Breeding methodologies and related plant material

This topic is led in the Genetics and Breeding of Grapevine (GAV) team at the UMR SVQV, by Komlan AVIA.

Objectives

Viticulture in France and across Europe holds immense cultural and economic importance as a key export sector within the agri-food industry. However, it now faces not only heightened competition from other wine-producing countries, but also the need to swiftly adapt to climate change and respond to increasing social and regulatory pressures to significantly reduce the use of plant protection products. These products are heavily used to combat numerous vine diseases, especially downy mildew and powdery mildew, making viticulture one of the largest consumers of such treatments. In this context, the development of new grapevine varieties resistant to fungal diseases has become a crucial strategy to meet the sector’s challenges and fulfill the objectives of the European Green Deal, as reflected in the French different « Ecophyto » plans.

Since 2000, the UMR SVQV has been committed to a breeding program (known as INRAE-ResDur), using both conventional hybridization and advanced breeding methods such as marker-assisted selection (MAS) to create varieties that address emerging needs in viticulture. More recently, new selection methodologies based on genomic and multi-omic data have also been introduced. The ultimate goal is to register varieties with polygenic resistance to the main fungal diseases, as well as enhanced resilience to abiotic stresses (e.g., drought, spring frosts, etc.) that increasingly affect the sector, all while producing wines of commercial quality.

Approaches and resources

1 INRAE-ResDur: conventional phenotypic selection coupled with MAS

The selection of new varieties in the INRAE-ResDur program takes place in three stages over a period of fifteen years after the pre-breeding stage (Figure 1). The first stage (Early Selection), which consists in identifying individuals endowed with a polygenic architecture of targeted resistances, is carried out in greenhouses on young seedlings. The second stage (Intermediate Selection) in field trails, provides information on resistance levels, main agronomic traits and the organoleptic profile of the wines. It takes place in the vineyard and involves INRAE's Experimental Viticultural Units. The third and final stage (Final Selection) complies with a regulatory requirement and establishes the Value for Sustainable Cultivation and Use (VSCU) of candidate varieties for inclusion in the catalogue.

To support the change of scale required for the development of resistant varieties from INRAE’s program, while securing their deployment, an industrial project supported by BPI France has recently been funded. This project named InnoVitiPlant, relies on a consortium coordinated by Agri-Obtentions and is structured around 3 INRAE units (UMR SVQV, UMR SAVE and UMR EGFV) and IFV. Through the combination of the skills brought together, this project addresses (i) the sustainability of the genetic solution via the diversification of the gene pyramiding and (ii) the implementation of a tool for epidemiological surveillance and acquisition of agro-oenological references, (iii) by mobilizing the rootstock lever to adapt resistant vineyards to climate change and finally (iv) by enabling the adaptation of the plant production system to accelerate the availability of innovations in vineyards. Scientific and technical coordination for INRAE is done by Guillaume Arnold of the GAV team.

Figure 1: Grapevine breeding scheme used in the INRAE-ResDur program

2 Regional breeding programs

With the success of the INRAE-ResDur program, the French wine industry has shown a strong interest in the principle of grapevine breeding for disease resistance, an interest which has resulted in the launch of a dozen regional programs to create new varieties resistant mainly to mildew and powdery mildew, with a particular emphasis on the regional typicity of the wines (Figure 2). Hundreds of genotypes have been obtained from crosses between elite INRAE or IFV genitors and emblematic grape varieties from different regions and are currently being evaluated to select future resistant varieties typical of each region. These programs have been the subject of tripartite INRAE-IFV-Interprofessional agreements. The UMR SVQV has also coordinated a PNDV project called VitisExplorer (2022-2023) aimed at structuring the agronomic and oenological data from all the regional varietal creation programs into a unique database (https://observatoire.plan-deperissement-vigne.fr/vitis-explorer/app/)

Figure 2: Regional breeding programs for the selection of new grapevine varieties resistant to cryptogamic diseases with regional wine typicity.

3 Optimizing selection methodology

Despite the success of the INRAE-ResDur program led by the UMR SVQV, the lengthy selection cycle for new varieties, spanning over fifteen years, remains a significant barrier to the rapid development and diversification of resistant cultivars. Beyond disease resistance, there is a pressing need to define new vine ideotypes that integrate specific agronomic and oenological traits tailored to diverse production contexts and the evolving challenges of climate change. However, the complex genetic architecture underlying many of these traits often limits the effectiveness of traditional marker-assisted selection. The recent surge in the application of predictive modeling in agriculture presents a valuable opportunity to design and refine novel strategies that can modernize existing breeding schemes. As such, future selection frameworks should increasingly rely on integrative approaches that harness genomics and other omics data sources to accelerate and enhance varietal improvement.

