Comparative transcriptomic responses of olive drupes pre-treated with Trichoderma atroviride culture filtrate or Candida oleophila cells during Phytophthora oleae infection in a postharvest scenario

Soft rot of olive drupes caused by Phytophthora oleae is an emerging disease first reported in Italy. In this study, RNA-seq analysis was used to investigate the transcriptional responses of olive drupes to P. oleae . Two biological pre-treatments were also evaluated, consisting of the culture filtrate of the antagonistic filamentous fungus Trichoderma atroviride and a cell suspension of the antagonistic yeast Candida oleophila . Both treatments were applied 24 h before pathogen inoculation. Although complete protection was not achieved, both pre-treatments significantly reduced rot severity in inoculated drupes. Severity of Phytophthora rot was assessed at 24, 72, and 168 hours post inoculation (hpi) using an empirical rating scale. Both biological pre-treatments significantly reduced rot severity, with comparable reductions of 56% for T. atroviride culture filtrate and 52% for C. oleophila cells. At 72 hpi, clear differences in lesion size were observed, and this time point was therefore selected for RNA-seq analysis. A total of 2,307, 1,714, and 1,816 genes were differentially expressed in drupes inoculated with P. oleae alone, pre-treated with T. atroviride culture filtrate and subsequently inoculated with P. oleae , or pre-treated with C. oleophila and subsequently inoculated with P. oleae , respectively, compared with wounded control drupes. Selected RNA-seq-responsive genes were further validated by RT-qPCR at 24, 72, and 168 hpi. The combined RNA-seq and RT-qPCR results indicate that both biological pre-treatments were associated with marked modulation of defense- and stress-related transcriptional responses in olive drupes, while also revealing partially distinct regulatory signatures during P. oleae infection.