Status and Prospects of Systems Biology in Grapevine Research

Matus, José Tomás; Ruggieri, Valentino; Romero, Francisco J.; Moretto, Marco; Wong, Darren Chern Jan

doi:10.1007/978-3-030-18601-2_8

Cited by 3 publications

(3 citation statements)

References 148 publications

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“…Several grapevine transcription factors have been isolated and studied in the past decade as regulators of berry metabolism and environmental and pathogen responses. Many of these characterizations have been enhanced by the use of heterologous systems, while only recently by means of systems biology approaches ( Falchi et al 2019 ; Matus et al 2019 ). However, central mediators of developmental transitions involving all these biological processes have not been identified to date.…”

Section: Discussionmentioning

confidence: 99%

The transcription factor VviNAC60 regulates senescence- and ripening-related processes in grapevine

et al. 2023

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Grapevine (Vitis vinifera L.) is one of the most widely cultivated fruit crops because the winemaking industry has huge economic relevance worldwide. Uncovering the molecular mechanisms controlling the developmental progression of plant organs will prove essential for maintaining high-quality grapes, expressly in the context of climate change, which impairs the ripening process. Through a deep inspection of transcriptomic data, we identified VviNAC60, a member of the NAC transcription factor family, as a putative regulator of grapevine organ maturation. We explored VviNAC60 binding landscapes through DNA affinity purification followed by sequencing and compared bound genes with transcriptomics datasets from grapevine plants stably and transiently overexpressing VviNAC60 to define a set of high-confidence targets. Among these, we identified key molecular markers associated with organ senescence and fruit ripening. Physiological, metabolic, and promoter activation analyses showed that VviNAC60 induces chlorophyll degradation and anthocyanin accumulation through the up-regulation of STAY-GREEN PROTEIN 1 (VviSGR1) and VviMYBA1, respectively, with the latter being up-regulated through a VviNAC60-VviNAC03 regulatory complex. Despite sharing a closer phylogenetic relationship with senescence-related homologues to the NAC transcription factor AtNAP, VviNAC60 complemented the non-ripening(nor) mutant phenotype in tomato (Solanum lycopersicum), suggesting a dual role as an orchestrator of both ripening- and senescence-related processes. Our data support VviNAC60 as a regulator of processes initiated in the grapevine vegetative- to mature-phase organ transition and therefore as a potential target for enhancing the environmental resilience of grapevine by fine-tuning the duration of the vegetative phase.

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Section: Discussionmentioning

confidence: 99%

The transcription factor VviNAC60 regulates senescence- and ripening-related processes in grapevine

et al. 2023

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“…Several grapevine transcription factors have been isolated and studied in the past decade as regulators of berry metabolism and environmental and pathogen responses. Some of these characterizations have been enhanced by systems biology approaches (40,41). However, central mediators of developmental transitions involving all these biological processes have not been identified to date.…”

Section: Discussionmentioning

confidence: 99%

Initiation of organ maturation and fruit ripening in grapevine is controlled by the CARPO-NAC transcription factor

D’Incà

Foresti

Orduña

et al. 2021

Preprint

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Grapevine is a woody temperate perennial plant and one of the most important fruit crops with global relevance in both the fresh fruit and winemaking industries. Unfortunately, global warming is affecting viticulture by altering developmental transitions and fruit maturation processes. In this context, uncovering the molecular mechanisms controlling the onset and progression of ripening could prove essential to maintain high-quality grapes and wines. Through a deep inspection of previously published transcriptomic data we identified the NAC family member VviCARPO (Controlled Adjustment of Ripening and maturation of Plant Organs) as a key regulator of grapevine maturation whose induction precedes the expression of well-known ripening associated genes. We explored VviCARPO binding landscapes through DAP-seq and overlapped its bound genes with transcriptomics datasets from stable and transient VviCARPO overexpressing grapevine plants to define a set of high-confidence targets. Among these, we identified key molecular ripening markers. Physiological, metabolic and promoter activation analyses showed that VviCARPO induces chlorophyll degradation and anthocyanin accumulation through the up-regulation of VviSGR1 and VviMYBA1, respectively, with the latter being up-regulated through a VviCARPO-VviNAC03 regulatory complex. Despite showing a closer phylogenetic relationship to senescent-related AtNAP homologues, VviCARPO complemented the nor mutant phenotype in tomato, suggesting it may have acquired a dual role as an orchestrator of both ripening- and senescence-related processes. Our data supports CARPO as a master regulator of the grapevine vegetative-to-mature phase organ transition and therefore an essential target for insuring fruit quality and environmental resilience.SIGNIFICANT STATEMENTCARPO is a grape NAC transcription factor central to fruit ripening and tissue senescence. This regulator influences multiple biological pathways common to both processes including cell wall metabolism, chlorophyll degradation, pigment production and hormone synthesis/signaling through regulation of their key genes. As various external stresses and changing climatic conditions influence vegetative growth and berry ripening, CARPO could prove a useful genetic and breeding target towards maintaining necessary crop performance and fruit-quality characteristics.

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“…Moving forward from single-omic studies and gene-to-gene network exploring tools, the construction of gene - to - metabolite networks via integrative approaches represents a promising strategy for identifying novel gene functions and unprecedent links between genes and metabolites ( Hirai et al., 2005 ; Saito et al., 2008 ). This concept has been reviewed in grapevine ( Wong and Matus, 2017 ; Matus et al., 2019 ), stating the need for appropriate tools to visualize the integration of multi-omic datasets. The first tool developed for data integration in grapevine was ‘VitisNet’ ( Grimplet et al., 2009 ; Grimplet et al., 2012 ), which allowed the multiple combinations of omics data by overlapping user data to 247 curated grapevine molecular networks, reporting more than 16,000 genes; unfortunately, this tool is no longer accessible.…”

Section: An Illustration Of Data Integration and Meta-analysis Using ...mentioning

confidence: 99%

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

et al. 2022

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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.

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Status and Prospects of Systems Biology in Grapevine Research

Cited by 3 publications

References 148 publications

The transcription factor VviNAC60 regulates senescence- and ripening-related processes in grapevine

The transcription factor VviNAC60 regulates senescence- and ripening-related processes in grapevine

Initiation of organ maturation and fruit ripening in grapevine is controlled by the CARPO-NAC transcription factor

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

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