To this end, Clémentine Borrelli is currently pursuing a doctoral thesis within the GAV team, leveraging the extensive plant material generated through the INRAE-ResDur program (comprising over 1,100 genotypes cultivated across vineyards and supported by multi-year, multi-site phenotypic data). Her research focuses on developing and refining genomic and phenomic selection models and evaluating their efficiency in comparison to traditional phenotypic selection methods employed within the ResDur framework.

Complementing this effort, the ANR Ecophyto Maturation project SelGenVit (2020–2024) has established and deployed a reference population for multi-omics prediction at several sites across France. This reference panel serves as a foundational tool for building and validating predictive models using material derived from regional varietal breeding programs. Ultimately, the goal is to enable faster and more accurate selection of future grapevine varieties, regardless of the ideotypes defined (Figure 3)

Figure 3: Integrating genomic selection (B) into the grapevine breeding scheme to improve the current breeding approach (A)

4 Phenotyping methodology for agronomic traits

While the costs of sequencing and genotyping have significantly decreased, phenotyping, an essential component in elucidating the genetic basis of traits for varietal innovation, remains a major bottleneck due to its high costs, time demands, and labor intensity. As artificial intelligence and predictive modeling increasingly depend on large, high-quality datasets, there is a growing need to reimagine our approach to phenotyping. In this context, we are actively developing and optimizing high-throughput phenotyping tools utilizing advanced sensors such as LIDAR, RGB and multispectral cameras, and spectroscopy, with a particular focus on applications in viticulture (e.g., the PhenoVigne platform, Figure 4). This work is coordinated by Éric Duchêne of the GAV team and aims to enhance the scalability and precision of phenotypic data acquisition in the field.

Figure 4: PhenoVigne for high-throughput phenotyping in vineyards

Staff, GAV team

• Anne ALAIS
• Guillaume ARNOLD
• Komlan AVIA
• Clémentine BORRELLI
• Éric DUCHÊNE
• Nathalie JAEGLI
• Vincent DUMAS
• Raymond MASSON
• Christine ONIMUS
• Emilce PRADO
• Aurélie UMAR-FARUK

Sources of funding

To carry out this research, the GAV team received funding from FranceAgriMer, INRAE as part of the Varietal Innovation program, ANR, BPIFrance and Horizon Europe.

Support from Agri-Obtention and IFV for the registration of new varieties under the ENTAV-INRA dual brand.

Results

Publications

• Avia, K & Le Cunff L. (2024). Varietal innovation in viticulture: challenges and prospects for the industry. Revue des Œnologues n° 191 (April 2024), pp 11-13.
• Chedid E., Avia K., Dumas V., Ley L., Reibel N., Butterlin G., Soma M.,Lopez-Lozano, R., Baret F., Merdinoglu D. & Duchêne, É. (2023). LiDAR Is Effective in Characterizing Vine Growth and Detecting Associated Genetic Loci. Plant Phenomics, 5, 0116. https://doi.org/10.34133/plantphenomics.0116
• Avia K., Schneider C., Onimus C., Arnold G., Dumas V., Umar-Faruk A., Butterlin G., Dorne M.-A., Alais A., Jaegli N., Lacombe M.-C., Piron M.-C., Prado E., Wiedemann-Merdinoglu S., Mestre P., Duchêne É., Merdinoglu D. (2023). The French grapevine breeding program ResDur: state of the art and perspectives. IVES Conference Series. https://hal.inrae.fr/hal-04231604
• Trapp O., Avia K., Eibach R., Töpfer R. (2023). How to deal with the Green Deal - Resistant grapevine varieties to reduce the use of pesticides in the EU. IVES Conference Series. https://hal.inrae.fr/hal-04231667
• Schneider C., Onimus C., Prado E., Dumas V., Wiedemann-Merdinoglu S., Dorne M-A, Lacombe M-C, Piron M-C, Umar-Faruk A., Duchêne É., Mestre P. & Merdinoglu D. (2018). Grapevine, breeding, resistance, marker-assisted selection, pyramiding, durability. 10.17660/ActaHortic.2019.1248.30

Grapevine resistant varieties

Twelve new Vitis vinifera varieties with polygenic resistance to downy and powdery mildew from the INRAE-ResDur program registered in the official catalogue of grapevine varieties.

Access the fact sheets of INRAE-ResDur varieties registered in the catalogue: