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.

DOI:

Publication date: June 14, 2024

Issue: Open GPB 2024

Type: Article

Authors

Silvia Vezzulli1*§, Marco Moretto, 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…

Unveiling the fungal diversity of Falanghina grapes and the role of autochthonous Saccharomyces and non-Saccharomyces yeasts in wine fermentation

Falanghina, a typical wine from the Sannio (Campania region, Italy), hosts a complex fungal microbiota that significantly influences both fermentation dynamics and sensory characteristics.

The evolution of the aromatic composition of carbonic maceration wines

The vinification by Carbonic maceration (CM) involves the process whereby the whole bunches are subjected to anaerobic conditions during several days. In this anaerobic condition, the grape endogenous enzymes begin an intracellular fermentation. This situation favors that whole grapes split open and release their juice into the tank, increasing the liquid phase that is fermented by yeasts [1]. Then, two types of wines are obtained; one from the free-run liquid in the tank (FCM) and other from the liquid after pressing the whole grape bunches (PCM). PCM wines are recognized as high quality young wines because their fruity and floral aromas[2] that although they are very intense at the end of the winemaking they gradually disappear during conservation.

Terroir, climat et sol

Le sol et le climat occupent une place prépondérante dans le concept de terroir, pour lequel l’OIV s’apprête à adopter une définition internationale. Les travaux de recherche qui ont été menés depuis une trentaine d’années sur ces thèmes et qui ont été, pour les plus importants, présentés dans les 7 premiers Congrès Internationaux des Terroirs Viticoles ont considérablement modifié les connaissances sur le fonctionnement des terroirs viticoles dans le monde et le comportement des consommateurs avertis par rapport aux vins de terroirs.

How can historical cultivars mitigate the effects of climate change?

IFV, INRAe and the national network “Partenaires de la Sélection Vigne” representing 37 organizations from the different wine regions, have been working increasingly closely over the last 2 decades towards the preservation of the French varietal patrimony. There are approximately 600 patrimonial varieties according to INRAe and SupAgro Montpellier experts, including ancient cultivars (400) and intravarietal crossbreeds obtained since the 19th century. In the context of a drastic reduction in such varieties from the mid 1980’s in favor of mainstream varieties, it was essential to carry out an inventory of old vines and vineyards. INRAe Vassal collection plays a key role here as it holds the largest diversity available, along with a rich bibliography and herbariums, offering us the opportunity to document and double check the identity of a cultivar, consolidating the expertise of ampelographers. The work is carried out in several stages, from verifying the existence of a variety in a small region, through to rehabilitation. During this session, the authors present the process that leads to the official registration of a variety. After this, IFV selection center takes over to initiate the process of selection and propagation. A specific focus within regions such as the Alps, Champagne and the South-West will provide details of the full procedure. Bia, Bouysselet, Chardonnay rose, Mecle and the aptly named Tardif, are some of the cultivars that have followed this procedure. Furthermore, a recent regulation established by INAO on “varieties of interest for adaptation purposes” might boost uptake by growers. Since 2006, 36 historical cultivars have been registered. Most of these have been neglected in the past due to late maturity, lack of sugar and high titratable acidity at harvest time. Such characteristics are today considered as positive qualities, not only in mitigation of the effects of climate change, but also as an opportunity for restoring diversity…

Application of grape pomace and stem extracts on Vitis vinifera L. cv. Monastrell: Increased stilbene content of grapes and wines

Pomace and grape stems are the main solid organic waste from winery industries, resulting from the pressing and/or fermentation processes it is generated in large amounts in many parts of the world