipate an imminent collapse of the entire oyster industry in Eastern Canada if growers are unable to maintain viable production.

Since 2019, Genome Canada (through Genome Atlantic and Génome Québec) has funded a collaboration between researchers at Université Laval and L’Étang Ruisseau Bar Ltée (ERB)/Mallet Oysters, in Shippagan, NB—the largest shellfish hatchery and supplier of oyster seed in the region—to use genomics to improve the growth, quality and disease-resistance of farmed oysters. In May 2025, Genome Canada announced a new environmental DNA (“eDNA”) surveillance project that will develop a tool to help predict the potential impact of MSX and Dermo parasites, and provide early warning of their spread—enabling more effective mitigation measures.

A rapid response to this threat hinges on ERB’s breeding program, which could allow selective breeding for MSX resistance. With additional investment from Genome Canada, ERB and the scientists at Université Laval, led by Jean-Sébastien Moore, PhD, will identify genetic variation linked to MSX-resistance and using genomic selection to rapidly develop and commercialize the first MSX-resistant oysters in Canada. The goal is to outpace the spread of the disease.

The researchers will identify resistance-linked genetic variation in the ERB breeding population using a pangenome-wide association study. Such studies analyze the genetic diversity of many individuals to identify genomic regions that co-vary specific traits, like disease resistance. These full genome approaches are costly and time-consuming, so an important goal of the project is then to use these genomic data to develop a new low-density single-nucleotide polymorphism (SNP) panel specific for MSX resistance. Combined with previously developed SNP panels targeting production-related traits, this new panel will provide a complementary tool to select simultaneously for increased performance and resistance.  

The availability of MSX-resistant oysters will have significant benefits to ERB and help protect its business. The entire industry in the provinces of Eastern Canada (QC, NB, PEI, NS, NL) will also benefit from access to resistant seed to maintain production in the face of high disease pressure. ERB’s location in northern NB is key, since the ERB hatchery will likely be one of the last areas to be affected by MSX and will be able to continue supplying the region with oyster seed.

Since MSX resistance will be directly incorporated into an existing commercial product with strong sales and a consistent customer base, the pathway to commercialization and implementation is direct and straightforward. This investment is an opportunity to mitigate widespread impacts while fostering Canadian innovation.