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…

The terroir of winter hardiness: a three year investigation of spatial variation in winter hardiness, water status, yield, and berry composition of riesling in the niagara region using geomatic technologies

Grapevine winter hardiness is a key factor in vineyard success in many cool climate wine regions. Winter hardiness may be governed by several factors in addition to extreme weather conditions – e.g. soil factors (texture, chemical composition, moisture, drainage), vine water status, and yield– that are unique to each site.

Aromatic maturity is a cornerstone of terroir expression in red wine

Harvesting grapes at adequate maturity is key to the production of high-quality red wines. Enologists and wine makers define several types of maturity, including technical maturity, phenolic maturity and aromatic maturity. Technical maturity and phenolic maturity are relatively well documented in the scientific literature, while articles on aromatic maturity are scarcer. This is surprising, because aromatic maturity is, without a doubt, the most important of the three in determining wine quality and typicity (including terroir expression). Optimal terroir expression can be obtained when the different types of maturity are reached at the same time, or within a short time frame. This is more likely to occur when the ripening takes place under mild temperatures, neither too cool, nor too hot. Aromatic expression in wine can be driven, from low to high maturity, by green, herbal, fresh fruit, ripe fruit, jammy fruit, candied fruit or cooked fruit aromas. Green and cooked fruit aromas are not desirable in red wines, while the levels of other aromatic compounds contribute to the typicity of the wine in relation to its origin. Wines produced in cool climates, or on cool soils in temperate climates, are likely to express herbal or fresh fruit aromas; while wines produced under warm climates, or on warm soils in temperate climates, may express ripe fruit, jammy fruit or candied fruit aromas. Growers can optimize terroir expression through their choice of grapevine variety. Early ripening varieties perform better in cool climates and late ripening varieties in warm climates. Additionally, maturity can be advanced or delayed by different canopy management practices or training systems.

Climatic zoning of viticultural production periods over the year in the tropical zone: application of the methodology of the Géoviticulture MCC system

L’objectif de cette recherche est le zonage climatique des périodes viticoles de l’année dans la Vallée du São Francisco, région brésilienne productrice de vins située en climat tropical semi-aride. Dans cette région, la production peut être échelonnée sur tous les mois de l’année.

Predatory Arthropods associated with potential locally-adapted native insectary plants for Australian vineyards

Three locally-adapted native plants were evaluated to determine their capacity to provide insectary benefits to predatory arthropods in association with vineyards, and thereby to enhance biological control of insect pests. Native plants are preferred as supplementary flora, as they are naturally adapted to Australia’s climatic conditions.

Legal protection of the vitivinicultural terroirs in Yamanashi Prefecture, Japan

This study analyses the actual situation regarding the legal protection of the vitivinicultural terroirs in Yamanashi Prefecture, the centre of Japanese wine industry with more than 150 years of wine-making tradition.