Proteomics Integrated with Transcriptomics of Clubroot Resistant and Susceptible

Clubroot disease, caused by Plasmodiophora brassicae, is a threat to Brassica 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 B. napus, carrying the resistance of turnip (B. rapa 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) (q < 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 PLANT INVERTASE/PECTIN METHYLESTERASE INHIBITOR (BnaC04T0003100WE), KELCH MOTIF (BnaC02T0374800WE), LACCASE (BnaA02T0019200WE), and antioxidant-related transcripts [GLUTATHIONE S-TRANSFERASES (BnaA03T0280900WE) and 4-HYDROXYPHENYLPYRUVATE DIOXYGENASE (BnaA09T0641500WE)]. Our findings offer valuable new targets for breeding clubroot-resistant B. napus.