Transcriptomic and genomic analysis highlights the basis of ZYMV tolerance in zucchini

Background: Cucurbita pepo is high susceptible to Zucchini yellow mosaic virus (ZYMV) and the resistance found in several wild species does not provide complete or broad-spectrum resistance. In this study, a source of tolerance introgressed in C. pepo (381e) from C. moschata, in True French (TF) background, was investigated 12 days post inoculation (DPI) at transcriptomic and genomic levels. Results: A comparative RNA-seq experiment on TF (susceptible to ZYMV) and 381e (tolerant to ZYMV), allowed to evaluate 33,000 expressed transcripts and to identify 146 differentially expressed genes (DEGs) in 381e, mainly involved in photosynthesis, transcription, cytoskeleton organization and callose synthesis. By contrast, the susceptible line True French triggered oxidative processes related to response to biotic stimulus, and key regulators of plant virus intercellular movement. Moreover, the genome mapping of transcripts allowed the identification of two chromosome regions rich in SNPs (Single Nucleotide Polymorphisms), putatively introgressed from C. moschata, containing genes exclusively expressed in 381e. Conclusion: The transcriptome reprogramming of 381e ZYMV challenged revealed a globally restoring of cellular activities and a reduced virus movement and replication. Furthermore, genes putatively involved in ZYMV tolerance were detected in C. moschata introgressed genomic regions. Our work provides new insight into the plant virus recovery process and a better understanding of the molecular basis of 381e tolerance.