Transcriptomics Analysis of Tomato Ripening Regulated by Carbon Dioxide

Tomatoes are a perishable and seasonal fruit with a high economic impact. Carbon dioxide (CO2), among several other reagents, is used to extend the shelf-life and preserve the quality of tomatoes during refrigeration or packaging. To obtain insight into CO2 stress during tomato ripening, tomatoes at the late green mature stage were conditioned with one of two CO2 delivery methods: 5% CO2 for 14 days (T1) or 100% CO2 for 3 h (T2). Conventional physical and chemical characterization found that CO2 induced by either T1 or T2 delayed tomato ripening in terms of color change, firmness, and carbohydrate dissolution. However, T1 had longer-lasting effects. Furthermore, ethylene production was suppressed by CO2 in T1, and promoted in T2. These physical observations were further evaluated via RNA-Seq analysis at the whole-genome level, including genes involved in ethylene synthesis, signal transduction, and carotenoid biosynthesis. Transcriptomics analysis revealed that the introduction of CO2 via the T1 method downregulated genes related to fruit ripening; in contrast, T2 upregulated the gene encoding for ACS6, the enzyme responsible for S1 ethylene synthesis, even though there was a large amount of ethylene present, indicating that T1 and T2 regulate tomato ripening via different mechanisms. Quantitative real-time PCR assays (qRT-PCR) were used for validation, which substantiated the RNA-Seq data. The results of the present research provide insight into gene regulation by CO2 during tomato ripening at the whole-genome level.