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…

Free amino acid composition of must from 7 Vitis vinifera L. cv. in Latium (Italy)

Free amino acid concentrations in must of 7 Vitis vinifera cultivars (Cabernet Franc, Syrah, Merlot, Montepulciano, Sangiovese, Cesanese d’Affile, Carmenere) grown in the Latium region (Italy) were monitored from 2003 to 2005. The cultivars were located in a homogeneous soil and climatic zone and with the same training system (Cordon Spur).

Study of cross-modal interactions through sensory and chemical characteristics of italian red wines

This work aimed at investigating red wine olfactory–oral cross-modal interactions, and at testing their impact on the correlations between sensory and chemical variables. Seventy-four Italian red whole wines (WWs) from 10 varieties, and corresponding deodorized wines (DWs), were evaluated by sensory descriptive assessment.

Grape ripening: why berry transpiration and xylem backflow matter

At the beginning of ripening, grape berries switch their water import pathway from the xylem to the phloem. However, the cause of the decline in xylem inflow remains a matter of debate. Applying xylem-mobile dye in conjunction with root or shoot pressurization demonstrated that the direction of xylem flow was reversible and responded to pressure manipulation.

Intravarietal diversity: an opportunity for climate change adaptation

Merlot grapevine is the second wine cultivar most planted in the world and especially in the Bordeaux wine region. This cultivar has many advantages in producing high quality wine; however, in the last decade, climate change has increased the sugar concentration in berries at harvest and shortened the maturation cycle. If this has been up to now a great opportunity to improve wine quality profile, we are touching the tipping point. High sugar concentration at harvest induces high alcool content in wine which can negatively impact wine quality. There are many viticultural and oenological practices possible to limit this effect. In this study we focus on plant material through intra-varietal diversity of Merlot cultivar.

The use of cation exchange resins for wine acidity adjustment: Optimization of the process and the effects on tartrate formation and oxidative stability

Acidity adjustments are key to microbial control, sensory quality and wine longevity. Acidification with cation exchange resins -in acid cycle- offers the possibility to reduce the pH by exchanging wine cations, such as potassium (K+), for hydrogen ions (H+). During the exchange process, the removal of potassium and calcium ions contributes to limiting the formation of tartrate salts, thus offering an alternative solution to conventional methods for tartrate stability. Moreover, the reduction of wine pH and the removal of metals catalyzers (e.g. iron) could positively impact the wine’s oxidative stability. Therefore, the aims of this work were (a) to optimize the ion exchange process by testing different volumes and concentrations of sulfuric acid (H2SO4) during the acid cycle, (b) evaluate the effects of the ion exchange process on the formation of tartrate salts, and (c) analyze the oxidative stability of the treated wines.