Comparative analysis of the rhizosphere microbiome and transcriptome in clubroot-susceptible and resistant rapeseed (Brassica napus).

Clubroot disease, caused by Plasmodiophora brassica, severely threatens the rapeseed industry in China, with an annual affected area exceeding 667000 hectares. To elucidate the mechanisms in clubroot resistance, we compared the differences in soil physicochemical properties, rhizosphere microbiome, and transcriptomic responses between a susceptible variety, HYZ62 (disease index 54.86), and a resistant variety, HYZ5R (disease index 17.05), following P. brassicae infection. The results showed that the electrical conductivity of HYZ5R (R) was 1.73 and 1.57 times that of HYZ62 (S) in the inoculated and uninoculated treatments, respectively. Compared to the 17.18% decrease in alkali-hydrolysable nitrogen content in HYZ62 (S) after inoculation, its content in HYZ5R (R) showed no significant difference. The rhizosphere microbial community significantly differed between HYZ5R (R) and HYZ62 (S), with HYZ5R (R) exhibiting higher relative abundances of several microbial genera, such as Burkholderia-Caballeronia-Paraburkholderia, Humibacter, Dyella, and Trichoderma. Although Bacillus had a significantly higher relative abundance in the rhizosphere of uninoculated HYZ62 (S), its relative abundance decreased by 30.36% after infection. Transcriptome analysis revealed that, compared to HYZ62 (S), the expression of pattern-triggered immunity-related genes, such as CML, WRKY, and PR1, was higher in HYZ5R (R) and was more strongly induced upon inoculation. Effector-triggered immunity-related genes, such as RIN4, RPS5, and HSP90, were consistently expressed at higher levels. In contrast, HYZ62 (S) showed a broad suppression of defense-related gene expression after inoculation. Furthermore, although P. brassicae infection generally suppressed defense-related secondary metabolic pathways, including phenylpropanoid biosynthesis, the expression levels of multiple genes in this pathway remained higher in HYZ5R (R). Together, these results suggest that the higher relative abundances of specific microbial taxa in the rhizosphere and the high expression of defense-related genes are associated with the clubroot resistance in HYZ5R (R).