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…

Characterization of four Chenin Blanc-rootstock combinations to assess grapevine adaptability to water constraint

Climate change impacts water availability for agriculture, notably in semi-arid regions like South Africa, necessitating research on cultivar and rootstock adaptability to water constraints. To evaluate the performance (vegetative and reproductive) of different Chenin Blanc-rootstock combinations to the two water regimes, a field experiment was established in a model vineyard at Stellenbosch University, South Africa. Chenin Blanc vines grafted onto four different rootstocks (110Richter, 99Richter, 1103Paulsen and US 8-7) were planted in 2020. The vines are managed under two contrasting water conditions – dryland and irrigated (industry norm).

Effect of different pH values on the interaction between yeast mannoproteins and grape seed flavanols

The consequences of the global climate change in the vitiviniculture are revealed as a gap between phenolic and technological grape maturities, higher grape sugar concentration that leads to high wine alcohols levels, lower acidities and high pH values, among others. The unbalanced phenolic maturity caused in this scenario leads to harsh astringency and to instable colour of wines. Previous studies have reported that the addition of yeast mannoproteins (MPs) to wines may have positive effects on these two organoleptic properties due to their capability to interact with wine polyphenols [1]; however, studies about the effect of the pH on these interactions have not been carried out so far.

Metabolomics screening of Vitis sp. interspecific hybrids to select natural ingredients with cosmetic purposes

Introducing natural ingredients using green chemistry practices is a major challenge in cosmetics industry to follow the market trend. Among the plants of cosmetic interest, vine products show a remarkable diversity of natural substances with high potential for the cosmetic and dermatological sectors. To date, research focuses on well-known compounds like E-resveratrol and E-ε-viniferin,

Unraveling the complexity of high-temperature tolerance by characterizing key players of heat stress response in grapevine

Grapevine (Vitis spp.) is greatly influenced by climatic conditions and its economic value is therefore directly linked to environmental factors. Among these factors, temperature plays a critical role in vine phenology and fruit composition. In such conditions, elucidating the mechanisms employed by the vine to cope with heat waves becomes urgent. For the past few years, our research team has been producing molecular and metabolic data to highlight the molecular players involved in the response of the vine and the fruit to high temperatures [1]. Some of these temperature-sensitive genes are currently undergoing characterization using transgenesis approaches coupled or not with genome editing, taking advantage of the Microvine genotype [2].

Effects of abscisic acid treatment on Vitis vinifera L. Savvatiano and Mouchtaro grapes and wine characteristics

Grapes development is determined by grape cultivar and vineyard climatic conditions and consequently affecting the phenolic and aroma on grapes and wines. Abscisic Acid (ABA) plays a key role in the promotion of fruit ripening and fruit anthocyanin content. Herein, we report the impact of ABA to grape ripening and wine quality.