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…

Under-vine management effects on grapevine production, soil properties and plant communities in South Australia

Under-vine (UV) management has traditionally consisted of synthetic herbicide use to limit competition between weeds and grapevines. With growing global interest towards non-synthetic chemical use, this study aimed to capture the effects of alternative UV management at two commercial Shiraz vineyards in South Australia, where the sole management variables were UV management since 2016. In adjacent treatment blocks, cultivation (CU) was compared to spontaneous vegetation (SV) in McLaren Vale (MV), and herbicide was compared to SV in Eden Valley (EV). Soil water infiltration rates were slower and grapevine stem water potential was lower in CU compared to SV in MV, with the latter having a plant community dominated by soursob (Oxalis pes-caprae) during winter; while in EV, there was little separation between the treatments. Yields were affected at both sites, with SV being higher in MV and HE being higher in EV. In MV, the only effect on grape must was a lower 13C:12C isotope ratio in CU, indicating greater grapevine water stress. In the grape must at EV, SV had higher total soluble solids, total phenolics, anthocyanins, and yeast available nitrogen; and lower pH and titratable acidity. Pruning weights were not affected by the treatments in MV, while they were higher in HE at EV. Assessments revealed that the differing soil types at the two sites were likely the main determinants of the opposing production outcomes associated with UV management. In the silty loam soil of MV, the higher yields in SV were likely due to more plant-available water, as a potential result of the continuous soil bio-pores formed by winter UV vegetation. Conversely, in the loamy sand soils of EV with a lower cation exchange capacity, the lower yields and pruning weights in SV suggest the UV vegetation competed significantly with the grapevines for available water and nutrients.

Exogenous dsRNA applications to identify novel candidate susceptibility genes to downy mildew

One of the major threats to viticulture is represented by fungal pathogens. Plasmopara viticola, an oomycete causing grapevine downy mildew, is one of the principal causes of grape production losses. The most efficient management strategies are represented by a combination of agronomical practices, fungicides’ applications, and use of resistant varieties. Plant resistance is conferred by the presence of resistance (R) genes. Opposed to them, susceptibility (S) genes are encoded by plants and exploited by pathogens to promote infection. Loss or mutation of S genes can limit the ability of pathogens to infect the host. By exploiting post-transcriptional gene silencing, known as RNA intereference (RNAi), it is possible to knock-down the expression of S genes, promoting plant resistance.

Terroir aspects of harvest timing in a cool climate wine region: physiology, berry skin phenolic composition and wine quality

Preliminary experiment of harvest timing was carried out in Eger wine district, Hungary in 2009. In situ physiological responses, berry quality parameters and wine quality of the Kékfrankos grapevine were studied at two growing sites (Eger-K6lyuktet6 – non-stressed, flat vineyard, and Eger-Nagyeged hill – water stressed, steep slope vineyard).

Stability of 3-mercaptohexanol during white wine storage in relationship to must pre-fermentative fining

3-Mercaptohexanol (3MH) is a volatile thiol occurring in several white and red wines, where it can contribute to fruity attributes. Its content is typically high in wines from certain grape varieties, in particular Sauvignon blanc, where it is considered a varietal marker. The strong nucleophilic character of thiols makes 3MH rather unstable during wine storage, due to the presence of several strong electrophilic species. Among these electrophilics, those arising from the oxidation of flavan3-ols such as catechin and epi-catechin have been indicated as critical for 3MH stability. Accordingly, there is a generalized interest towards the ability of vinification practices to reduce 3MH loss during aging through the management of wine flavan-3-ols content.

Focus on terroir studies in the eger wine region of Hungary

In 2001, the Hungarian Ministry of Agriculture and Rural Development designated the Institute of Geodesy, Cartography and Remote Sensing (FÖMI) to elaborate a Geographic Information System (GIS) supported Vineyard Register (VINGIS) in Hungary. The basis of this work was a qualification methodology (vineyard and wine cellar cadastre system) dating back to several decades, however, in the 1980s and 1990s the available geographical maps and information technology did not provide enough accuracy for an overall evaluation of viticultural areas. The reason for the VINGIS elaboration and development was an obligation resulting from the EU membership to ensure the agricultural subsidies for the wine–viticulture sector.