Our activities are structured according to 3 axes. The first axis aims to develop biological resources and powerful analytical tools intended to better explore genetic and genomic diversity. The second axis focuses on the characterization of sources of genomes diversity and evolution. The third axis deals with the identification of the variability of interest for specific traits.
Axis 1: Resource Development
Part of our activities is based on the establishment and characterization of biological resources for analysis of diversity and variability of interest. We have developed a collection of nearly 300 accessions of cultivated and wild African rice and participated in the complete sequencing of 260 of them as part of the”Investissement d’Avenir” program (PIA) IRIGIN France Génomique ANR-10-INBS-09. We also developed large populations of interspecific or inter-subspecific lines, and in particular a population of Nested Association Mapping (NAM) lines from crosses between the two subspecies of Asian rice.
We are also highly involved in the development of genetic analysis tools (MapDisto and CSSL Finder) or genomic analysis tools, such as Gigwa, for the large-scale management of genomic variants, or TOGGLe, a NGS workflow manager dedicated to biologists.
Finally, the progress of genomic analysis, associated with high-throughput phenotyping tools, requires the implementation of new approaches and new tools allowing the management of "massive" data and the integration of "multi-scale" data to favor an optimum use of these data. In this context, we are involved in the development of the AgroLD knowledge base (www.agrold.org), also supported by the South Green Bioinformatics platform (http://www.southgreen.fr), and the IBC PIAs ( http://www.ibc-montpellier.fr/wp/wp5) and IFB -the French node of Elixir- (http://www.france-bioinformatique.fr) with the ambition to provide tools and methods necessary to exploit the data and knowledge produced on rice (and more broadly other tropical plants).
Axis 2: Diversity and evolution of genomes analyses
Access to such genomics data, but also to transcriptomics, methylome or others data, allows us to better understand the structural and functional diversity of rice genomes, and thus their evolution and control mechanisms. Then, we explore through pangenomics approaches genome structure evolution during speciation and domestication. the pangenome concept proposes that individuals from the same species do not share the same genomic and genetic content, but share just a subset (the core-genome), the remaining part being more or less specific (dispensable-genome). For that purpose, we use the IRIGIN project data, but also the one coming from the 3,000 Rice Genome Project.
Axis 3: Analysis of the variability of interest for specific traits
We are also involved in programs of gene and allele identification for breeding. We are particularly interested in the resistance to biotic stress, including the resistance to Rice yellow mottle virus (RYMV), a major biotic constraint in Africa, and Rice hoja blanca virus (RHBV), the second leading cause of biotic stress in Central and South America, and Striga, a parasitic plant found in Africa and Asia. These programs benefit from the genetic and genomic resources developed within the team and are developed in collaboration with partner institutes (International Center for Tropical Agriculture, CIAT, Colombia, for resistance to Striga and RHBV, Africa Rice Center, Côte of Ivory, for RYMV, University of Sheffield, United Kingdom, for Striga). Genetic mapping and association genetics (GWAS) have identified genes or QTLs of interest. Thus, two major genes involved in RYMV resistance and their different allelic forms have been identified. Two candidate genes for resistance to RYMV and RHBV are also being characterized. The knowledge acquired in these programs contributes to a better knowledge of plant / pathogen interactions, especially plants / viruses, and some of them are already valued in breeding programs.