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…

The history of the first demarkated wine region of the world – the Tokaj wine region

The optimal climatic conditions of the region were proved in 1867, when a leaf-print of Vitis tokaiensis was found in a stone from miocen age (13 million years ago).

Read More

The use of zirconia dioxide enclosed in a metallic cage for the stabilisation of Chardonnay white wine

White wines are commonly stabilised by removing the heat unstable proteins through adsorption by bentonite, an effective but inefficient wine processing step. Alternative absorbents are thus sought and zirconium dioxide (zirconia) is recognised as a promising candidate.

Read More

StartupLab and HackaVitis: open innovation and technology transfer in the wine sector

The study analyzes a set of open innovation actions promoted by the innovation environments of the Instituto Federal do Rio Grande do Sul (IFRS), in cooperation with entities, companies in the sector and the Department of Innovation, Science and Technology of Rio Grande do Sul.

Read More

Revisiting the effect of subsurface irrigation and partial rootzone drying on canopy size and yield of Cabernet Sauvignon using remote sensing techniques

Irrigation is an essential tool for grape production, especially where rainfall does not meet the optimal water requirements needed to achieve yield and quality targets. Increased evaporative demand of grapevines due to changing climate conditions, and a growing awareness for sustainable farming, require the improvement of irrigation techniques to maximize water use efficiency, i.e. using less water to achieve the same yields or the same water but larger yields. In this study, the performance of Cabernet Sauvignon vines was compared under three irrigation techniques: conventional aboveground drip irrigation, subsurface irrigation installed directly under the vine row, and partial rootzone drying in which two subsurface lines were buried in the middle of the two interrow spacings on each side of the vine row with irrigation alternated between the two lines based on soil moisture content.

Read More

“Silex vitioeno module porte-greffe”: an information system to gather experimental results on grapevine rootstocks

Maintaining stable yields and quality over time is a major challenge for the wine industry. Within the context of climate change, the choice of the rootstock is an important lever for adapting to current and future climatic conditions. Within a vineyard, the choice of the rootstock depends on the environmental conditions, the scion variety and the objectives of production. Many experimental data on the performances of rootstock already exist and can guide our decision-making.

Read More