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…

Crowdsourced the assessment of wine rating: professional wine competition rating vs vivino rating

We evaluate wine ratings by comparing data from two crowdsourcing platforms – Vivino, which aggregates the opinions of a large number of wine lovers, and Global Wine Medal Rating, which aggregates the scores from more than 1030 international wine competitions since 2020.

Evoluzione stagionale delle temperature ed andamento della maturazione nel vitigno Aglianico: risultati di un quadriennio di osservazioni in Campania

In viticoltura, la comprensione dell’influenza della temperatura dell’aria sulla dinamica della maturazione assume importante rilievo in relazione all’ ottimizzazione dell’ epoca di raccolta da cui dipende in modo significativo la qualità del prodotto finale.

What do we know about the kerosene/petrol aroma in riesling wines?

1,1,6-Trimethyl-1,2-dihydronaphthalene (TDN) is a controversial aroma component found in Riesling wines. It belongs to the family of C13-norisoprenoids and is mainly associated with kerosene/petrol notes. TDN can add complexity to the wine aroma at medium – low concentrations and deteriorate the wine bouquet when its content is high. No TDN aromas are usually perceived in young Riesling wines, but they can appear after several years of aging due to the gradual formation of TDN. Management of TDN in Riesling wines is an actual task, since global warming can promote formation of this compound and compromise the aromatic composition of wine. Therefore, the aim of the current work was, firstly, to study the sensory particularities of TDN in Riesling wine at various concentrations. Secondly, to investigate the ability of bottle closures to absorb (scalp) TDN from Riesling wine under various storage conditions. These studies also include the comparative assessment of our findings with previously published data. METHODS: sensory analysis, GC-MS (SBSE), HPLC,1H-NMR and other methods related to the synthesis and determination of TDN. RESULTS: First of all, the method of the synthesis of highly purified TDN (95% and 99.5%) was optimized [1].

Challenges and opportunities for increasing organic carbon in vineyard soils: perspectives of extension specialists

Context description and research question: an increasing number of farmers are considering the impact of conservation practices on soil health to guide sustainable management of vineyards. Understanding impacts of soil management on soil organic carbon (SOC) is one lever for adoption of agroecological practice with potential to help maintain or improve soil health while building SOC stocks to mitigate climate change (Amelung et al., 2020).

Changes in the composition and extractability of flavonoids in Cabernet-Sauvignon: influence of site, climate and vine water status

The purpose of the study was to monitor berry development as a function of site, vine water status and climate in order to improve our understanding of the role played by climate change on secondary metabolites relevant to wine quality.