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…

Comportement du cépage Mourvèdre dans l’aire d’Appellation d’Origine Contrôlée de Bandol

The Appellation d’Origine Contrôlée of Bandol covers an area of ​​1365 ha, 83% of which are planted with vines, the annual production being around 40,000 hl. Among the wines produced, there are mainly reds which assert themselves over time, but also rosés characterized by their pale colour, generally orange; the whites represent a small part of the production. The main grape variety of this AOC is Mouvèdre, of Spanish origin, which is also found in Provence and Languedoc.

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.

Conventions and methods towards landscape quality: an application in the Douro (Portugal)

[lwp_divi_breadcrumbs home_text="IVES" use_before_icon="on" before_icon="||divi||400" module_id="publication-ariane" _builder_version="4.19.4" _module_preset="default" module_text_align="center" text_orientation="center" custom_margin="65px||18px||false|false"...

Influence of maceration time and temperature on some bioactive compounds in Malvazija istarska white wines

The rising trend of moderate wine consumption as a part of a healthy lifestyle promotes white wines with higher phenolic content because of their bioactive properties. Duration and temperature of the maceration process have a marked impact on the content and composition of wine phenolics. The aim of this study was to explore the effect of applying maceration processes of different durations and temperature on total phenolic content and flavan-3-ol compounds concentration of Malvazija istarska (Vitis vinifera L.) wines, an autochthonous Croatian white grape variety. Vinification took place at the Institute of Agriculture and Tourism (Poreč) where pre-fermentative two days cryomaceration treatment at 8 °C (CRYO), seven days maceration treatment at 16 °C (M7), and prolonged post-fermentative maceration treatments at 16 °C for 14 days (M14), 21 day (M21), and 42 days (M42) were studied and compared to non-maceration control treatment (C). Total phenolic content was determined by the Folin-Ciocalteu colorimetric method using a UV/VIS spectrophotometer and the results were expressed as gallic acid equivalents (mg/L GAE).

Il turismo del vino: dalla logica individuale a quella di distretto

In alcuni lavori condotti alcuni anni or sono, abbiamo analizzato per un verso le tendenze della domanda di prodotti enologici, ed il comportamento del consumatore, e per un altro verso le motivazioni alla base delle scelte dell’enoturista, ovvero di colui che va per vigne e cantine per fruire di risorse enogastronomiche.