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Background <p><i>Sclerotinia sclerotiorum</i> is a destructive necrotrophic fungus, that causes stem rot in <i>Brassica napus</i>, 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 <i>B. napus</i> remains poorly understood.</p> Results <p>We conducted an integrative transcriptomic analysis of three resistant and three susceptible <i>B. napus</i> 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 (<i>SFH8</i>), <i>FKBP17</i>, and transcription factors such as <i>HCA2</i>, <i>VAL2</i>, and <i>WRI4</i> could strongly implicated in immune signaling and hormonal pathways.</p> Conclusion <p>Our findings establish AS as a critical and genotype-dependent regulatory layer in <i>B. napus</i> defense against <i>S. sclerotiorum</i>. Linking splicing dynamics with co-expression networks and highlighting key hub regulators can pave the way for improving <i>B. napus</i> resistance in the future.</p>

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

  • 期刊论文

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  • 发表日期：

    2026年1月20日

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  • Sehrish Sarfraz,
  • Sumbal Wahid,
  • Feng Gao,
  • Zetao Bai,
  • Li Qin,
  • Yizhou He,
  • Yuanyuan Zhang,
  • Cong Zhou,
  • Li Xu,
  • Lingyi Zeng,
  • Fan Liu,
  • Lijiang Liu,
  • Chaobo Tong,
  • Meili Xie,
  • Shengyi Liu

摘要

Background

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.

Results

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.

Conclusion

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.