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…

Qualité des vins et Terroirs. Incidence du milieu naturel sur la composition aromatique des vins

The northern vineyards produce wines with a high aromatic richness. The wines of Alsace are appreciated for the diversity of their aromas, the typicality of which was for a long time judged mainly according to the grape variety of origin. Alsatian winegrowers have however widely sensed the importance of the environment of the vine on the quality of the wines. Efforts are made to try to harmonize in a reasoned way the interaction between the natural environment and the plant material with a view to developing the character of the grape variety through the fine expression of the terroir and making the quality and typicality even more inimitable. wines produced in Alsace.

Organoleptic and analytical impacts of the color of glass of the bottles on Chasselas wine

This study was performed on Chasselas wine to assess the impact of exposure to wine light according to several glass color of bottles. The aim was to highlight any differences whether from an organoleptic or analytical point of view depending on the color. For this, four different shades were compared, dead leaf, green, cinnamon and transparent. A control, not treated with light, was also included in the study…

Different strategies for the rapid detection of Haze‐Forming Proteins (HFPs)

Over the last decades, wine analysis has become an important analytical field, with emphasis placed on the development of new methodologies for characterization and elaboration control.

The application of soil biological indicators to support soil conservation practices and landscape quality in viticulture

Le but de notre travail a été d’étudier l’influence de différents systèmes de la gestion du sol en viticulture sur des paramètres biologiques de sol comme indicateurs de la protection et de la qualité du sol. La conservation de sol est indispensable pour une viticulture durable et la protection du terroir. Nos résultats ont montré, que la matière

A comprehensive ecological study of grapevine sensitivity to temperature; how terroir will shift under climate change

Fossil fuel combustion continues to drive increases in atmospheric carbon dioxide, consequently elevating the global annual mean temperature and specifically increasing the growing season temperatures in many of the world’s most important wine growing regions (IPCC 2014; Jones et al 2005). Grapes are sensitive to changes in growing season temperatures, and past models have shown a direct link between warming temperatures and earlier harvest dates (Cook and Wolkovich 2016). Globally, there have been shifts of 1-2 weeks for wine growing regions (Wolkovich et al 2017 and references within). The phenological shifts resulting from growing season temperature increases are documented internationally, and models predicting phenology using temperature are becoming more precise (Parker et al 2011).