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…

Adsorption of tetraconazole by organic residues and vineyard organically-amended soils 

Spain is the country with the largest wine-producing area in the EU and its productivity is largely controlled applying fungicides. However, residues of these compounds can move and contaminate surface and groundwater. The objective of this work was to evaluate the capacity of bioadsorbents from different origin to adsorb and immobilize tetraconazole by themselves or when applied as organic soil amendment, and to prevent soil and water contamination by this fungicide. The adsorption of tetraconazole by 3 organic residues: spent mushroom substrate (SMS), green compost (GC) and vine pruning sawdust (VP), as well as by vineyard soils unamended and amended individually with these residues at 1.5% (w/w) was evaluated using the batch equilibrium technique.

Indice bioclimatique de qualité Fregoni

La viticulture dans le monde est sous l’étroite dépendance des conditions climatiques. En effet, la culture de la vigne est concentrée entre 30° et 50° de latitude Nord et 30° à 40° de latitude Sud

Application of satellite-derived vegetation indices for frost damage detection in grapevines

Wine grape production is increasingly vulnerable to freeze damage due to warming climates, milder winters, and unpredictable late spring frosts. Traditional methods for assessing frost damage in grapevines which combine fieldwork and meteorological data, are expensive, time-consuming, and labor-intensive. Remote sensing could offer a rapid, inexpensive way to detect frost damage at a regional scale. Remote sensing approaches were used to assess freeze damage in grapevines by evaluating satellite-derived vegetation indices (VIs) to understand the severity and spatial distribution of damage in several New York vineyards immediately after a frost event (May 17th-18th, 2023). PlanetScope 3m satellite images acquired before and after the freeze were used to map damage and measure changes in VIs for vineyards in the Finger Lakes region.

A global and regional study on winegrowers’ perceptions and adaptations to climate change

Aim: The aim of this study was to explore the current and future state of the wine sector in the context of climate change, where the goal was to obtain greater understanding on winegrowers’ perceptions and adaptations to a changing climate and its associated impacts. The study sought to provide both a global and regional perspective on these issues.

Mechanical fruit zone leaf removal and deficit irrigation practices interact to affect yield and fruit quality of Cabernet Sauvignon grown in a hot climate

Cabernet Sauvignon is the top red wine cultivar in CA, however, the hot climate in Fresno is not ideal for Cabernet Sauvignon, particularly for berry color development. Fruit-zone leaf removal and irrigation were studied previously to have the significant effect on grape yield performance and berry quality. But the timing of leaf removal and the timing of irrigation are still inconclusive. Also, mechanical fruit-zone leaf removal is relatively new in CA. Our study aims to identify the interactive effect of mechanical fruit-zone leaf removal and irrigation on Cabernet Sauvignon’s yield performance and fruit quality and find the ideal timing of leaf removal and irrigation to maximize the berry color while maintaining the sustainable yield level.