terclim by ICS banner
IVES 9 IVES Conference Series 9 Defining gene regulation and co-regulation at single cell resolution in grapevine

Defining gene regulation and co-regulation at single cell resolution in grapevine

Abstract

Conventional molecular analyses provide bulk genomic/transcriptomic data that are unable to reveal the cellular heterogeneity and to precisely define how gene networks orchestrate organ development. We will profile gene expression and identify open chromatin regions at the individual cells level, allowing to define cell-type specific regulatory elements, developmental trajectories and transcriptional networks orchestrating organ development and function. We will perform scRNA-seq and snATAC-seq on leaf/berry protoplasts and nuclei and combine them with the leaf/berry bulk tissues obtained results, where the analysis of transcripts, chromatin accessibility, histone modification and transcription factor binding sites showed that a large fraction of phenotypic variation appears to be determined by regulatory rather than coding variation and that many variants have an organ-specific effect. By bioinformatics approaches we will identify cell and gene clusters, interpreting the heterogeneity from single-cell transcriptomes; subsequently, we will perform in situ hybridizations to corroborate already predicted cell-type annotations and to identify new cell-type marker genes, required for the cell identity definition, and for the experimental validations of scRNA-seq data. The realization of a single cell resolution spatiotemporal transcriptomic and chromatin accessibility map of grapevine berry will allow to link gene expression profiles to cellular and developmental processes, uncovering part of the molecular mechanisms of ripening and slowly providing the key in maintaining high quality grapes and wine. Building organ-scale gene expression maps is essential to drive technological innovation such as reprogramming cell identity and inducing phenotypic changes via cell-type-specific gene editing.

DOI:

Publication date: June 14, 2024

Issue: Open GPB 2024

Type: Poster

Authors

Chiara Foresti1*, Michele Morgante2, Paola Paci3, Sara Zenoni1

1Department of Biotechnology, University of Verona, Verona, Italy
2IGA and Department of Agri-food, Environmental and Animal Sciences, University of Udine, Italy
3Institute for System Analysis and Computer Science “Antonio Ruberti”, National Research Council, Rome, Italy

Contact the author*

Keywords

Single-cell RNA-seq, single nucleus ATAC-seq, gene expression regulation, gene network, developmental trajectories

Tags

IVES Conference Series | Open GPB | Open GPB 2024

Citation

Related articles…

DOES LIGNIN AN ACCEPTABLE MARKER OF GRAPESEED MATURATION AND QUALITY?

Usually the winemaker consider polyphenols from the grape berry as an actor of the wine quality. There are frequently consider as a marker of grape maturity. It is commonly known that winemaker consider tannins and anthocyanins as main polyphenol actors for winemaking practices and wine quality. Here we will focus on the characterisation of lignins in grape seeds. Previous studies suggest that the seed is lignified [1], which could explain the change in colour of the seed when it reaches maturity and thus provide a reliable indicator for describing the maturity stage in the seed.

Rootstocks: how the dark side of the vine can enlight the future?

Global challenges, including adaptation to climate change, decrease of the environmental impacts and maintenance of the economical sustainability shape the future of viticulture.

Lamp – a modern tool for the detection of fungal infections in the vineyard

AIM: Loop-mediated isothermal amplification (LAMP) [1] is a modern technology for fast and sensitive amplification of specific DNA sequences under isothermal conditions. Its simple handling and no need for dedicated equipment together with an evaluation of the amplification event by in-tube detection make this method advantageous and economically affordable for on-site investigations in the industry.

Impact of non-fruity compounds on red wines fruity aromatic expression: the role of higher alcohols

A part, at least, of the fruity aroma of red wines is the consequence of perceptive interactions between various aromatic compounds, particularly ethyl esters and acetates, which may contribute to the perception of fruity aromas, specifically thanks to synergistic effects.1,2 The question of the indirect impact of non-fruity compounds on this particular aromatic expression has not yet been widely investigated. Among these compounds higher alcohols (HA) represent the main group, from a quantitative standpoint, of volatiles in many alcoholic beverages. Moreover, some bibliographic data suggested their contribution to the aromatic complexity by either increasing or masking flavors of wine, depending of their concentrations.

The sensitivity to ABA affects the cross-talk between scion/rootstock in tolerant grapevines to drought stress

Drought caused by climate change has a dramatic incidence on the vineyard. Despite employing specific rootstocks tolerant to drought like 110 Richter, the vineyard continues to experience various losses, revealing the importance of the scion cultivar in the adaptation to drought stress. In this regard, Merlot, a widely cultivated grapevine, exhibited reduced drought tolerance compared to less cultivated varieties like Callet, a local cultivar originating from the Balearic Islands that demonstrated greater resilience to drought. Therefore, understanding the drought stress response in both cultivars and the cross-talk between scion and rootstock is key to unveiling possible differences that could affect to the adaptation to drought in vineyard.