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…

Soil, vine, climate change – what is observed – what is expected

To evaluate the current and future impact of climate change on Viticulture requires an integrated view on a complex interacting system within the soil-plant-atmospheric continuum under continuous change. Aside of the globally observed increase in temperature in basically all viticulture regions for at least four decades, we observe several clear trends at the regional level in the ratio of precipitation to potential evapotranspiration. Additionally the recently published 6th assessment report of the IPCC (The physical science basis) shows case-dependent further expected shifts in climate patterns which will have substantial impacts on the way we will conduct viticulture in the decades to come.
Looking beyond climate developments, we observe rising temperatures in the upper soil layers which will have an impact on the distribution of microbial populations, the decay rate of organic matter or the storage capacity for carbon, thus affecting the emission of greenhouse gases (GHGs) and the viscosity of water in the soil-plant pathway, altering the transport of water. If the upper soil layers dry out faster due to less rainfall and/or increased evapotranspiration driven by higher temperatures, the spectral reflection properties of bare soil change and the transport of latent heat into the fruiting zone is increased putting a higher temperature load on the fruit. Interactions between micro-organisms in the rhizosphere and the grapevine root system are poorly understood but respond to environmental factors (such as increased soil temperatures) and the plant material (rootstock for instance), respectively the cultivation system (for example bio-organic versus conventional). This adds to an extremely complex system to manage in terms of increased resilience, adaptation to and even mitigation of climate change. Nevertheless, taken as a whole, effects on the individual expressions of wines with a given origin, seem highly likely to become more apparent.

Climate, Viticulture, and Wine … my how things have changed!

The planet is warmer than at any time in our recorded past and increasing greenhouse emissions and persistence in the climate system means that continued warming is highly likely. Climate change has already altered the basic framework of growing grapes for wine production worldwide and will likely continue to do so for years to come. The wine sector can continue to play an important role in leading the agricultural sector in addressing climate change. From developing on…

WHICH IMPACT FOR PROANTHOCYANIDIC TANNINS ON RED WINE FRUITY AROMA? SENSORY AND PHYSICOCHEMICAL APPROACHES

Previous research on the fruity character of red wines highlighted the role of esters. Literature provides evidence that, besides these esters, other compounds that are not necessarily volatiles may have an important impact on the overall aroma of wine, contributing to a modulation of its global aromatic expression. The goal of this work was to assess the olfactory consequences of a mixture between esters and proanthocyanidic tannins, through sensory and physico-chemical approaches.
Sensory analysis of numerous aromatic reconstitutions, including triangular tests, detection thresholds, and sensory profiles, were conducted in order to evaluate the sensory impact of tannins on red wine esters perception.

Comparison of the free radical-scavenging activity in infected oidium and sound dolcetto grape cultivar grown in a terroir of Central Italy

The importance of polyphenols, which are present in many vegetables and grapes too, is well-know and documented. Specific research works about the red grape

Assessment of plant water consumption rates under climate change conditions through an automated modular platform

The impact of climate change is noticeable in the present weather, making water scarcity the most immediate mediator reducing the performance and viability of crops, including grapevine (Vitis vinifera L.). The present study developed a system (hardware, firmware, and software) for the determination of plant water use through changes in weight through a period. The aim is to measure the differences in grapevine water consumption in response to climate change (+4oC and 700 ppm) under controlled conditions. The results reveal a correlation between daily plant consumption rates and reference evapotranspiration (ETo).