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Abstract: Tomato fruit ripening is triggered by the demethylation of key genes, which alters their transcriptional levels thereby initiating and propagating a cascade of physiological events. What is unknown, is how these processes are altered when fruit are ripened using postharvest practices to extend shelf-life, as these practices often reduce fruit quality. To address this, postharvest handling-induced changes in the fruit DNA methylome and transcriptome, and how they correlate with ripening speed, and ripening indicators such as ethylene, ABA, and carotenoids, were assessed. This study comprehensively connected changes in physiological events with dynamic molecular changes. Ripening fruit that reached ‘Turning’ (T) after dark-storage at 20°C, 12.5°C, or 5°C chilling (followed by 20°C rewarming), were compared to fresh-harvest fruit ‘FHT’. Fruit stored at 12.5°C, had the biggest epigenetic marks and alterations in gene expression, exceeding changes induced by postharvest chilling. Fruit physiological and chronological age were uncoupled at 12.5°C, as the time-to-ripening was the longest. Fruit ripening to Turning at 12.5°C was not climacteric; there was no respiratory or ethylene burst, rather, fruit were high in ABA. Clear differentiation between postharvest-ripened and ‘FHT’ was evident in the methylome and transcriptome. Higher expression of photosynthetic genes and chlorophyll levels in ‘FHT’ fruit, pointed to light as influencing the molecular changes in fruit ripening. Finally, correlative analyses of the -omics data putatively identified genes regulated by DNA methylation. Collectively, these data improve our interpretation of how tomato fruit ripening patterns are altered by postharvest practices, and long-term are expected to help improve fruit quality.

Postharvest chilling injury (PCI) is a physiological disorder that contributes to the global loss and waste of fruit and vegetables. Ectopic expression of C-Repeat Binding Factor (CBF) transcription factors in tomato (Solanum lycopersicum L.) alleviates vegetative chilling injury, but their influence on PCI is unknown. We developed a dexamethasone (DEX)-inducible system with the aim of limiting high ectopic expression of Arabidopsis thaliana CBF1 (AtCBF1) to fruit, and only during postharvest chilling. Our aim was (1) to optimize the DEX-inducible system for high AtCBF1 expression in the organ and conditions of interest, i.e., fruit postharvest cold storage, and (2) to determine if AtCBF1 could lessen PCI symptoms. Here, we describe the testing and validation of transformed lines from this system. In all tests, fruit were stored under PCI-inducing or non-PCI-inducing conditions. Across storage time, fruit immersion in 50 μM DEX for one hour prior to 2.5 °C storage or rewarming, induced AtCBF1 expression 11- to 91-fold (mean: 33-fold, median: 29-fold), significantly higher than the 0.2- to 3.2-fold (mean: 1.5-fold, median: 1.3-fold) without DEX. Fruit color, surface pitting and decay incidence were used to indicate PCI. For genotype OE-8, PCI symptoms lessened during cold storage without DEX application compared to the wild-type. For line OE-2, DEX led to riper fruit at both 2.5 and 12.5 °C, while PCI-like symptoms developed under control temperatures (12.5 °C), after rewarming. In OE-6 fruit, DEX elicited a mild increase in the rate of ripening during the first week of cold storage compared to the wild-type. Our findings show that AtCBF1 ectopic expression influenced fruit surface color or PCI symptom-development, and highlight that PCI is tightly interconnected with ripening. This is the first report of the use of a chemical-inducible system to ectopically express a gene to study a postharvest trait, and provides a basis for investigating the role of CBF1 on PCI and ripening.