Comparative Transcriptomic Analysis of Two Tomato Cultivars with Different Shelf-Life Traits

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Abstract
Tomato (Solanum lycopersicum) is a perishable fruit because of its fast water loss and susceptibility to pathogens in the post-harvest stage, which leads to huge economic losses every year. In this study, firstly from 19 tomato cultivars, we screened out two cultivars, Riogrand and SalarF1, having long and short shelf-life spans, respectively. Secondly, shelf-life analysis was carried out for both cultivars at room temperature. Results exhibited that Riogrand showed higher firmness and less weight loss than SalarF1. The ethylene production was higher in SalarF1, compared with Riogrand during post-harvest storages. We performed transcriptomic analysis of both cultivars in different storage stages. We discovered 2913, 2188, and 11,119 differentially expressed genes (DEGs) for three post-harvest stages (0, 20, and 40 Days Post-Harvest (DPH)), respectively. These genes are enriched in ethylene biosynthesis and response, as well as cell wall-related genes. Ethylene response factor (ERF) ERF2 and ERF4 were highly expressed in SalarF1 with a short shelf life in 40 DPH, and the ethylene biosynthetic genes ACO1, ACO4, ACS6, and ACS2 were significantly upregulated in SalarF1. Regarding cell wall loosening and cell wall-related genes XTH3, XTH7, XTH23, 1,3;1,4-β-D-Gluc-like, pGlcT1, Cellulase, PGH1, PL5, PL-like 1, PL-like 2 exhibited the highest levels of significance, being notably upregulated in the last stage of SalarF1. The quantitative real-time polymerase chain reaction (qRT-PCR) analysis validated these gene expressions, which is in line with the transcriptome analysis. The findings suggested that the extension of tomato fruit shelf life is mostly dependent on ethylene biosynthesis, signaling pathway genes, cell wall loosening, and cell wall-associated genes.

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