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…

Impact of smoke exposure on the chemical composition of grapes

Vineyard exposure to smoke can lead to grapes and wine which exhibit objectionable smoky and ashy aromas and flavours, more commonly known as ‘smoke taint’ [1, 2]. In the last decade, significant bushfires have occurred around the world, including near wine regions in Australia, Canada, South Africa and the USA, as a consequence of the warmer, drier conditions associated with climate change. Considerable research has subsequently been undertaken to determine the chemical, sensory and physiological consequences of grapevine exposure to smoke. The sensory attributes associated with smoke-tainted wine have been linked to the presence of several smoke-derived volatile phenols, such as guaiacols, syringols and cresols [2].

Monitoring gas-phase CO2 in the headspace of champagne glasses through diode laser spectrometry

During Champagne or sparkling wine tasting, gas-phase CO2 and volatile organic compounds invade the headspace above glasses [1], thus progressively modifying the chemical space perceived by the consumer. Gas-phase CO2 in excess can even cause a very unpleasant tingling sensation perturbing both ortho- and retronasal olfactory perception [2]. Monitoring as accurately as possible the level of gas-phase CO2 above glasses is therefore a challenge of importance aimed at better understanding the close relationship between the release of CO2 and a collection of various tasting parameters.

Exploring the inner secrets of grapevine: a journey through plant-microbe interactions

Throughout centuries of anthropocentric breeding, plants have been selectively bred to enhance their quality traits and yield, often overlooking the importance of neglected attributes, like those involved in the interactions with beneficial microorganisms. This phenomenon led to an alteration in the distribution of photosynthetic products, shifting from defence mechanisms to growth, commonly described as ‘domestication syndrome’. Addressing the losses stemming from this condition is imperative just as unravelling the concealed communication between grapevines and beneficial microorganisms.

Adsorption capacity of phenolics compounds by polyaniline materials in model solution

The aim of this work was to study the trapping capacity of four polyaniline polymers towards phenolic compounds in wine-like model solutions. METHODS: The model wine solution was composed of 12% (v/v) and 4 g/L of tartaric acid adjusted to pH = 3.6. A series of centrifuge tubes (15 mL) were filled with 10 mL of model solution enriched with 50 mg/L of five phenolic compounds (i.e., Gallic acid, caffeic acid, (+)-catechin, (-)-epicatechin, and rutin), and treated with different doses of PANI polymer (i.e., 0, 2, 4 and 8 g/L). After the addition of the polymer, the samples were stirred using a platform shaker at room temperature (20 ºC) for 2, 8, 16 and 24 h. All treatments included three replications.

Study of the aromatic oxidation markers of Tempranillo long aged wines

The aromatic quality of wines after a long aging period in bottle is one of key points for oenologists. The objective of this work is to determine the main representative aromatic compounds found in long aged wines from D.O.Ca. Rioja. This study was made by 32 wines from 1971 to 2010 vintages. Sotolon, acetaldehyde, phenylacetaldehyde, 1,1,6-trimethyl-1,2-dihydronaptalene (TDN), β-damascenone, Y-decalactone and Y-dodecalactone were determined as the most important oxidation markers by GC-MS analysis. Moreover, sensory analysis using triangular tests were performed from wines with and without the addition of the mentioned compounds. Four different concentrations of each odorant were added, as individual compounds and as mixtures. The additions were ranged from values close to the reference odour thresholds up to high level concentrations. The most identified aroma was sotolon, which is commonly associated to curry and coffee liqueur aromatic notes. Other oxidative compounds were easily detected by panellists, such as Y-decalactone (peach compote), Y-dodecalactone (ripe fruit). The mixtures of the odorants were most easily detected than the individual compounds. It should be noted that acetaldehyde and phenylacetaldehyde were rarely perceived and distinguished.