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A new scientific approach: addressing genetic progress through an integrated approach

The aim of the consortium is to improve the knowledge available to its members to facilitate the creation of pertinent plant varieties, grown alone or in mixes, using (or not) cover crops and/or combinations, as well as their insertion into novel culture systems. The objective will be to understand the functioning of genes, genomes and the plasticity of their responses to biotic and abiotic constraints and agronomic practices.

The agricultures of tomorrow need to be supported by innovative concepts and uses of genetics. The actions undertaken will take into account the knowledge of plant genes and genomes, detailed phenotyping of plant traits, the characterisation of biotic and abiotic environments and the management, integration and exploitation of the big data generated and made accessible according to FAIR recommendations.

The initiative will involve regular consultation and active collaboration with the research and R&D communities in the areas of biocontrol, biostimulation, agronomy and soil sciences in the first instance.

The three thematic priorities of PlantAlliance are the following:

1.     Genes and genomes - Fundamental plant biology & plant breeding

Knowledge on gene function and genome structure of crops and their wild relatives will be gained by the following studies:

1. Genetic and/or epigenetic determinism of the traits of interest,
2. Potential of the pan-genome for plant breeding, by exploiting the distributed genomes found only in certain varieties, compared to the core genome, which is found in all varieties of a species,
3. Genetic variability in crops and wild relatives, considering both lines and non-fixed populations.  

Plant breeding methods will be renewed by:

1. New pre-breeding methods, practices and technologies for the mobilisation of natural and induced genetic variability,
2. Accelerated domestication of wild relatives for crop diversification and protection by the use of new tools for translational biology,
3. Study and implementation of new breeding tools, in particular with regard to the control of reproduction and recombination,
4. Continuation of research in genome editing, in particular for the creation of new alleles,
5. Enrichment of genomic selection by taking into account structural variants, epistasis, an extended diversity and interactions with the environment.

2.     Plants and the environnement - phenotyping & enviro-typing

Technologies for plant phenotyping and environmental characterisation will be mobilised to adapt plants to diverse environments and culture systems by the following studies:

1. Identification of relevant measurements that are correlated with a trait or phenotype, and the development of detection methods and sensors,
2. Molecular phenotyping, including of a wider range of metabolites, to provide product quality markers and new resources for plant defence,
3. Biotic, physical and chemical characterisation of the environment,
4. Effect of the microbiote (rhizosphere and phyllosphere) on plant growth, development and vigour,
5. Interactions between crop pathogens/pests and their host plants to explore new ways to manage these organisms,
6. Multiscale models to predict their behaviour of crop plants in varying environments,
7. Evaluation of varieties, mixtures and populations in innovative cropping systems.

3.     Interdisciplinarity approachs for ecosystem services

Public and private stakeholders are aware of the need to build the foundations for the interdisciplinary research and development that will occur over time during the period of PlantAlliance. By “ecosystem services”, the members of PlantAlliance mean the restoration and preservation of biodiversity, the preservation of soil and water quality in production areas, carbon sequestration and reduced carbon release in the atmosphere as part of agricultural practices. Items underneath will be studied:

1. The contribution of genetics to the implementation of biocontrol solutions and novel agricultural practices,
2. The integration of all disciplines including genetics, to provide ecosystem services,
3. Socio-economic studies to facilitate the coexistence of various types of agriculture and the sustainability of new practices.

Species: cash crops, scondary species to be promoted and species to be domesticated

France is the world’s leading exporter of seeds for several species that make up a major share of agricultural products consumed and used by humans and animals. It must maintain this position while continuing efforts in the agroecological transition via a diversification of breeding objectives and species.

In this context, major targets have already been identified to help meet these challenges. Yield stability remains a major target, based on resistance to bio-aggressors and resilience to variations in the abiotic environment, as well as product quality. The range of species needs to be widened beyond the crops currently being worked on in the first wave of the Investment for the Future Programme (PIA) in the nine projects endorsed by the GIS BV2, notably by integrating species that are promising with regard to hardiness and diversification. An indicative list, likely to evolve in the future, is indicated below:

• Cereals - Major species are wheat, maize, barley and rice. Spelt (adapted to low input) and sorghum (drought tolerant) are candidates for diversification.
• Oil-protein crops - Major species are rapeseed, sunflower, pea and faba bean. Targets for diversification include soybean, flax, pulses (target species for human and soil health,) and camelina (rustic brassicaceae marketable as soil cover).
• Perennials - Major species are grapevine, temperate and tropical fruit species (apple, pear, Prunus, banana). Towards varieties adapted to climate change and resilient to emerging diseases.
• Vegetables - Focus on tomato, symbol of a tasty and healthy diet and a pivotal species for translational biology in the Solanaceae family (potato, chilli pepper, bell pepper, eggplant). Cucurbits, leaf-vegetables and root-vegetables include major crop and model species, such as melon, lettuce and carrot.
• Industrial - Major species are sugar beet and potato (starch production). Diversification targets include miscanthus and/or other perennial species for the production of biomass and bio-based materials.
• Pastures - Varieties adapted to mixtures and to polyculture livestock systems.
• Multi-service cover crops (CIMS) - Composition of mixtures for intermediate and cover crops.
• Ornamentals - A large variety of species are being worked on by numerous VSEs that rarely have the means to pursue research. Major species are rose bush and bulb plants.
• Microalgae - Keeping in mind PlantAlliance priority themes, microalgae will play a role regarding biomass, lipids, bio-stimulants and biocontrol products. Microalgae will also be considered as a model to boost carbon capture and photosynthesis efficiency.

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