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:
Issue: Open GPB 2024
Type: Article
Authors
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
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Keywords
QTL browser, database, manual curation, Vitis ontology, FAIR