Multi-omics profiling elucidates defense-related pathways and metabolites against clubroot in Chinese cabbage

Clubroot disease, caused by Plasmodiophora brassicae Woronin, leads to substantial yield losses in Brassica crops worldwide, including Chinese cabbage. Nevertheless, the molecular mechanisms underlying host defense responses remain poorly understood. In this study, we assessed clubroot resistance by comparing the resistant line 'CR Jingqiu Xinsanhao' (JQX3) with the susceptible cultivar 'Zhongbai 76' (ZB76) through histological analysis of root tissues and monitoring of disease progression in pot trials. Integrated transcriptomic and metabolomic approaches were employed to characterize the defense mechanisms of JQX3 against P. brassicae infection. Marked metabolic reprogramming was detected during both the primary (3 days after inoculation, DAI) and secondary (10 DAI) infection stages. Four pathways—tyrosine metabolism, phenylpropanoid biosynthesis, valine, leucine and isoleucine biosynthesis, and glucosinolate biosynthesis—were significantly enriched at both time points. Notably, differential expression of key enzymatic genes and accumulation of intermediates in the lignin biosynthesis pathway underscored the importance of lignification in the JQX3–P. brassicae interaction. Furthermore, the intermediates p-coumaric acid and coniferaldehyde markedly inhibited P. brassicae spore germination, demonstrating their direct antifungal activity and potential as natural agents for disease control. These findings elucidate key defense-related pathways in Chinese cabbage and offer valuable insights for the development of sustainable clubroot management strategies. Overall design: RNA-seq profiling of JQX samples at 0 DAI (CK), 3 DAI and 10 DAI.