Proteomics Integrated with Transcriptomics of Clubroot Resistant and Susceptible Brassica napus in Response to Plasmodiophora brassicae Infection

Clubroot disease, caused by <i>Plasmodiophora brassicae</i>, is a threat to <i>Brassica</i> crops; therefore, understanding of host-resistance is important for developing clubroot-resistant cultivars. Using multi-omics analysis of clubroot-resistant (CR) and -susceptible (CS) near-isogenic lines (NILs) of <i>B. napus</i>, carrying the resistance of turnip (<i>B. rapa</i> var. rapifera), we characterized the host resistance mechanisms. Through proteome analysis, we identified 6626 differentially abundant proteins (DAPs) (2353 in CR-NILs, 4273 in CS-NILs) (<i>q</i> < 0.05), of which 50 in CR- and 62 in CS-NILs were detected across the disease developmental stages. Notable proteins included those involved in reactive oxygen species scavenging (BnaA09T0647200WE)], cell-wall modifications (BnaA04T0244300WE) and glucosinolate biosynthesis (BnaA01T0266700WE) in the CR-NILs. Additionally, disease-resistance proteins like ENHANCED DISEASE RESISTANCE 2-like (BnaA03T0055600WE) and hairpin-induced family protein YLS9 (BnaA08T0237900WE) showed increased abundance in CR-NILs. In contrast, CS-NILs exhibited decreased abundance of defense-related proteins, including proteins containing CUPIN domain (BnaA09T0578800WE) and LACCASE (BnaA02T0019200WE). Integration of proteome data with transcriptome data revealed 33 genes in CR- and 32 in CS-NILs showing a consistent pattern, including the genes related to <i>PLANT INVERTASE/PECTIN METHYLESTERASE INHIBITOR</i> (BnaC04T0003100WE), <i>KELCH MOTIF</i> (BnaC02T0374800WE), <i>LACCASE</i> (BnaA02T0019200WE), and antioxidant-related transcripts [<i>GLUTATHIONE S-TRANSFERASES</i> (BnaA03T0280900WE) and <i>4-HYDROXYPHENYLPYRUVATE DIOXYGENASE</i> (BnaA09T0641500WE)]. Our findings offer valuable new targets for breeding clubroot-resistant <i>B. napus</i>.