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…

Crowdsourced the assessment of wine rating: professional wine competition rating vs vivino rating

We evaluate wine ratings by comparing data from two crowdsourcing platforms – Vivino, which aggregates the opinions of a large number of wine lovers, and Global Wine Medal Rating, which aggregates the scores from more than 1030 international wine competitions since 2020.

Pierce’s disease of grapevines, a new threat to the wine industry in Southern Europe

Pierce’s disease (PD) is considered a potential threat to european viticulture (EPPO a2 list of pathogens since 1981). In the usa, infections caused by the vector-borne bacterium xylella fastidiosa have caused recurrent damage to vineyards in California and the southeastern states. However, vineyards in Europe have remained free of PD until recently, when it was first detected on the island of Mallorca in 2017. The reasons for the absence of PD in continental Europe have not been convincingly explained.

Elucidating the biological function of EPFL9 in grapevine roots

Epidermal Patterning Factors are a class of cysteine rich peptides known to be involved in many developmental processes. The role of EPF1, EPF2 and EPFL9 in controlling leaf stomata formation has been well described in model plants and cereals, and recently also in grapevine, while little is known about their activity in other organs. The aim of our study is to investigate whether VviEPFL9-2 can have a specific biological function in grapevine roots, where it resulted to be expressed. As grapevine is cultivated in the form of a grafted plant, we focused our study on the commonly used rootstock Kober 5BB (Vitis berlandieri x Vitis riparia). VviEPFL9-2 was edited in Kober 5BB plants using Agrobacterium tumefaciens transformation of embryogenic calli and the CRISPR/Cas9 technology. The phenotypic evaluation in greenhouse indicated that, as expected, the leaves of knock-out (KO) plants have a significant lower stomatal density compared to WT, associated with a lower stomatal conductance.

Elementi in traccia e ultratraccia nell’uva: possibili applicazioni ai fini della tracciabilità geografica

Nel presente studio si è ricercata la possibilità di associare l’uva al territorio mediante parametri chimici indipendenti da variabili climatiche ed antropiche.

Petiole phosphorus concentration is controlled by the rootstock genetic background in grapevine: is this a key for understanding rootstock conferred vigour?

Grapevine, Vitis vinifera, requires grafting on Phylloxera tolerant rootstocks of American origin in most viticultural areas of the world. The most commonly used species in rootstock creation are V. berlandieri, V. riparia and V. rupestris. Rootstocks not only provide tolerance to Phylloxera but assure the supply of water and mineral nutrients to the scion. The objective of this work was to determine to what extent rootstocks of different parentages alter the mineral composition of petioles of grapevine.