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.

Download the abstract

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…

Phloem anatomy traits predict maximum sugar accumulation rates

Heat and water stress can accelerate berry sugar accumulation and lead to excessive sugar-to-acid ratios at harvest, producing bland, overly-alcoholic wines. Selecting grapevines for slower sugar accumulation could help maintain wine quality under future, hotter conditions, but these efforts have been stymied by our limited understanding of the traits determining sugar accumulation rates. Here, we measured traits characterizing the structure and anatomy of the sugar transport system – the phloem – in 16 winegrape cultivars and tested for relationships with sugar accumulation rates and cultivar climate classifications.

Read More

Biodiversity and biocontrol ability of Trichoderma natural populations in soil vineyards from Castilla y León region (Spain)

Trichoderma is a microorganism present in many agricultural soils and some of its species could be used as natural biological control agents. In this work, the presence of natural populations of Trichoderma was estimated in soil vineyard and its biocontrol capacity against Phaeoacremonium minimum, one of the main agent causals of grapevine trunk diseases instead of using pesticides. Moreover, physicochemical variables in soil such as pH, organic matter and nutrients were evaluated to determine a possible correlation to natural populations of Trichoderma.

Read More

Methodological approach to zoning

An appellation or geographic indication should be based on the terroir concept in order to ensure its integrity. The delimitation of viticultural terroirs must include two consecutive or parallel steps, namely (a) the characterisation of the environment and identification of homogenous environmental units (basic terroir units, natural terroir units) taking all natural factors into account, as well as (b) the characterisation of the viticultural and oenological potential of these units over time.

Read More

Evoluzione stagionale delle temperature ed andamento della maturazione nel vitigno Aglianico: risultati di un quadriennio di osservazioni in Campania

In viticoltura, la comprensione dell’influenza della temperatura dell’aria sulla dinamica della maturazione assume importante rilievo in relazione all’ ottimizzazione dell’ epoca di raccolta da cui dipende in modo significativo la qualità del prodotto finale.

Read More

Evolution of acetaldehyde concentration during wine alcoholic fermentation: online monitoring for production balances

During alcoholic fermentation, acetaldehyde is the carbonyl compound quantitatively the most produced by yeasts after ethanol. The dynamics of acetaldehyde production can be divided into 3 phases. Early formation of this compound is observed during the lag phase at the beginning of fermentation before any detectable growth [1].

Read More