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…

Viticultural sites and their valorisation in Istria (Croatia)

Pratiquement tout le territoire d’Istrie possède les bonnes conditions naturelles pour la viticulture, laquelle dans ce lieu a une tradition millénaire. La viticulture était et reste toujours la plus importante branche de production agraire et d’économie. Les sites viticoles en Istrie sont caractérisés par des diverses conditions naturelles.

Read More

Temperature effects on the biosynthesis of aroma compounds in glera grapes

This paper describes the first year results of a study that investigated the effects of altitude and related temperature parameters on the biosynthesis of aromas in the Italian cultivar Glera.

Read More

The role of vine trunk height in delaying grape ripening: insights for viticultural adaptation strategies

Global changes in temperature patterns necessitate the development of viticultural adaptation strategies. One promising approach involves modifying the training system and elevating trunk height. This study explored the potential of raising the vine trunk as an adaptive strategy to counteract the effects of increasing temperatures and delay ripening. Thermal conditions, radiation levels, and must composition were measured at different heights (10 and 150 cm) in a commercial vineyard of the minority variety Maturana Blanca, trained on a vertical cordon.

Read More

Exploring the genomic diversity of yeast involved in spontaneous fermentation. from studies to select autochthonous strains of different italian’s wineries to extensive phylogenetic survey about the italians’ population of s. cerevisiae

Modern winemakers must ensure effective alcoholic fermentation without losing the intrinsic biodiversity of the different oenological contexts. In this sense, the population of saccharomyces cerevisiae characteristic of wineries that traditionally do not use selected yeasts can represent an interesting reservoir of biodiversity.

Read More

USING CHECK-ALL-THAT-APPLY (CATA) TO CATEGORIZE WINES: A DECISION-MAKING TOOL FOR WINE SELECTION

Bordeaux is the largest appellation vineyard in France. This contrasting vineyard with varied terroirs offers all styles of wine, resulting from the blending of several grape varieties. If these different profiles make the renown of Bordeaux wines, it can appear as a constraint when the aim is to study Bordeaux wines in their diversity. The selection of a representative sample can be performed by a sensory analysis carried out by trained panelists or by wine professionals, which can take several forms: consensus among experts, conventional descriptive analysis, typicality or quality evaluation. However, because of time, economic, and logistical constraints, these methods have limited applications. As an alternative to classical descriptive analysis, more intuitive methods that do not require training have been proposed recently to describe wines using an expert panel such as Napping, Free Choice or Flash Profiling, CATA or RATA.

Read More