terclim by ICS banner
IVES 9 IVES Conference Series 9 The grapevine QTLome is ripe: QTL survey, databasing, and first applications

The grapevine QTLome is ripe: QTL survey, databasing, and first applications

Abstract

Overarching surveys of QTL (Quantitative Trait Loci) studies in both model plants and staple crops have facilitated the access to information and boosted the impact of existing data on plant improvement activities. Today, the grapevine community is ready to take up the challenge of making the wealth of QTL information F.A.I.R.. To ensure that all valuable published data can be used more effectively, the myriad of identified QTLs have to be captured, standardised and stored in a dedicated public database.
As an outcome of the GRAPEDIA initiative, QTL-dedicated experts from around the world have gathered to compile the grapevine QTLome: the complete information (e.g., map positions, associated phenotypes) describing all experimentally supported QTLs for a specific trait. This has led to the collection of more than 150 published QTL papers and to the FAIRification of the fields relevant to the grapevine QTL database. A grapevine-QTL frontend application for uploading data has been developed to support QTL curators.
For each specific trait, the QTLome will be anchored firstly to the grapevine reference PN40024.T2T(v5) genome/annotation and secondly to the published diverse genome assemblies. The generated “Grapevine QTL browser” will (i) enhance the understanding of the genetic architecture of diverse phenotypes, (ii) reveal consistent QTLs across studies (consensus genomic intervals), which are particularly valuable for marker-assisted breeding, (iii) assist the identification of candidate genes (relevant alleles) and their integration into biological/biotechnological applications. The potential of this resource will be demonstrated by a case study.

Download the abstract

DOI:

Publication date: June 14, 2024

Issue: Open GPB 2024

Type: Article

Authors

Silvia Vezzulli1*§, Marco Moretto1§, Paola Bettinelli1, Javier Tello2, Pablo Carbonell-Bejerano2, Agnès Doligez3, Elsa Chedid4, Marina de Miguel4, Elisa Marguerit4, Éric Duchêne5, Ludger Hausmann6, Franco Röckel6, Daniela Holtgräwe7, Noam Reshef8, Varoostha Govender9, Justin Lashbrooke9, Claudia Muñoz-Espinoza10, Marco Meneses11, Patricio Hinrichsen11, Summaira Riaz12, Chin Feng Hwang13, Lance Cadle-Davidson14, Diana Bellin15, Alessandra Amato15, Marianna Fasoli15, José Tomás Matus16, Lakshay Anand17, Camille Rustenholz5, Laura Costantini1

1 Fondazione Edmund Mach, Research and Innovation Centre, San Michele all’Adige, Trento, Italy
2 Instituto de Ciencias de la Vid y del Vino, CSIC, Universidad de la Rioja, Gobierno de La Rioja, Logroño, Spain
3 AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
4 EGFV, Université de Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
5 SVQV, INRAE-University of Strasbourg, Colmar, France
6 Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
7 Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, Bielefeld, Germany
8 Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
9 Department of Genetics, Stellenbosch University, Matieland, South Africa
10 Department of Plant Production, Faculty of Agronomy, Universidad de Concepción, Chillán, Chile
11 Instituto de Investigaciones Agropecuarias, INIA La Platina, Santiago, Chile
12 Crop Diseases, Pests and Genetics Research Unit, USDA-ARS San Joaquin Valley Agricultural Sciences Center, Parlier, California, USA
13 State Fruit Experiment Station at Mountain Grove Campus, Missouri State University, Springfield, Missouri, USA
14 USDA-ARS Grape Genetics Research Unit, Geneva, New York, USA
15 Department of Biotechnology, University of Verona, Verona, Italy
16 Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Valencia, Spain
17 Environmental Epigenetics and Genetics Group, Department of Horticulture, University of Kentucky, Lexington, Kentucky, USA

§ equally contributed

Contact the author*

Keywords

QTL browser, database, manual curation, Vitis ontology, FAIR

Tags

IVES Conference Series | Open GPB | Open GPB 2024

Citation

Related articles…

Recherche de relations entre terroir et caractéristiques sensorielles des eaux-de-vie de Cognac

[lwp_divi_breadcrumbs home_text="IVES" use_before_icon="on" before_icon="||divi||400" module_id="publication-ariane" _builder_version="4.19.4" _module_preset="default" module_text_align="center" module_font_size="16px" text_orientation="center"...
Read More

Research on the origin and the side effects of chitosan stabilizing properties in wine

Fungal chitosan is a polysaccharide made up of glucosamine and N-acetyl-glucosamine and derived from chitin-glucan of Aspergillus niger or Agaricus bisporus. Fungal chitosan has been authorized as an antiseptic agent in wine since 2009 (OIV) and in organic wine in 2018. At the maximum dose of 10g/hl, it was shown to eliminate Brettanomyces bruxellensis, the main spoilage agent in red wines. Fungal chitosan is highly renewable, biocompatible (ADI equivalent to sucrose) and non-allergenic. However, winemakers often prefer to use sulfites (SO2), though sulfites are classified as priority food allergens, than chitosan. Indeed, many conflicting reports exist regarding its efficiency and its side effects towards beneficial wine microorganisms or wine taste. These contradictions could be explained by the heterogeneity of the fungal chitosan lots traded, the diversity of the wines (chemical composition, winemaking process), but also, by the recently highlighted huge genetic diversity prevailing in wine microbial species.

Read More

Ultra-High Pressure Homogenization (UHPH): a technique that allows the reduction of SO2 in winemaking

Ultra-High Pressure Homogenization (UHPH) is an innovative, efficient and non-thermal technology that can be applied at different stages in winemaking in order to reduce or avoid the use of sulphites. During 2022 vintage, a batch of Xarel·lo must was processed by UHPH at 300 MPa with an inlet temperature (Ti) of 4 ºC. In order to verify the influence of the UHPH treatment in wine characteristics, alcoholic fermentations with this must (UHPH) were carried out and compared with a control batch (without SO2 addition (C)) and a sulphited batch, in which 60 mg/L of total SO2 (SO2) were added.

Read More

Effects of different organic amendments on soil, vine, grape and wine, in a long-term field experiment in Chinon vineyard (France)

In a long-term experiment carried out in Chinon vineyard (37, France) during 23 years, the effects of several organic amendments were studied on soil, vine, grapes and wine. Four main treatments were compared on a calcareous sandy soil: control without organic amendment, dry crushed pruning wood at 2.1.t-1.ha-1.year-1 (D1), cow manure at 10 t-1. ha-1.year-1 (D1) and cow manure applied at 20 t-1.ha-1.year-1 (D2). D1 levels were calculated to fill the annual humus losses by mineralization.

Read More

Impact of varying ethanol and carbonation levels on the odor threshold of 1,1,6-trimethyl-1,2-dihydronaphtalene (petrol off-flavor) and role of berry size and Riesling clones

1,1,6-trimethyl-1,2-dihydronaphtelene (TDN) evokes the odor of “petrol” in wine, especially in the variety Riesling. Increasing UV-radiation due to climate change intensifies formation of carotenoids in the berry skins and an increase of TDN-precursors1. Exploring new viticultural and oenological strategies to limit TDN formation in the future requires precise knowledge of TDN thresholds in different matrices. Thresholds reported in the literature vary substantially between 2 µg/L up to 20 µg/L2,3,4 due to the use of different methods. As Riesling grapes are used for very different wine styles such as dry, sweet or sparkling wines, it is essential to study the impact of varying ethanol and carbonation levels.

Read More