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…

Pharmacological basis of the J-shaped curve in biological effects of wine

The classical pharmacological model assumes that the effect of a drug is proportional to the fraction of receptors occupied by the drug. In the simplest circumstances, the relationship between dose of a drug and response, when plotted on a logarithmic scale for drug concentration, is described by a sigmoidal curve. It presumes the existence of a threshold dose, below which no biological effect appears, and a maximal response in the form of a plateau, when a further increase in the dose of drug has no effect.

Prediction of sauvignon blanc quality gradings with static headspace−gas chromatography−ion mobility spectrometry (SHS−GC−IMS) and machine learning

The main goal of the current study is the development of a cost-effective and easy-to-use method suitable for use in the laboratory of commercial wineries to analyze wine aroma. Additionally, this study attempted to establish a prediction model for wine quality gradings based on their aroma, which could reveal the important aroma compounds that correlate well with different grades of perceived quality METHODS: Parameters of the SHS−GC−IMS instrument were first optimized to acquire the most desirable chromatographic resolution and signal intensities. Method stability was then exhibited by repeatability and reproducibility. Subsequently, compound identification was conducted. After method development, a total of 143 end-ferment wine samples of three different quality gradings from vintage 2020 were analyzed with the SHS−GC−IMS instrument. Six machine learning methods were employed to process the results and construct a quality prediction model. Techniques that aim to explain the model to extract useful insights were also applied.

Unconventional methods to delve deeper into the influence of temperature and nutrition on Chardonnay wine profiles

Temperature and yeast nutrition profoundly impact wine quality and sensory attributes by modulating yeast aroma production and release during fermentation. While temperature and nitrogen’s individual effects are well-studied, their combined influence, including nutrient type and addition timing, remains underexplored. hence, this study aimed to investigate the simultaneous effects of these factors on fermentation kinetics, aroma production and sensory profile, particularly in a Chardonnay wine production selected as a quite aromatically neutral base.

Consistency of the hydraulic traits and stomatal responses in grapevines with contrasting hydraulic vulnerability

Different from wild species in arid and semiarid conditions, cultivated species are very sensitive to drought and, beyond some stress thresholds, food production is not possible

The use of cation exchange resins for wine acidity adjustment: Optimization of the process and the effects on tartrate formation and oxidative stability

Acidity adjustments are key to microbial control, sensory quality and wine longevity. Acidification with cation exchange resins -in acid cycle- offers the possibility to reduce the pH by exchanging wine cations, such as potassium (K+), for hydrogen ions (H+). During the exchange process, the removal of potassium and calcium ions contributes to limiting the formation of tartrate salts, thus offering an alternative solution to conventional methods for tartrate stability. Moreover, the reduction of wine pH and the removal of metals catalyzers (e.g. iron) could positively impact the wine’s oxidative stability. Therefore, the aims of this work were (a) to optimize the ion exchange process by testing different volumes and concentrations of sulfuric acid (H2SO4) during the acid cycle, (b) evaluate the effects of the ion exchange process on the formation of tartrate salts, and (c) analyze the oxidative stability of the treated wines.