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Article|31 Jan 2022|OPEN
Multi-omics data integration provides insights into the post-harvest biology of a long shelf-life tomato landrace
Riccardo Aiese Cigliano1 ,† , Riccardo Aversano2 ,† , Antonio Di Matteo2 ,† , Samuela Palombieri3 ,† , Pasquale Termolino3 ,† , Claudia Angelini4 , Hamed Bostan2 , Maria Cammareri3 , Federica Maria Consiglio3 , Floriana Della Ragione5 , Rosa Paparo3 , Vladimir Totev Valkov6 , Antonella Vitiello3 , Domenico Carputo2 , Maria Luisa Chiusano2 , Maurizio D’Esposito5,7 , Silvana Grandillo3 , Maria Rosaria Matarazzo5 , Luigi Frusciante2 and Nunzio D’Agostino2 , , Clara Conicella,3 ,
1Sequentia Biotech SL, Carrer de Valencia, 08009, Barcelona, Spain
2Department of Agricultural Sciences, University of Naples Federico II, Via Universita’ 100, 80055 Portici, Italy
3Institute of Biosciences and Bioresources, National Research Council of Italy, Via Universita‘ 133, 80055 Portici, Italy
4Institute for Applied Calculus, National Research Council of Italy, Via P. Castellino 111, 80131, Napoli
5Institute of Genetics and Biophysics "Adriano Buzzati Traverso", National Research Council of Italy, Via P. Castellino 111, 80131, Napoli
6Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80131 Napoli, Italy
7Deceased
*Corresponding author. E-mail: unzio.dagostino@unina.it,onicell@unina.it
Riccardo Aiese Cigliano,Riccardo Aversano,Antonio Di Matteo,Samuela Palombieri and Pasquale Termolino contributed equally to the study.

Horticulture Research 9,
Article number: uhab042 (2022)
doi: https://doi.org/10.1093/hr/uhab042
Views: 23

Received: 19 Jun 2021
Revised: 18 Jan 2022
Accepted: 15 Oct 2021
Published online: 31 Jan 2022

Abstract

In this study we investigated the transcriptome and epigenome dynamics of the tomato fruit during post-harvest in a landrace belonging to a group of tomatoes (Solanum lycopersicum L.) collectively known as “Piennolo del Vesuvio”, all characterized by a long shelf-life. Expression of protein-coding genes and microRNAs as well as DNA methylation patterns and histone modifications were analysed in distinct post-harvest phases. Multi-omics data integration contributed to the elucidation of the molecular mechanisms underlying processes leading to long shelf-life. We unveiled global changes in transcriptome and epigenome. DNA methylation increased and the repressive histone mark H3K27me3 was lost as the fruit progressed from red ripe to 150 days post-harvest. Thousands of genes were differentially expressed, about half of which were potentially epi-regulated as they were engaged in at least one epi-mark change in addition to being microRNA targets in ~5% of cases. Down-regulation of the ripening regulator MADS-RIN and of genes involved in ethylene response and cell wall degradation was consistent with the delayed fruit softening. Large-scale epigenome reprogramming that occurred in the fruit during post-harvest likely contributed to delayed fruit senescence.