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…

Wine metabolomics and sensory profile in relation to terroir: A case study focusing on different wine-growing areas of Piacenza Province (Italy)

Aim: In this work, we have optimized a robust methodology for investigating possible correlations between the phytochemical profile of wine and the terroir (including the climate), considering the specific wine-growing area. In particular, the untargeted metabolomic and sensorial profiles of Gutturnio DOC commercial wines (both still and “frizzante” types) from different production areas in the Piacenza province were determined. The geographical areas taken into consideration for this study consisted in Val Tidone, Val Nure and Val d’Arda.

Read More

Viticultural zoning in the province of San Juan, Argentina. Preliminary results, year 2000

La région viticole de San Juan (Argentine) est marquée par des températures très élevées et des variations diurnes faibles. La valorisation de la connaissance de cet environnement et de ses interactions avec le fonctionnement de la vigne et le lien au vin passent par l’étude de ses terroirs et de leur caractérisation. Le point de départ de ce travail est l’étude des zones mésoclimatiques aptes à la culture de la vigne de la Province de San Juan et à la caractérisation des sols de cette même région. L’objectif est de définir le potentiel vitivinicole des zones considérées.

Read More

Field performance of red and white “pilzwiderstandsfähige” (PIWI) cultivars in the south of Uruguay

As knowledge about the oenological potential of disease-tolerant grape varieties (PIWI) continues to grow and consumer demand for product safety and sustainable production increases, more governments worldwide are permitting the cultivation of these varieties [1].

Read More

Direct SPME GC-MS determination of volatile congeners in wines without sample pre-treatment

In this work “ethanol as an internal standard” method was used for the SPME GC-MS quantification of volatile congeners in wines. Our aim was to develop a fast and simple method of wine analysis without additional procedures, reagents etc. A row of standard solutions containing some frequently found congeners in wine was prepared gravimetrically. Suggested method was compared with traditional internal standard method.

Read More

From the current probabilistic approach to a deterministic production process, a clear step towards digital transformation in the wine sector

Currently, to consistently ensure the maintenance of a wine-style while benefiting from the utmost rigor made possible by the winemaking process, the composition of the wine blend is made using sensory control. This is performed after the wine is made with no real possibility of deterministic intervention.

Read More