Balancing selection in Plasmodiophora brassicae and its impact on resistance breakdown.
Gossen, B.D., Sedaghatkish, A., and McDonald, M.R. 2023. Balancing selection in Plasmodiophora brassicae and its impact on resistance breakdown. Clubroot Workshop, September 24, 2023 at the 16th Intern Rapeseed Congress, Sydney, Australia.
Résumé en langage clair
Plasmodiophora brassicae Wor., which causes clubroot of brassica crops, is an obligate Chromist pathogen that can persist in soil for many years as resting spores. Single genes for clubroot resistance often provide almost complete symptom reduction, but there has been rapid breakdown of clubroot resistance, especially when spore concentration in soil is high. The underlying causes of this consistent rapid breakdown have not been studied in detail.
Survival of resting spores over time
Estimates of resting spores in soil are intrinsically highly variable, given the localized nature of most clubroot infestations, which often present as spreading patches of infection. However, the reproducibility of such estimates has improved rapidly, moving from visual counts to PCR, qPCR and most recently ddPCR. Long-term studies of resting spore survival have demonstrated that spore concentration in soil in Canada initially declines quickly, but the decline slows after 2–3 years (type-III survival curve). However, resting spores are quite sensitive to freeze-thaw action, so the decline may be less dramatic in regions with less intense winters.
Whole-genome sequencing / Single-spore sequences
Whole-genome sequencing was used to compare the genotype of collections of P. brassicae (clubs) made before and after a shift in pathotype at two sites in Ontario, Canada that occurred as a response to a change in host or host resistance. At both locations, the genotype of the new, virulent pathotype was very substantially different from that of the initial pathotype, with roughly1/2 of genes containing SNPs that were not detected in the initial population. This supported other studies which indicated that more than one pathotype of P. brassicae could be present in a field population of the pathogen.
Recent collaboration with a team at McGill University to sequence the whole genome from single resting spores of P. brassicae has demonstrated that multiple genotypes, each substantially different from the others, were present in the resting spores from a single clubbed root at a single site. One genotype, presumably the predominant pathotype at the site, was present at a much higher frequency than the other genotypes.
Balancing selection / Conclusions
Balancing section occurs when entire genotypes of an organism are preserved in a population over time, although often at low frequency. This result is not common in nature, but given that an individual Brassica seedling might develop hundreds of simultaneous root hair infections, it shouldn’t be surprising that some avirulent genotypes establish cortical infections and produce resting spores in each root. The observation that multiple genotypes are present in the resting spore population of a single club demonstrates that field populations of P. brassicae are genetically diverse, likely including genotypes adapted to other conditions, other hosts, and even other host genes for resistance. This diversity is certainly connected with the rapid breakdown of single resistance genes when spore populations in soil are high. Genotypes with virulence genes to overcome host resistance are already present in the population and are selected for when a resistant host is grown.