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…

Low-cost sensors as a support tool to monitor soil-plant heat exchanges in a Mediterranean vineyard

Mediterranean viticulture is increasingly exposed to more frequent extreme conditions such as heat waves. These extreme events co-occur with low soil water content, high air vapor pressure deficit and high solar radiant energy fluxes and result in leaf and berry sunburn, lower yield, and berry quality, which is a major constraint for the sustainability of the sector. Grape growers must find ways to proper and effectively manage heat waves and extreme canopy and berry temperatures. Irrigation to keep soil moisture levels and enable adequate plant turgor, and convective and evaporative cooling emerged as a key tool to overcome this major challenge. The effects of irrigation on soil and plant water status are easily quantifiable but the impact of irrigation on soil and canopy temperature and on heat convection from soil to cluster zone remain less characterized. Therefore, a more detailed quantification of vineyard heat fluxes is highly relevant to better understand and implement strategies to limit the effects of extreme weather events on grapevine leaf and berry physiology and vineyards performance. Low-cost sensor technologies emerge as an opportunity to improve monitoring and support decision making in viticulture. However, validation of low-cost sensors is mandatory for practical applicability. A two-year study was carried in a vineyard in Alentejo, south of Portugal, using low-cost thermal cameras (FLIR One, 80×60 pixels and FLIR C5, 160×120 pixels, 8-14 µm, FLIR systems, USA) and pocket thermohygrometers (Extech RHT30, EXTECH instruments, USA) to monitor grapevine and soil temperatures. Preliminary results show that low-cost cameras can detect severe water stress and support the evaluation of vertical canopy temperature variability, providing information on soil surface temperature. All these thermal parameters can be relevant for soil and crop management and be used in decision support systems.

Plant nitrogen assimilation and partitioning as a function of crop load

Aims: The optimization of nitrogen use efficiency (NUE, i.e. uptake, assimilation and partitioning) is a solution towards the sustainable production of premium wines, while reducing fertilization and environmental impact. The influence of crop load on the accumulation of N compounds in fruits is still poorly understood. The present study assesses the impacts of bunch thinning on NUE and the consequences on the free amino N (FAN) profile in fruits.

Training rats to drink red wine: effects of different drinking approaches on drinking/feeding habits, weight gain and survival from myocardial infarction

The habit of regular, moderate wine consumption, particularly with meals, is associated with protective effects from coronary heart disease. Epidemiological studies looking at myocardial protection/recovery focus mainly on the effects of red wine due to its high content in antioxidants, especially polyphenols. In several previous studies, conducted in our laboratory, we have concentrated on the effects of moderate consumption of white wine, by experimental animals (rats), gaining a significant experience in technical and procedural challenges. The scientific literature, and our past experience, suggests that rats are resilient towards consumption of full bodied, barrique red wines.

Unveiling the Grapevine Red Blotch Virus (GRBV) host-pathogen arms-race via multi-omics for enhanced viral defense 

The Grapevine Red Blotch Virus (GRBV) poses a critical challenge to the wine sector, lacking a uniquely identified vector. Current control methods involve costly and labor-intensive vine removal, emphasizing the urgency for targeted alternatives. The limited understanding of intricate host-virus interactions underscores the need for foundational knowledge to develop innovative disease control strategies. These include efforts to boost the plant’s RNA interference (RNAi) response, including RNA-based topical applications.

Untangling belowground response of grapevines to cover crop competition

Cover crops are planted in vineyards for multiple benefits including soil conservation, weed management, regulation of grapevine vegetative growth