Characterizing genetic resources to assess their potential for agroecology

Diversifying agricultural systems has been identified as a lever for accelerating the agroecological transition and adapting to the challenges posed by climate change. It requires increased diversity in both production systems and genetic resources used (genotypes, varieties, breeds, species). There is no single elite genetics for a species that is compatible with all systems and environments. Therefore, it is necessary to develop research that optimizes the use of genetic diversity within and between species to support the evolution of agricultural systems.

Genetic resources conserved in France represent a largely unrecognized national heritage, particularly in terms of their potential for agroecology. Accumulated over time, they include in situ populations and collections hosted by biological resource centers, with two characteristics: 1) storage often initiated before the genomics boom (lack of genomic characterization of accessions) and 2) a lack of phenotypic measurements related to selection objectives for agroecology. Therefore, it is important to characterize the genomic diversity of all available genetic resources to identify particularly promising genotypes and prioritize their phenotyping under agroecological production conditions. Genomics and high-throughput phenotyping generate large-scale data that fall within the realm of digital technologies for agroecology.

This axis aims to support projects that will:

• genetically and genomically characterize available animal and plant genetic resources, including epigenetic variability;
• study symbiotic and commensal microbial communities that contribute to the phenotypic variability of their hosts (holobionts scale);
• develop phenotyping for agroecological traits, identifying the most relevant and cost-effective measures for new objectives related to environmental footprint, resilience to climate challenges, efficiency, health, animal welfare, and more.

The funded projects contributing to this axis

Flagship research projects from the start of the program

• AgroDiv, Genomic and functional characterization of the diversity of domestic plants and animals as a keystone for agroecology: from genome to phenotype.
• HOLOBIONTS, Animal holobionts: a new biological scale to explore genetic diversity and refine selection strategies in agroecology.
   

Winner of the 2024 call for projects

• ADAAPT, agroecology and digital agriculture via animal and plant epigenetics.
   

Infrastructure projects

• PATASEL, Animal phenotyping for the agroecological transition of livestock systems.
• AgroEcoPhen, High-throughput phenotyping of plants for agroecology.
   

Winners from the 2023 thesis and postdoctoral call for projects

• "EAGLE - Artificial Intelligence for Translational Genetics in Agronomy" Ph.D. Thesis.
• "Constructing a bioinformatics pipeline to predict genomic shift in cultivated and wild fruit trees in response to climate change" Ph.D. Thesis.
   

Winner from the 2024 thesis and postdoctoral call for projects

• "Causality models and omics data integration to identify determinants of microbiome recruitment by plants", Postdoctorate.