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…

Challenges for the Implementation of commercial inoculum of arbuscular fungi in a commercial Callet vineyard (Vitis vinifera L.)

Over the past 70 years, scientific literature has consistently illustrated the advantageous effects of arbuscular mycorrhiza fungi (AMF) on plant growth and stress tolerance. Recent reviews not only reaffirm these findings but also underscore the pivotal role of AMF in ensuring the sustainability of viticulture. In fact, various companies actively promote commercial inoculants based on AMF as biofertilizers or biostimulants for sustainable viticulture. However, despite the touted benefits of these products, the consistent effectiveness of AMF inoculants in real-world field conditions remains uncertain.

Zonazione dell’area viticola doc durello

Il lavoro di zonazione riveste un ruolo importante per capire le potenzialità e la vocazionalità di una specifica area viticola. La viticoltura dovrebbe essere vista in funzione dell’obiettivo enologico che si vuole realizzare e quindi particolare importanza riveste il risultato delle vinificazioni delle uve provenienti dai vigneti delle diverse aree della zona di produzione oggetto d’indagine. La zonazione dell’area a DOC Monti Lessini Durello ha preso in esame la varietà “Durella”, vitigno autoctono del territorio, che rappresenta la maggior parte della produzione vitivinicola della zona.

TOWARDS THE SHELF-LIFE PREDICTION OF OLD CHAMPAGNE VINTAGES DEPENDING ON THE BOTTLE CAPACITY

Today, nearly one billion bottles of different sizes and capacities are aging in Champagne cellars while waiting to be put on the market. Among them, several tens of thousands of prestigious cuvees elaborated prior the 2000s are potentially concerned by prolonged aging on lees. However, when it comes to champagne tasting, dissolved CO₂ is a key compound responsible for the very much sought-after effer-vescence in glasses [1]. Yet, the slow decrease of dissolved CO₂ during prolonged aging of the most prestigious cuvees raises the issue of how long a champagne can age before it becomes unable to form CO₂ bubbles during tasting [2].

New markers for monitoring “fresh mushroom aroma” in wine: A dual approach using microbiological and chemical tools from the vineyard to winery–A synthesis of recent research advances

The ‘fresh mushroom off-flavour’ has been recognized by the wine industry as an emerging defect since the 2000s. For many years, this off-flavour was not specifically characterized and rather grouped under ‘earthy’ and ‘musty’ taints. However, it has become increasingly problematic due to its rising prevalence. In some vineyards, incidents of this off-flavour now occur as frequently as once every five years. This trend may be associated with climatic changes affecting regions that are more prone to warm and wet seasons.

Explorando el potencial bioprotector de levaduras nativas no-Saccharomyces en la vinificación: resultados preliminares

The use of the term bioprotection in winemaking refers to the use of non-chemical methods to prevent the development of undesirable microorganisms (yeasts and/or bacteria). The reason for studying this method is mainly as a natural alternative to the addition of sulfites during the pre-fermentation stages. In winemaking, the addition of s02 has multiple functions, the main ones being antiseptic and antioxidant power.