terclim by ICS banner
IVES 9 IVES Conference Series 9 VitExpress, an open interactive transcriptomic platform for grapevine

VitExpress, an open interactive transcriptomic platform for grapevine

Abstract

We developed VitExpress, an open interactive transcriptomic platform for grapevine, using our newly assembled and annotated Chasselas genome as a reference. This platform provides a genome browser and integrated web tools for expression profiling, and a set of statistical tools (StatTools) for the identification of highly correlated genes. The implementation of the correlation finder tool for MybA1, a major regulator of the anthocyanin pathway, identified candidate genes associated with anthocyanin metabolism, whose expression patterns were experimentally validated as discriminating between black and white grapes. These resources and innovative tools for mining genome-related data are anticipated to foster advances in several areas of grapevine research.

DOI:

Publication date: July 6, 2024

Issue: Open GPB 2024

Type: Poster

Authors

Guillaume Madignier1,2, Anis Djari1, Olivia Di Valentin1, Thibault Gillet1, Pierre Frasse1, Amel Djouhri1, Guojian Hu1,2, Sebastien Julliard3, Mingchun Liu4, Yang Zhang4, Farid Regad1, Julien Pirrello1, Elie Maza1,*, and Mondher Bouzayen1,*

1Laboratoire de Recherche en Sciences Végétales–Génomique et Biotechnologie des Fruits-UMR5546, Université de Toulouse, CNRS, Université Paul Sabatier, Institut Polytechnique de Toulouse, Auzeville Tolosan 31326, France
2Fondation Jean Poupelain, Cognac, Javrezac 16100, France
3Conservatoire du vignoble charentais, Institut de Formation de Richemont, Cherves-Richemont 16370, France
4Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China

Contact the author*

Keywords

Transcriptomic platform, RNA-seq, Statistics, Data mining, Anthocyanin pathway

Tags

IVES Conference Series | Open GPB | Open GPB 2024

Citation

Related articles…

VineyardFACE: Investigation of a moderate (+20%) increase of ambient CO2 level on berry ripening dynamics and fruit composition

Climate change and rising atmospheric carbon dioxide concentration is a concern for agriculture, including viticulture. Studies on elevated carbon dioxide have already been on grapevines, mainly taking place in greenhouses using potted plants or using field grown vines under higher CO2 enrichment, i.e. >650 ppm. The VineyardFACE, located at Hochschule Geisenheim University, is an open field Free Air CO2 Enrichment (FACE) experimental set-up designed to study the effects of elevated carbon dioxide using field grown vines (Vitis vinifera L. cvs. Riesling and Cabernet Sauvignon). As the carbon dioxide fumigation started in 2014, the long term effects of elevated carbon dioxide treatment can be investigated on berry ripening parameters and fruit metabolic composition.
The present study aims to investigate the effect on fruit composition under a moderate increase (+20%; eCO2) of carbon dioxide concentration, as predicted for 2050 on both Riesling and Cabernet Sauvignon. Berry composition was determined for primary (sugars, organic acids, amino acids) and secondary metabolites (anthocyanins). Special focus was given on monitoring of berry diameter and ripening rates throughout three growing seasons. Compared to previous results of the early adaptative phase of the vines [1], our results show little effect of eCO2 treatment on primary metabolites composition in berries. However, total anthocyanins concentration in berry skin was lower for eCO2 treatment in 2020, although the ratio between anthocyanins derivatives did not differ.
[1] Wohlfahrt Y., Tittmann S., Schmidt D., Rauhut D., Honermeier B., Stoll M. (2020) The effect of elevated CO2 on berry development and bunch structure of Vitis vinifera L. cvs. Riesling and Cabernet Sauvignon. Applied Science Basel 10: 2486

Functionality of different inter-stimulus rinse protocols for the sensory analysis of wildfire affected wines

From the effect of global climate change, wildfire occurrence during grape ripening has increased. These wildfires produce smoke that can carry organic compounds to a vineyard. These smoke compounds are adsorbed in the grape berry and result in wines with elevated levels of smoke-related phenols. These wines are described as having a smokey, burnt, and dirty aroma (Kristic et al, 2015). Not only are volatile phenols carried by smoke, but additionally glycoconjugate forms of these phenols are present as will. These have been found to have a large impact on the flavor of wines, being the cause of a lasting ashy aftertaste post consumption (Parker et al, 2012). When evaluating the sensory profile of these wines when tasted one after the other, there is an observed problem due to the lasting nature of these undesirable attributes and high level of carry-over from sample to sample. The aim of this work is to evaluate the extent this carryover occurs, along with the best sensory practices to mitigate its influence via different inter-stimulus rinse protocols.

Control of microbial development in wines elaborated by carbonic maceration

Carbonic Maceration (CM) winemaking is typically used in different European regions. But It is paradoxical that being a traditional processing system and widely used in many wineries, some of the phenomena that take place and the parameters that characterize them are barely known. In this vinification system the intact grape clusters are placed in a carbon dioxide (CO2) enriched medium, and they immediately change from a respiratory metabolism to an anaerobic fermentative metabolism called intracellular fermentation, which is carried out by grape enzymes. But some grapes located in the lower zone of the tank are crushed by the weight of the ones above and release must, which is fermented by yeasts.

IMPACT OF HARVEST DATE ON THE FINE MOLECULAR COMPOSITION OF MUST AND BORDEAUX RED WINE (VAR. MERLOT, CABERNET SAUVIGNON). FOCUS ON ACIDITY AND SENSORY IMPACT AFTER FIVE YEARS OF AGING

Climate change has brought several impacts that are becoming increasingly intense during the last few years and put at risk the quality of the berries or even the plant’s sustainability. Such extreme climatic events impact the composition of the wine while modulating its quality and the consumer preferences (Tempère et al., 2019). The three most important changes that take place in the must are: 1) decrease acidity, 2) increase of the concentration of sugar, hence increase of alcohol in the wine, and 3) modification
of the sensory balance and the development for example of cooked fruit aromas.

Impact of canopy management on thiol precursors in white grapes: a six-year field study

The mechanisms behind thiol precursor accumulation in grapes remain incompletely understood, nor are the ways in which they can be improved by agronomic practices. A six-year field trial studied the physiological response of the Swiss white cultivar Vitis vinifera Arvine, rich in varietal thiols and precursors, to canopy management, i.e. leaf removal and canopy height.. Five treatments were set up in a randomized block design to assess the impacts of 1) pre-flowering LR (i.e. pre-flowering or full-flowering stages) and 2) compensating for the leaf area removed in the cluster zone by increasing the trimming height (i.e. 100 or 150 cm canopy height), compared with a non-defoliated control treatment.
Intensive pre-flowering LR severely reduced yield potential (–47% on average) and reduced the concentration of 3-mercaptohexanol precursors (P-3MH) in the must (–21%; p-value < 0.10).