Comparative transcriptomic and transcript-based network analyses revealed genotype-specific alternative splicing induced by Sclerotinia sclerotiorum in Brassica napus

Sclerotinia sclerotiorum is a destructive necrotrophic fungus, that causes stem rot in Brassica napus, severely reducing yield worldwide. While host resistance is shaped by complex transcriptional and post-transcriptional regulation, the contribution of alternative splicing (AS) to cultivar-specific resistance in B. napus remains poorly understood. We conducted an integrative transcriptomic analysis of three resistant and three susceptible B. napus cultivars pre- and post-inoculation to characterize genotype-specific AS, gene expression changes, and transcript-based co-expression networks during pathogen infection. A total of 1,176 differentially alternatively spliced (DAS) genes were identified from the comparison between the transcriptomes of the infection-induced (II) and cultivar-related (CR) groups. Surprisingly, we found that 91% of DAS genes were genotype specific, highlighting the strong cultivar dependence of AS responses. Intron retention was the predominant AS event, and ~ 80% of the DAS genes were also differentially expressed, suggesting a complex connection between splicing and expression regulation. Weighted gene co-expression network analysis (WGCNA) based on transcripts identified key modules related to the pathogen response, identifying hub regulators involved in membrane trafficking, transcriptional control, and stress-associated metabolism. Prominent DAS genes such as SEC14-like lipid transfer protein (SFH8), FKBP17, and transcription factors such as HCA2, VAL2, and WRI4 could strongly implicated in immune signaling and hormonal pathways. Our findings establish AS as a critical and genotype-dependent regulatory layer in B. napus defense against S. sclerotiorum. Linking splicing dynamics with co-expression networks and highlighting key hub regulators can pave the way for improving B. napus resistance in the future.