Deciphering transcriptional regulation mechanisms underlining fruit development and ripening in Vitis vinifera

BACKGROUND: Grapes (Vitis vinifera) are an important woody crop cultivated in a broad range of environmental conditions. Grapefruit development is a physiological process whose molecular regulatory networks are still not sufficiently investigated. OBJECTIVE: The primary aim of the work was to identify which key genes, molecular mechanisms and networks were involved in fruit ripening and development through a comparison of available transcriptomic data at different stages during grape development and ripening. Secondly, we aimed at identifying among these fruit-related genes, which genes play also a functional role in other developmental and physiological processes in reproductive tissues (bud and flower). METHODS: The two objectives were obtained through a meta-analysis on 9 RNA-Sequencing (RNA-Seq) studies. Raw data was downloaded from publicly available resource and re-analyzed to find out the significant differentially expressed genes (DEGs) (p-value <0.05). Gene enrichment and functional analysis were done using MapMan and PageMan. DAVID web server was used to identify gene ontology. NetworkAnalyst was used for finding out the protein-protein interaction. RESULTS: 721 (178 were up-regulated and 534 were down-regulated) differentially regulated genes in fruit development were in common between all the four fruit studies. The gene set enrichment analysis performed on these commonly regulated genes showed that the following biological processes were significantly affected during the fruit development: induction of major CHO metabolism, starch and lactoylglutathione lyase and repression of cell wall-related pathways, photosynthesis and cytokinin synthesis. Some of the key genes involved in ethylene, brassinosteroid and cytokinin were down-regulated in the late stage of fruit ripening, while two key abscisic acid-related genes were up-regulated. Fruit ripening up-regulated some key genes encoding Homeobox (HB17), AP2EREBP (RAP2), C2C2-CO-like, WRKY (WRKY9), MYB (MYB62) while repressing several key genes encoding bHLH, MYBs, WRKYs and C2H2. CONCLUSION: This comprehensive meta-analysis allowed identifying which genes should be the main targets of a grape breeding strategy to improve physiological processes linked to fruit development and ripening. These data will be used for future sustainable biotechnologies strategies based on small-molecule treatments and genome editing.