Comparative transcriptome analysis of canola carrying clubroot resistance from ‘Mendel’ or Rutabaga and the development of molecular markers

Clubroot resistance has been introgressed into spring canola from various sources; however, the molecular basis of this using multiple resistances has not yet been investigated. We conducted a comparative transcriptomic study using resistance introgressed from rutabaga (RtR) and winter canola cv. ‘Mendel’ (MdR) and identified ~3500 upregulated genes of which 8–9% genes were involved in primary and secondary metabolic pathways. Treatment of the susceptible plants with trehalose suggested that the modulation of primary metabolism can increase resistance to clubroot. While comparing the DEGs from BnaA08 (RtR) and BnaA03 (MdR), we found that the gene CRF4 could be essential for mediating resistance. We also developed SSR markers from the upregulated genes for use in breeding. •Conducted a comparative transcriptomic study by using canola carrying clubroot resistance located on BnaA03 or BnaA08.•Showed that the primary and secondary metabolic pathways are involved in host defense in response to P. brassicae infection.•Identified the gene CRF4 in canola lines carrying these resistances indicating its possible role in clubroot resistance.•Demonstrated that trehalose may play an important role in elicitation of plant defense.•Developed molecular markers based on differentially expressed genes for use in molecular breeding.