Portable nanopore sequencing platform for white mold strain detection and resistance breeding
A genomics-based methodology using MinION portable sequencers to detect and characterize Sclerotinia sclerotiorum (white mold) strain variation across Quebec and Ontario. Enables in-field sampling, geotagged isolate collection, and genomic profiling to guide development of genetic resistance in dry bean and other pulse crops threatened by increasing disease pressure.
Overview
White mold, caused by the fungus Sclerotinia sclerotiorum, is one of the most destructive diseases of dry bean and other pulse crops, capable of causing up to 100% yield loss under favorable conditions. With wetter climate patterns expanding across eastern Canada, disease incidence is expected to rise, while control options remain limited. This research delivers a portable, genomics-driven methodology for collecting, sequencing, and characterizing S. sclerotiorum strains directly from field locations. By mapping the genomic variation of the pathogen across a geographic range, the platform provides breeders and pathologists with the foundational intelligence needed to develop pulse cultivars with durable genetic resistance.
Technical specifications
- Field-ready sampling workflow: Geotagged collection of sclerotia from a planned south-to-north longitudinal transect across Quebec and Ontario, creating a structured isolate library with known geographic origin.
- Portable nanopore sequencing: Barcoded amplicon libraries are prepared, purified, and quantified before being run on a MinION nanopore device, enabling sequencing outside of centralized laboratory facilities.
- Comparative genomic analysis: Reads are aligned to the common bean reference genome, followed by assembly, identification of polymorphic regions among isolates, and calculation of a distance matrix to quantify genetic diversity.
- Resistance breeding application: The resulting strain catalog supports dissection of Phaseolus vulgaris white mold resistance QTL and helps breeders target germplasm with enhanced resistance.
- Disease surveillance value: Establishes a baseline methodology for in-field detection of S. sclerotiorum strains that can be deployed to guide genetic resistance strategies across pulse crop hosts.
Technology readiness level
The project is in the early-to-mid research and development phase. A small set of isolates with known contrasting genetic makeup is currently being constructed to validate the approach. Future work will execute the full sampling plan across the two-province transect, perform nanopore sequencing on field-collected sclerotia, and complete the comparative genomic analysis. The methodology is designed to produce a publicly useful strain reference set that downstream breeding programs and disease management initiatives can build upon.
About Pulse Breeding, Genomics and Phenomics Research Laboratory
The Pulse Breeding and Genetics Lab, located within the Department of Plant Science at McGill University, is a research group focused on the genetic improvement of pulse legumes, including common beans, chickpeas, and dry peas. The lab utilizes field data to conduct research in areas such as genomics, quantitative genetics, abiotic stress tolerance, disease resistance, and high-throughput phenotyping. By integrating emerging technologies into agricultural systems, the team aims to develop superior cultivars that enhance yield, quality, and nutritional profiles for sustainable production. Their work combines fundamental research with applied plant breeding to generate new knowledge and drive agricultural innovation.
This research is critical for supporting the pulse industry, farmers, and end-users by providing solutions that improve productivity and sustainability in Quebec, Canada, and internationally. The lab engages in collaborative efforts with the private and public sectors, offering opportunities for industrial partners to leverage their expertise and equipment for accelerated product development and R&D. Furthermore, the laboratory plays a significant role in education by training MS and PhD students in the fields of plant breeding and genetics, ensuring the development of scientific leadership to advance global food security and nutrition.
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