Objective
To develop and implement genomics-based diagnostic tools for the identification of key Plasmodiophora brassicae pathotypes, supporting enhanced surveillance, improved clubroot management, and better integration with current phenotypic classification systems.
Project Description
Clubroot is a major threat to crop production in Canada, resulting in significant economic losses. The most effective management strategy to date has been the deployment of clubroot-resistant (CR) canola cultivars. Currently, P. brassicae isolates are classified into pathotypes based on their virulence phenotypes on the Canadian Clubroot Differential (CCD) set. While effective, this system is labor-intensive and time-consuming, requiring access to biosecure greenhouse facilities and up to eight weeks to complete. These limitations constrain the number of samples that can be processed annually and delay timely management decisions. The repeated use of CR cultivars has also driven shifts in the virulence of P. brassicae populations, leading to increased prevalence of rare pathotypes and the emergence of new strains capable of overcoming resistance. For example,
only four years after the release of first-generation CR cultivars in 2009, resistance-breaking pathotypes were detected in Alberta. The rapid diversification of P. brassicae populations underscores the need for enhanced surveillance methods, particularly scalable, high-throughput diagnostic tools capable of testing both plant roots and soil samples. Moreover, because symptom-based pathotyping requires substantial greenhouse space and long processing times, it is difficult to provide as a routine service through commercial diagnostic laboratories. Thus, a key research priority is the development of genomics-based molecular diagnostics for pathotype identification. Such tools could complement host differential sets such as the CCD, providing actionable information through the early detection of pathotypes. Our research group has contributed to this area by developing PCR-based tools for molecular diagnostics, including rhPCR and SNaPshot assays. These approaches have enabled the identification of two major pathotype clusters, each comprising multiple pathotypes that are closely related at the sequence level. We also performed variant calling on 45 P. brassicae isolates representing 13 pathotypes, identifying polymorphic regions, including single-nucleotide polymorphisms (SNPs) and structural variants (SVs), which support the two major genetic clusters and suggest recombination within populations. In parallel, we generated high-quality de novo genome assemblies for seven single-spore isolates and constructed the first P. brassicae pangenome. This resource includes complete genomes for pathotypes relevant to the Canadian Prairies, including non-resistance-breaking (3H, 6C) as well as resistance-breaking types (2A, 3A, 4A, 5X, 6B).
Developed under the recently completed Project 2022F110R, co-funded by Alberta Canola, RDAR, and the WGRF, these genomic resources provide a strong foundation for SNP-based assays with applications in pathotype identification. However, the discovery of these polymorphic regions has not yet been translated into practical diagnostic tools, as broader testing across multiple isolates is still required and scalable, high-throughput platforms remain to be developed. The current proposal builds directly on these outcomes by focusing on the validation of candidate SNPs and, more
importantly, the development and implementation of diagnostic tools for industry use. Concurrently, the Strelkov lab is working with the Clubroot Steering Committee and partners to refine the CCD set. Integrating genomic data with phenotypic refinement will help ensure that the CCD set more accurately reflects the diversity and relationships among P. brassicae pathotypes, since current genomic analyses have not fully reproduced the same pathotype groupings observed through virulence phenotyping. Strengthening the alignment between genotype and phenotype will support more effective marker discovery and validation, particularly for differentiating key pathotypes capable of overcoming resistance. It will also reduce identification time from several weeks to just a few days. Complementing this effort, our Project 2025F3620R, jointly funded by Alberta Canola, RDAR, and SaskOilseeds, is expanding genomic knowledge of clubroot by improving available genome assemblies and sequencing additional isolates to investigate the genetic mechanisms driving the emergence of new virulent pathotypes. While that initiative focuses on understanding how pathotype diversity arises and strengthening the Canadian P. brassicae genome database, the current proposal emphasizes translating genomic discoveries into practical, scalable diagnostic tools while directly supporting refinement of the CCD set.
