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…

Measurement of grape vine growth for model evaluation

Within a research project for simulating the nitrogen turnover in vineyard soils and the nitrogen uptake by the grape vine, a previously developed plant growth model (Nendel and Kersebaum 2004) had to be evaluated. A dataset was obtained from a monitoring experiment at three vineyard sites with different soil types, conducted in the years 2003 and 2004.

Read More

Varietal differences between Shiraz and Cabernet sauvignon wines revealed by yeast metabolism

This study investigated if compositional differences between Shiraz and Cabernet Sauvignon grape varieties could influence the production of yeast-derived compounds. This work was based on the analysis of 40 experimental red wines made in triplicate fermentations from grapes harvested from two consecutive vintages in New South Wales (Australia). Grapes were picked at three maturity stages using berry sugar accumulation as physiological indicator, from nine commercial vineyards located in three different climatic regions (temperate, temperate-warm and warm-hot). A range of 30 yeast-derived wine volatiles including esters and alcohols were quantified by HS/SPME-GC/MS. Ammonia, amino-acids and lipids were analysed in the corresponding grapes. The juice total soluble solids (°Brix) in addition to the wine alcohol and residual sugar levels were also measured. The influence of grape maturity on wine ester composition was also variety dependent, particularly for higher alcohol acetate and ethyl ester of branched acids. This study highlights that varietal differences observed in Shiraz and Cabernet Sauvignon wines involve fermentation-derived compounds irrespective of the site (soil, climate, viticultural practices).

Read More

From vineyard to a glass of wine: the effect of abscisic acid application on mouhtaro, a rare autochthonous variety of greece

In a context of a sustainable viticulture, a new uprising strategy to improve grape and wine composition (or quality) is the exogenous application of plant activators(Gil-Muñoz et al., 2017)

Read More

Applicability of spectrofluorometry and voltammetry in combination with machine learning approaches for authentication of DOCa Rioja Tempranillo wines

The main objective of the work was to develop a simple, robust and selective analytical tool that allows predicting the authenticity of Tempranillo wines from DOCa Rioja. The techniques of voltammetry and absorbance-transmission and fluorescence excitation emission matrix (A-TEEM) spectroscopy have been applied in combination with machine learning (ML) algorithms to classify red wines from DOCa Rioja according to region (Alavesa, Alta or Oriental) and category (young, crianza or reserva).

Read More

Terroir, climat et sol

Le sol et le climat occupent une place prépondérante dans le concept de terroir, pour lequel l’OIV s’apprête à adopter une définition internationale. Les travaux de recherche qui ont été menés depuis une trentaine d’années sur ces thèmes et qui ont été, pour les plus importants, présentés dans les 7 premiers Congrès Internationaux des Terroirs Viticoles ont considérablement modifié les connaissances sur le fonctionnement des terroirs viticoles dans le monde et le comportement des consommateurs avertis par rapport aux vins de terroirs.

Read More