Transcriptome analysis of three olive cultivars to investigate the molecular response to Xylella fastidiosa infection

Over the past decade, the spread of the bacterium Xylella fastidiosa subsp. pauca, the causal agent of olive quick decline syndrome (OQDS), has profoundly altered the agriculture and landscape heritage of the Salento area in Apulia, Southern Italy. Despite significant efforts to control and contain the disease, OQDS has not yet been successfully managed. Therefore, a comprehensive understanding of the molecular mechanism underlying the plant’s response to the pathogen is essential. With the aim to investigate the pathways potentially involved in the response to Xylella fastidiosa and identify candidate resistance genes, we performed a comparative transcriptome analysis of three olive cultivars with diverse levels of susceptibility to the pathogen: ‘Leccino’ (resistant), ‘Donna Francesca’ (putatively tolerant), and ‘Oliva Rossa’ (susceptible). The plants were grown in a certified greenhouse at DiSSPA (University of Bari), and, for each cultivar, three biological replicates of both mock-inoculated and infected plants were analyzed. The total RNA was extracted from leaf and petiole tissues using a commercial kit and the RNA-seq libraries were generated and sequenced on the Illumina Novaseq 6000 platform. Data analysis revealed a complex gene expression pattern with more than 800 differentially expressed genes, including several defense-related genes. A subset of candidate genes, identified among those differentially expressed in the three cultivars, were validated by RT-qPCR and further investigated.