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.

Download the abstract

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…

Efficacy of tannins of different botanical origin as partial or total substitute of SO2 to preserve a Cortese white wine during storage in cellar

While SO2 is one of the oldest and widest additive used in enology for its well-known antioxidant, anti-laccase and antimicrobial properties, it can cause health problems in some individuals.

Read More

Comparative study of qualitative and quantitative characters of grape cultivar ‘Mavrodafni’ (Vitis vinifera L.) grown in different regions of the PDO Mavrodafni Patras

‘Mavrodafni’ (Vitis vinifera L.) is considered one of the oldest grapevine cultivars indigenous to the Greek vineyard, with western Peloponnese being its primary center of cultivation. ‘Renio’ is considered to be either a variant of ‘Mavrodafni’ or an altogether different cultivar. Both ‘Mavrodafni’ and ‘Renio’ can be found in the vineyards of the centers of cultivation, since ‘Renio’ is considered to be more productive compared to ‘Mavrodafni’, and for this reason, it has gradually replaced ‘Mavrodafni’ from cultivation over the course of time. The aim of the present study was to assay the mechanical properties, the polyphenolic content and the antioxidant capacity of skin extracts and must of berries coming from ‘Mavrodafni’ and ‘Renio’, cultivated in the same vineyard as well as in the different regions of cultivation of the PDO Mavrodafni Patras.

Read More

Mapping intra-plot topsoil diversity of Burgundy vineyards (Aloxe-Corton, France) from very high spatial resolution (VHSR) images

In this work, we present a method based on very high spatial resolution (VHSR) aerial images acquired in the visible domain and that map soil surface diversity at the hillslope

Read More

The impact of delayed grapevine budbreak on lemberger wine sensory compounds under variable weather conditions

Spring freeze events threaten grape production globally. As grape buds emerge from dormancy in spring, freezing temperatures have the potential to damage green tissues, decreasing yield potential and compromising fruit quality by harvest.

Read More

Fast, and full microbiological wine analysis using triple cellular staining.

We propose here a brand new large routine microbiological analysis method intended for oenology, in flow cytometry, using high performance equipment and triple selective cell staining, activated by fluorescence. The results and practical applications of the method are presented: Brettanomyces (Dekkera) Monitoring, fermentations monitoring, bottling and enological practices monitoring.The method allow a complete new microbiological tool for wine industry.The method has been accredited ISO 17025 in our laboratories.

Read More