Time-resolved transcriptome analysis reveals molecular signatures of Fusarium proliferatum DSM106835-induced sudden decline syndrome in date palm (Phoenix dactylifera L.).

The strategic Middle Eastern crop date palm is severely threatened by Fusarium proliferatum DSM106835 (Fp), the fungus causing sudden decline syndrome. To decipher the molecular basis of this interaction, we performed a time-series RNA-seq analysis to elucidate the dynamic transcriptomic responses in date palm roots and shoots to Fp infection at 4, 8, and 16 days post-infection (dpi). Thousands of genes showed altered expression, increasing dramatically over time: 4062 and 2741 differentially expressed genes in roots and shoots, respectively, at 4 dpi, rising to 10 670 and 4781 at 8 dpi, and 19 092 and 8570 by 16 dpi. The infection activated core defense pathways, including pathogen-triggered immunity and effector-triggered immunity, and key responses involved reactive oxygen species accumulation, cell wall remodeling, impaired photosynthesis, and reprogramming of hormone signaling pathways for ethylene, jasmonic acid, abscisic acid, and salicylic acid. Changes occurred in primary and secondary metabolism, covering carbohydrates, amino acids, lipids, and phenylpropanoids. Weighted gene co-expression network analysis identified tissue-specific gene modules and critical hub genes associated with Fp responses. This comprehensive analysis provides novel insights into date palm defense mechanisms against Fp infection. The identified key pathways and genes form a crucial foundation for targeted breeding or biocontrol strategies to enhance resistance against sudden decline syndrome.