AgroDiv

The ongoing climate change will have a significant impact on environmental conditions, negatively affecting agriculture in various ways, from water and input availability to changes in pest and disease distribution. To address the constraints of climate change while meeting agroecological objectives, one approach is to efficiently characterize previously untapped genetic diversity stored in ex situ and in situ collections before its utilization in selection. This will be conducted for major animal (rabbits, bees, trout, chickens, pigs, goats, sheep, cattle, etc.) and plant (wheat, corn, sunflower, melon, cabbage, turnip, apricot tree, peas, fava beans, alfalfa, tomatoes, eggplants, apple trees, cherry trees, peach trees, grapevines, etc.) species in French agriculture. It has been widely demonstrated that over the past millennia of domestication and centuries of selection, only a small fraction of the available genetic diversity worldwide has been widely exploited for these animal and plant species of interest. This highlights the need to reintroduce rare (e.g., local populations), ancient, or wild diversity into selection schemes to address the challenges of climate change and agroecological transition.

To achieve this goal, based on a collection of 20,476 and 7,466 accessions of the aforementioned plant and animal species, the AgroDiv project will be organized into six work axes:

• Collect and sample selected accessions, associating them with passport data providing all necessary information for authentication.
• Decrypt this genetic diversity using state-of-the-art genotyping and sequencing methods to provide, on an unprecedented scale, genetic variants characterizing them.
• Develop user-friendly search engines and multi-omic integration methods to quickly and efficiently filter collection and field trial data to "functionally" assess accessions or populations of interest for use in future alternative systems and selection schemes.
• Optimize and develop the tools necessary to explore available diversity through population genetics approaches (from genotyping data) and pan-genomics (from genome sequence data).
• Explore the phylogenetic diversity available in collections to characterize key functional genomic regions, either at the whole-genome scale or at specific loci.
• Transfer the knowledge acquired on the genetic diversity of each species studied into a translational research approach to exploit any gene-marker allele in one species for all species where the targeted trait is of interest.

The project will thus use and develop cutting-edge genomics and genetics approaches to deeply characterize biological material and evaluate its potential value for future use in the context of agroecological transition and climate change.

This project aims to generate knowledge and a general analytical framework through data and methods that will be widely distributed to the scientific community to sustain these research efforts, following FAIR principles and Open Science guidelines.

To achieve this, the AgroDiv project relies on a unique consortium of 191 recognized specialists in genetics, genomics, biostatistics, and bioinformatics from four research institutes: INRAE, CNRS, IRD, and Inria (as well as through Joint Research Units, Universities, CEA, CIRAD, AgroParisTech, and the Institut Agro Montpellier), working in both the animal and plant domains.