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…

Investigating spatial heterogeneity in powdery mildew pressure at the plot scale: A precision viticulture approach

Powdery mildew (Erysiphe necator) (PM) is the most important and impacting fungal disease of grapevine (Vitis vinifera L). This disease remains difficult to model and forecast accurately because (i) the first signs of the disease in the vineyard are hardly noticeable in the first 30- 40 days after the onset of the epidemic (three to four pathogen generations), and (ii) its spatial distribution within or between neighboring plots is heterogeneous.

Flor yeast diversity and dynamics in biologically aged wines

Wine biological aging is characterized by the development of yeast strains that form a biofilm on the wine surface after alcoholic fermentation. These yeasts, known as flor yeasts, form a velum that protects the wine from oxidation during aging. Thirty-nine velums aged from 1 to 6 years were sampled from “Vin jaune” from two different cellars. We show for the first time that these velums possess various aspects in term of color and surface aspects. Surprisingly, the heterogeneous velums are mostly composed of one species, S. cerevisiae. Scanning electron microscope observations of these velums revealed unprecedented biofilm structures and various yeast morphologies formed by the sole S. cerevisiae species.

REMEDIATION OF SMOKE TAINTED WINE USING MOLECULARLY IMPRINTED POLYMERS

In recent years, vineyards in Australia, the US, Canada, Chile, South Africa and Europe have been exposed to smoke from wildfires. Wines made from smoke-affected grapes often exhibit unpleasant smoky, ashy characters, attributed to the presence of smoke-derived volatile compounds, including volatile phenols (which occur in free and glycosylated forms). Various strategies for remediation of smoke tainted wine have been evaluated. The most effective strategies involve the removal of smoke taint compounds via the addition of adsorbent materials such as activated carbon, which can either be added directly or used in combination with nanofiltration. However, these treatments often simultaneously remove wine constituents responsible for desirable aroma, flavour and colour attributes.

Climate regionalization of Uruguayan viticulture for ecological sustainability

Ecological sustainability refers to developing viticulture in adequate environmental conditions.

Potential application of indigenous Pichia kluyveri for enhanced wine aroma quality

Aims: In previous work, five indigenous Pichia kluyveri strains, GS1-1, FS-2-7, HS-2-1, C730 and C732, were isolated and selected from spontaneous fermented wines from Ningxia and Gansu. The aims of this study were to 1) evaluate resistance of these strains to environmental stressors that may restrict their growth and the progress of alcoholic fermentation; 2) Investigate their fermentation dynamics; 3) Characterise aroma profiles of Cabernet Sauvignon wines made from mixed cultures of P. kluyveri and Saccharomyces cerevisiae.