MULTI-OMICS ANALYSIS SHEDS LIGHT ON HOW SHELF-LIFE OF TOMATO FRUIT IS PROLONGED

Improving fruit quality and storability is crucial to alleviate quantitative as well as qualitative post-harvest losses that occur worldwide, and particularly in developing countries. In this study, we investigated the regulatory networks underlying tomato fruit shelf-life in the landrace Lucariello (LUC) belonging to the so-called 'da serbo' tomatoes. LUC fruits have a regular timing of ripening associated with a prolonged shelf-life of more than 150 days. The physiochemical characterization of LUC fruits is consistent with their shelf-life extension. In particular, the changes in fruit firmness and fresh weight confirmed the delay in fruit softening and withering during post-harvest. We compared by multi-omics analysis fruits at 60 and 150 days of post-harvest to those at an advanced stage of ripening, i.e. red ripe fruits at 8 days after breaker coincident with the harvest. Gene expression was quantified by RNA-seq while epigenomic analysis included the profiling of DNA methylation, small non-coding RNAs, and post-translational modifications of histones. The expression profiles of LUC fruits were compared with those from public dataset of fruits during ripening in the short shelf-life cultivar Ailsa Craig (AC). Principal Component Analysis highlighted that LUC samples at harvest do not cluster with the corresponding stage of AC fruits thereby suggesting an overall delay of over-ripening program in LUC fruits. In particular, the delay appears to be highly correlated with the downregulation of RIPENING INHIBITOR (RIN), encoding a ripening-specific MADS-box transcription factor. RIN, as well as its targets such as PECTATE LYASE (PL), a fruit softening-specific gene, and LoxB, involved in the loss of cellular membrane integrity, showed a significant downregulation during ripening in LUC with respect to AC as observed by Real Time PCR. We argue that the decreased expression of these genes in LUC is an important factor in determining its extended shelf-life, since downregulation of these genes has been shown to result in fruits that are firmer for longer than controls. In order to understand the mechanisms underlying the observed transcriptional changes, an integrated analysis is now being carried out to investigate the regulation of gene expression in relation to epigenetic modulations