terclim by ICS banner
IVES 9 IVES Conference Series 9 Exploring the gene regulatory networks of WRKY family in grapevine (Vitis vinifera  L.) using DAP-Seq

Exploring the gene regulatory networks of WRKY family in grapevine (Vitis vinifera  L.) using DAP-Seq

Abstract

The recent development of regulatory genomics has raised increasing interest in plant research since transcriptional regulation of genes plays a pivotal role in many biological processes. By shedding light on the target genes of the various transcription factors (TFs), it is therefore possible to infer the influence they exert on the different molecular mechanisms. In this regard, the attention was focused on WRKYs, a family of TFs almost exclusively found in plant species. In grapevine, WRKYs are involved in several biological processes, playing a key role in berry development, hormonal balance and signalling, biotic and abiotic stresses responses, and secondary metabolites biosynthesis. In this study, DAP-Seq was used to investigate the regulatory activity of the whole WRKY family in gDNA from young leaves of Cabernet Franc. This approach allowed the definition of the WRKYs cistrome (i.e., the set of bound genes). 46 out of 59 WRKYs gave results, outlining a total number of 674,407 binding events along whole grapevine genome, of which 459,791 (68%) are localized in the perigenic region, according to its intense regulatory activity. Cistrome maps were integrated with gene centred co-expression networks based on a large transcriptomics dataset, and with the results of an ATAC-Seq. This allowed to isolate some High Confidence Targets, characterized by high degree of co-expression with the related TF and laying down in genomic regions of open chromatin. The networks generated can be used to provide a complete regulatory map of WRKY family, shedding light on its biological role in grapevine.

DOI:

Publication date: June 14, 2024

Issue: Open GPB 2024

Type: Article

Authors

Gabriele Magon1*, Giovanni Gabelli1, Carlotta Pirrello2, Sara Zenoni3, Valerio Licursi4, Luis Orduña Rubio5, Gabriele Magris6, Margherita Lucchin1, Josè Tomàs Matus5, Mario Pezzotti3, Michele Morgante6 and Alessandro Vannozzi1

1 Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), Università degli Studi di Padova, Viale dell’Università 16 – 35020 Legnaro (PD), Italy
2 Research and Innovation Center, Fondazione Edmund Mach, Via Edmund Mach 1 – 38098 San Michele all’Adige (TN), Italy
3 Department of Biotechnology, Cà Vignal 1 – Università degli Studi di Verona, Strada Le Grazie 15 – 37134 Verona (VR), Italy
4 Department of Biology and Biotechnology “Charles Darwin” – Università “La Sapienza” di Roma, Piazzale Aldo Moro 5 – 00185 Roma (RM), Italy
5 Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Carrer del Catedràtic Agustín Escardino Benlloch – 46980 Paterna, Valencia, Spain
6 Department of Agricultural, Food, Environmental and Animal Sciences (D4A) – Università degli Studi di Udine, Via delle Scienze 206 – 33100 Udine (UD), Italy

Contact the author*

Keywords

DAP-Seq, WRKY, transcription factors, gene regulation, regulatory network

Tags

IVES Conference Series | Open GPB | Open GPB 2024

Citation

Related articles…

Aroma composition of mono-varietal white wines for the production of Custoza

AIM: The appellation “Bianco di Custoza” or “Custoza”, born in 1971, is one of the oldest white wines Protected Designation of Origin in Italy.

Is your juice truly organic? An isotopic approach for certifying organic grape juice

The sustainability and authenticity of grape juice production have gained increasing attention, particularly regarding the environmental impact and health benefits of organic practices.

Simulating climate change impact on viticultural systems in historical and emergent vineyards

Global climate change affects regional climates and hold implications for wine growing regions worldwide. Although winegrowers are constantly adapting to internal and external factors, it seems relevant to develop tools, which will allow them to better define actual and future agro-climatic potentials. Within this context, we develop a modelling approach, able to simulate the impact of environmental conditions and constraints on vine behaviour and to highlight potential adaptation strategies according to different climate change scenarios. Our modeling approach, named SEVE (Simulating Environmental impacts on Viticultural Ecosystems), provides a generic modeling framework for simulating grapevine growth and berry ripening under different conditions and constraints (slope, aspect, soil type, climate variability…) as well as production strategies and adaptation rules according to climate change scenarios. Each activity is represented by an autonomous agent able to react and adapt its reaction to the variability of environmental constraints. Using this model, we have recently analyzed the evolution of vineyards’ exposure to climatic risks (frost, pathogen risk, heat wave) and the adaptation strategies potentially implemented by the winegrowers. This approach, implemented for two climate change scenarios, has been initiated in France on traditional (Loire Valley) and emerging (Brittany) vineyards. The objective is to identify the time horizons of adaptations and new opportunities in these two regions. Carried out in collaboration with wine growers, this approach aims to better understand the variability of climate change impacts at local scale in the medium and long term.

Arsenic in soil, leaves, grapes and wines

The presence of arsenic in food and beverages creates concern because of the toxicity of this element, classified as carcinogenic in humans. The arsenic concentration in soil, vine leaves and berries

Peptides diversity and oxidative sensitivity: case of specific optimized inactivated yeasts

Estimation of the resistance of a wine against oxidation is of great importance for the wine. To that purpose, most of the commonly used chemical assays that are dedicated to estimate the antioxidant (or antiradical) capacity of a wine consist in measuring the capacity of the wine to reduce an oxidative compound or a stable radical.