Transcriptomic and metabolomic integration as a resource in grapevine to study fruit metabolite quality traits

Abstract

Transcriptomics and metabolomics are methodologies being increasingly chosen to perform molecular studies in grapevine (Vitis vinifera L.), focusing either on plant and fruit development or on interaction with abiotic or biotic factors. Currently, the integration of these approaches has become of utmost relevance when studying key plant physiological and metabolic processes. The results from these analyses can undoubtedly be incorporated in breeding programs whereby genes associated with better fruit quality (e.g., those enhancing the accumulation of health-promoting compounds) or with stress resistance (e.g., those regulating beneficial responses to environmental transition) can be used as selection markers in crop improvement programs. Despite the vast amount of data being generated, integrative transcriptome/metabolome meta-analyses (i.e., the joint analysis of several studies) have not yet been fully accomplished in this species, mainly due to particular specificities of metabolomic studies, such as differences in data acquisition (i.e., different compounds being investigated), unappropriated and unstandardized metadata, or simply no deposition of data in public repositories. These meta-analyses require a high computational capacity for data mining a priori, but they also need appropriate tools to explore and visualize the integrated results. This perspective article explores the universe of omics studies conducted in V. vinifera, focusing on fruit-transcriptome and metabolome analyses as leading approaches to understand berry physiology, secondary metabolism, and quality. Moreover, we show how omics data can be integrated in a simple format and offered to the research community as a web resource, giving the chance to inspect potential gene-to-gene and gene-to-metabolite relationships that can later be tested in hypothesis-driven research. In the frame of the activities promoted by the COST Action CA17111 INTEGRAPE, we present the first grapevine transcriptomic and metabolomic integrated database (TransMetaDb) developed within the Vitis Visualization (VitViz) platform (https://tomsbiolab.com/vitviz). This tool also enables the user to conduct and explore meta-analyses utilizing different experiments, therefore hopefully motivating the community to generate Findable, Accessible, Interoperable and Reusable (F.A.I.R.) data to be included in the future.

A Review of Transcriptomics and Metabolomics in Plant Quality and Environmental Response: From Bibliometric Analysis to Science Mapping and Future Trends

“…In methodology and tools, with the explosive publication of more omics data, it is necessary to establish databases that generate searchable, accessible, interoperable, and reusable data for future use. The establishment of the grape transcriptomics and metabolomics integrated database (TransMetaDb) has set an example for other species [92]. In addition, with the progress in the field of computer science (i.e., machine learning, artificial intelligence, neural networks, etc.…”

Polyploidization and genomic selection integration for grapevine breeding: a perspective

“…For example, in a recent study conducted by ( Han et al., 2023 ), the authors used reference genome-based RNA-seq data analysis to identify the probable pathways involved in the freezing response in grapevines. Likewise, a few studies were conducted on grapevine breeding using various omics technologies ( Wang et al., 2021 ; Savoi et al., 2022 ). In addition to genomics, metabolomics, and transcriptomics, derived and innovative omics (such as epigenomics and epitranscriptomics) can also be used for comprehensive understanding of the complex epigenetic modifications in the induced polyploids.…”

Spatial Variability of Grape Berry Maturation Program at the Molecular Level

“…Over the past decade, the generation and analysis of large-scale transcriptomic datasets have played a crucial role in elucidating the molecular basis of grapevine berry development. Numerous investigations into gene expression patterns have established connections between molecular changes, primary and secondary metabolic pathways, and biological processes, together providing a comprehensive understanding of the transcriptomic program governing berry maturation [23]. However, little is known about the molecular differences during the ripening program associated with intra-vineyard variability of agronomic parameters.…”