Background Clubroot is an important disease of brassica crops world-wide. The causal agent, Plasmodiophora brassicae, has been present in Canada for over a century but was first identified on canola (Brassica napus) in Alberta, Canada in 2003. Genetic resistance to clubroot in an adapted canola cultivar has been available since 2009, but resistance breakdown was detected in 2013 and new pathotypes are increasing rapidly. Information on genetic similarity among pathogen populations across Canada could be useful in estimating the genetic variation in pathogen populations, predicting the effect of subsequent selection pressure on changes in the pathogen population over time, and even in identifying the origin of the initial pathogen introduction to canola in Alberta. Results The genomic sequences of 43 strains (34 field collections, 9 single-spore isolates) of P. brassicae from Canada, the United States, and China clustered into five clades based on SNP similarity. The strains from Canada separated into four clades, with two containing mostly strains from the Prairies (provinces of Alberta, Saskatchewan, and Manitoba) and two that were mostly from the rest of Canada or the USA. Several strains from China formed a separate clade. More than one pathotype and host were present in all four Canadian clades. The initial pathotypes from canola on the Prairies clustered separately from the pathotypes on canola that could overcome resistance to the initial pathotypes. Similarly, at one site in central Canada where resistance had broken down, about half of the genes differed (based on SNPs) between strains before and after the breakdown. Conclusion Clustering based on genome-wide DNA sequencing demonstrated that the initial pathotypes on canola on the Prairies clustered separately from the new virulent pathotypes on the Prairies. Analysis indicated that these ‘new’ pathotypes were likely present in the pathogen population at very low frequency, maintained through balancing selection, and increased rapidly in response to selection from repeated exposure to host resistance.

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Clubroot, caused by Plasmodiophora brassicae, dramatically reduces yields of brassica crops, and once present in a field, can persist in the soil for many years via long‐lived resting spores. Some nonhost crops can stimulate the germination of resting spores, which reduces clubroot inoculum because the pathogen cannot complete its life cycle in the absence of a living host. The effect of selected grasses and other field crops on the concentrations of spores in soil was assessed in two replicated and repeated short‐duration (8‐week) studies under controlled conditions. The spore concentration declined precipitously in the bare soil control relative to the initial spore concentration over the course of both studies. Cultivars of meadow bromegrass, smooth bromegrass and one cultivar of perennial ryegrass reduced the spore concentration compared to the bare soil control in both repetitions of one study, while two cultivars of perennial ryegrass did not reduce the spore concentration. In a second study, spring wheat, perennial ryegrass, barley and field pea reduced spores compared to the bare soil control, but soybean did not. Our hypothesis that larger root systems would produce larger reductions in spore numbers was not supported; there was no correlation between root weight and reduction in spore concentration. We conclude that perennial grasses, spring cereals and field pea can contribute to the reduction of clubroot spores in soil. The advantage of grass crops over annual crops for clubroot management is that movement of infested soil is minimized over the entire duration of the grass stand.

A Basidiomycete endomycorrhizal fungus, Piriformospora indica, colonizes and promotes the growth of canola and other Brassica crops, and can reduce diseases of other crops. Clubroot is an important disease of Bbrassica crops caused by the obligate, soil-borne pathogen Plasmodiophora brassicae. The effect of P. indica on clubroot severity in canola was assessed in replicated growth room studies. Seed was treated with P. indica using a proprietary process. Microscopic observation confirmed that canola roots grown from treated seed were colonized by P. indica. However, P. indica did not consistently reduce clubroot severity and did not promote the growth of canola.