A Multi-Omics approach to get insights into fruit senescence regulatory networks in a tomato landrace with long shelf-life.

A better understanding of regulatory networks underlying fruit senescence would greatly impact on fruit quality and storability. Tomato (Solanum lycopersicum L.) is currently the best model for studying ripening process in climacteric fleshy fruit. However, the boundary between fruit ripening and senescence is still unclear. The Italian landrace Lucariello (LUC), recognized as 'Pomodorino del Piennolo del Vesuvio', is characterized by a long shelf-life reaching more than 150 days after harvest, thus it represents an excellent model to investigate the relationship between ripening and senescence and a genetic resource to transfer its long shelflife to other cultivars. For a full characterization of Lucariello, a multi-omics approach was followed, in which the genome was resequenced, assembled and annotated. In addition, coding and non-coding RNAs, DNA methylation, and histone post-translational modifications (H3K4me3, H3K27me3, H3K9K14ac) were analysed in fruit pericarps at the red ripe stage, 60 and 150 days in post-harvest (dph). More than 10,000 genes were found to be differentially expressed across the time points and many were related to transcription factors and to fruit ripening. About 2,000 putative miRNAs were predicted as anti-correlated to DEG targets. Differentially enriched regions for H3K4me3, H3K27me3, H3K9K14ac and differentially methylated regions were identified around the transcription start site and correlated with gene expression. An integrated analysis is now being carried out to find activator and/or repressor candidates regulating senescence process in tomato fruits. All the genomic and epigenomic datasets are gathered into a dedicated and user-friendly web-based platform.