Ome-wide Studies of Grapevine Fruit Composition and Responses to Agro-environmental Factors in the Era of Systems Biology

Book excerpt: Fruits play a substantial role in the human diet as a source of vitamins, minerals, dietary fiber and a wide range of molecules relevant to health promotion and disease prevention. The characterization of genes involved in the accumulation of these molecules during fruit development and ripening, and in the overall plant’s response to the environment, constitutes a fundamental step for improving yield- and quality-related traits, and for predicting this crop’s behavior in the field. This is certainly the case for grapevine (Vitis vinifera L.), one of the most largely cultivated fruit crops in the world. The cultivation of this species is facing challenging scenarios driven by climate change – including increases in atmospheric carbon dioxide (CO2), solar radiation, and earth surface temperature, and decreases of water and nutrient availability. All these events will potentially affect the grapevine phenology, physiology, and metabolism in many growing regions and ultimately affect the quality of their fruits and of the most important derived product, the wine. The sequencing of the grapevine genome has given rise to a new era, characterized by the generation of large-scale data that requires complex computational analyses. Numerous transcriptomic and metabolomic studies have been performed in the past fifteen years, providing insights into the gene circuits that control the accumulation of all sorts of metabolites in grapevines. From now on, the integration of two or more ‘omics’ will allow depicting gene-transcript-metabolite networks from a more holistic (i.e. systems) perspective. This eBook attempts to support this new direction, by gathering innovative studies that assess the impact of genotypes, the environment, and agronomical practices on fruits at the ‘ome’-scale. The works hereby collected are part of a Research Topic covering the use of ‘omics’-driven strategies to understand how environmental factors and agronomical practices – including microclimate modification (e.g. sunlight incidence or temperature), water availability and irrigation, and postharvest management – affect fruit development and composition. These studies report well-settled transcriptomic and metabolomic methods, in addition to newly-developed techniques addressing proteome profiles, genome methylation landscapes and ionomic signatures, some of which attempt to tackle the influence of terroir, i.e. the synergic effect of (micro)climate, soil composition, grape genotype, and vineyard practices. A few reviews and opinions are included that focus on the advantages of applying network theory in grapevine research. Studies on vegetative organs in their relation to fruit development and on fruit-derived cell cultures are also considered.