Transcriptional Profiling Links LNC_501 to Cucumber Responses to Fusarium Wilt and Reveals Fatty‐Acid‐Metabolism Changes in Host and Pathogen

Fusarium wilt is a devastating soil-borne disease that severely limits cucumber production. However, the roles of long non-coding RNAs (lncRNAs) in cucumber resistance and the transcriptional interplay between cucumber roots and Foc during infection remain poorly understood. Here, we employed dual RNA-seq to simultaneously profile cucumber mRNAs, lncRNAs, and Foc transcripts in the roots of resistant and susceptible cucumber lines during the early stages of infection. Comparative transcriptome analysis revealed extensive transcriptional reprogramming in both host and pathogen and highlighted cell wall-related and fatty acid metabolism-related processes among the major responses associated with the cucumber-Foc interaction. Functional analyses in transgenic cucumber lines further supported LNC_501 as a putative negative regulator associated with resistance to Fusarium wilt. LNC_501 expression was inversely associated with that of a nearby glycine-rich cell wall structural protein gene, CsGRP1.8, and altered LNC_501 expression in transgenic plants was accompanied by opposite changes in CsGRP1.8 transcript abundance, suggesting a possible role for lncRNA-associated cell wall regulation in cucumber defense. In addition, fatty acid metabolism-related genes in both cucumber and Foc exhibited dynamic and host genotype-dependent expression patterns during infection, suggesting that fatty acid metabolism may be an important shared component of the cucumber-Foc interaction. Together, these findings identify LNC_501 as a candidate lncRNA associated with cucumber responses to Fusarium wilt and suggest a possible link between LNC_501, CsGRP1.8, and cell wall-related defense. They also highlight coordinated fatty acid metabolism changes in both cucumber and Foc during infection, providing a framework for future mechanistic studies of host-pathogen interaction.