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Background   Plasmodiophora brassicae  is a soilborne pathogen of the family Brassicaceae and the causal agent of clubroot disease. In Canada,  P. brassicae  is now one of the most important constraints to canola ( Brassica napus ) production, and is managed mainly by the deployment of resistant cultivars. In recent years, however, new strains of the pathogen have emerged that are capable of overcoming host resistance, posing new challenges for disease management. Despite its economic significance, molecular studies of  P. brassicae  are rare, mainly because this microorganism cannot be cultured outside of its host.    Results  Restriction site-associated DNA sequencing (RADseq) was used to examine the genetic diversity within  P. brassicae  single-spore and field isolates collected from across Canada. The isolates included individuals that were either capable or incapable of causing disease on clubroot resistant canola cultivars. Over 8750 variants were identified through RADseq. Population analysis indicated that most isolates belonged to one of two distinct populations, corresponding with the ability of isolates to cause disease on resistant cultivars. Within each population, there were low levels of genetic diversity. One thousand and fifty of the genetic variants that distinguished the two populations were nonsynonymous, altering the coding sequences of genes.    Conclusion  The application of RADseq revealed two distinct populations of  P. brassicae  in Canada, suggesting multiple introductions of the pathogen into the country. The genetic variation found here will be important for future research and monitoring of the pathogen.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4658-1) contains supplementary material, which is available to authorized users.

Genotyping of Plasmodiophora brassicae reveals the presence of distinct populations