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…

Design of microbial consortia to improve the production of aromatic amino acid derived compounds during wine fermentation

Wine contains secondary metabolites derived from aromatic amino acids (AADC), which can determine quality, stability and bioactivity. Several yeast species, as well as some lactic acid bacteria (LAB), can contribute in the production of these aromatic compounds. Winemaking should be studied as a series of microbial interactions, that work as an interconnected network, and can determine the metabolic and analytical profiles of wine. The aim of this work was to select microorganisms (yeast and LAB) based on their potential to produce AADC compounds, such as tyrosol and hydroxytyrosol, and design a microbial consortium that could increase the production of these AADC compounds in wines.

Effect of “Terroir” on quanti-qualitative paramethers of “vino nobile di Montepulciano”

In this last ten years period, there has been many integrated and interdisciplinary studies to determine the aptitude of different zones to viticulture (Lulli et al., 1989 ; Costantini, 1992 ; Fregoni et al., 1992). The researches needed some différent knowledges about environment characteristics (soil, climate), ecology, vineyard management, vine genetic, winemaking and sensory analysis. The interaction of all these knowledge produced the assessment about the environmental vocation (Scienza et al., 1992). By means of this metodology, the “viticultural vocation” joined the word “zoning”, that is the territory parting for its ecopedological and geographical characteristics in relation to adaptative answer of winegrape (Morlat, 1989).

In vitro regeneration of grapevine cv. Aglianico via somatic embryogenesis: preliminary studies for next genome editing applications  

Italy is a rich hub of viticultural biodiversity harboring hundreds of indigenous grape varieties that have adapted over centuries to the diverse climatic and geographic conditions of its regions. Preserving this biodiversity is essential for maintaining a diversified genetic pool, crucial for addressing future challenges such as climate change and emerging plant diseases. Rising temperatures, precipitation pattern variations, and extreme weather events can affect grape ripening, crop quality, and contribute to disease development. Integrated disease management necessitates exploration of novel strategies. Biotechnologies emerge as a significant player in tackling modern viticulture challenges.

PREVALENCE OF OAK-RELATED AROMA COMPOUNDS IN PREMIUM WINES

Barrel fermentation and barrel-ageing of wine are commonly utilised practices in premium wine production. The wine aroma compounds related to barrel contact are varied and can enhance a range of wine aromas and flavours, such as ‘struck flint’, ‘caramel’, ‘red berry’, ‘toasty’ and ‘nutty’, as well as conventional oaky characters such as ‘vanilla’, ‘spice’, ‘smoky’ and ‘coconut’. A survey of commercially produced premium Shiraz, Cabernet Sauvignon, Pinot Noir and Chardonnay wines was conducted, assessing the prevalence of compounds that have been proposed as barrel-ageing markers¹ including oak lactones, volatile phenols, furanones, aldehydes, thiazoles2,3, phenylmethanethiol⁴ and 2-furylmethanethiol.⁵

La perception des terroirs du vignoble des Coteaux du Layon

On peut être surpris de l’existence d’un vignoble de vins liquoreux, le vignoble des Coteaux du Layon, dans une zone septentrionale à la limite Nord de la culture de qualité de la vigne et ce d’autant plus que le cépage de ce vignoble, le Chenin ou Pineau de la Loire, est un cépage semi tardif. La première explication est à rechercher au niveau des facteurs naturels (données climatiques et géopédologiques) permettant la réalisation de ce type de produit. Il est nécessaire de souligner ici l’importance de chaque paramètre du terroir pris dans im sens large (géopédologique et climatique) et que toute variation de l’un d’entre eux, même non perceptible en première analyse à l’homme, peut avoir des incidences déterminantes sur la qualité des vins.