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…

CIEDE2000 colour difference value as a parameter for tracing the ageing process on wood aged spirits

It is quite common nowadays to carry out analyses which allow to control the ageing of spirits that are aged in wood casks. Many control parameters have been previously studied, such as the concentration of different phenolic compounds or the Total Polyphenol Index, in order to better understand the ageing process of wood aged spirits. On the other hand, it is frequent to analyse as a physical parameter the colour of those spirit samples, by stating them as an array of three coordinates from various colour spaces as CIE L*a*b* or CIE L*C*H*.

Effect of pH and ethanol on Lactiplantibacillus plantarum in red must fermentation: potential use of wine lees

Wine is the result of the alcoholic fermentation (AF) of grape must. Besides AF, wine can also undergo the malolactic fermentation (MLF) driven out by lactic acid bacteria (LAB). Among LAB, Oenococcus oeni and Lactiplantibacillus plantarum are the dominant species in wine. Even if O. oeni is the most common LAB undergoing MLF in wine, due to its high tolerance to wine conditions, L. plantarum can be used to undergo MLF in must. The moderate tolerance of L. plantarum to low pH and ethanol, may compromise the fermentative process in harsh wines.

Implications of herbicide, cultivation or cover crop under-vine soil management on the belowground microbiote

Soil management through cover crops in the lines of the vineyards is a common practice in viticulture, since it improves the characteristics of the soil. It has been shown that the cover crops can influence the cycle of nutrients, promote infiltration, decrease erosion, and enhance the soil microbiota biodiversity improving the grapevines. However, the area under the vines tends to be left bare by applying herbicides or tillage to avoid competition with the crop in hot climates. The use of cover crops under the vines might be a plausible alternative to the use of herbicides or cultivation, improving grapevine quality and soil characteristics. The aim of this research was to study the implications of different management of the soil under the vines (herbicide, cultivation or cover crops) on grapevine growth, water and nutritional status and belowground microbial communities.

Pruning vine-shoots as a new enological additive to differentiate and improve the quality of wines

The objective of these work was to demonstrate that toasted fragments of pruning vine-shoots added to the wines after fermentation provide them with differentiated aromatic notes and improve their quality.

Organic mulches improve vine vigour, yield and physiological response in a semi-arid region

Recycled organic mulch within the row in vineyard floor management has become an interesting ecological strategy to adapt the crop to climate change consequences in semi-arid regions.
This study aimed to assess the impact of three recycled organic mulches [straw (STR), grape pruning debris (GPD), and spent mushroom compost (SMC)] and two conventional soil management practices [herbicide (HERB) and under-row tillage (TILL)] on vegetative vigour (NDVI), production (kg/plant), and physiological parameters (δ13C in grapes and leaf gas exchange during four grapevine phenology stages). Additionally, temperature and water soil parameters were collected at three soil depths. Data was collected during the 2021 and 2022 grapevine growing seasons in La Rioja, Spain.