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…

Oenological potential of indigenous greek grape varieties and their clones

Vine clone selection aims at the survival of clones with particularly desireable attributes for the production of high quality wines. The purpose of this research was to study the enological potential of the clones of Greek indigenous grape varieties over two vintages, 2018 and 2019.
METHODS: Two clones of the white grape varieties Moschofilero (E26 and E27), Assyrtiko (E11 and 16), Roditis (25E16 and 02E1E21) and two clones of the red grape varieties Xinomavro (19 and E2E30) and Agiorgitiko (03E40 and 41E47) were vinified under the same protocol for the white wines and common for the red wines in 2018 and 2019. The resulting products were studied for several enological parameters such as alcohol content, volatile acidity, pH, total phenolics, anthocyanins and tannins for the red wines, as well as browning tests for the white wines. The aroma profile of these ten samples was investigated through sensory analysis with intensity rating of individual attributes on a five-point scale by a trained panel.

Addition of glutathione-rich inactivated yeasts to white musts: effects on wine composition and sensory quality

Glutathione plays a key role in preventing some oxidative processes during winemaking. This molecule limits the must enzymatic oxidation, reacts with caffeic acid and generates a colourless compound that prevents subsequent browning. It also has a protective effect on wine aroma, preventing the oxidation of the volatile compounds with a high sensory impact.

Oenological features of Sangiovese wine from vinification of whole grape berries

The present study was performed in a traditional winery located in the viticultural area of Brunello di Montalcino, Siena, Italy, in the vintage 2015. Actually, in this winery Sangiovese grape musts are fermented in large oak barrels by a single strain of Saccharomyces cerevisiae previously isolated in the same winery. Pumping over operations are carried out once or twice a day until the end of alcoholic fermentations. The aim of this work was to investigate on the oenological properties of Sangiovese wine produced with the traditional winemaking process adopted by the winery under study obtained from the fermentation of whole berries compared to that from crushed grape must. In particular, two lots of 65q of Sangiovese grapes from the same 3ha vineyard were vinified in 150hL oak barrels.

Unveiling Metschnikowia spp.: mechanisms and impacts of bioprotection in winemaking

Bioprotection, leveraging beneficial microorganisms, has emerged as a sustainable approach to modern winemaking, minimizing reliance on chemical preservatives like as sulfur dioxide (SO₂).

Integrated sustainability assessment in viticulture: An indicator-based approach applied to organic vineyards

Over the past two decades, sustainable vineyard management practices have become increasingly important as the wine industry is facing critical challenges, including climate change, biodiversity loss, and soil degradation.