DEBI -Diversity, Evolution and genomics of Biotic Interactions Team

Context and Issues

Rapeseed (Brassica napus) and related Brassica species have experimented successions of ancient and recent genome duplications. Polyploidisation can play important roles in the evolutionary fate of the genes involved biotic interactions, particularly in the regulation of specialized metabolism and nonself perception, through pseudogenization, subfunctionalization and neofunctionalization. B. napus is an allotetraploid species that harbours a narrow genetic diversity due to a low number of allopolyploidization events at the origin of this species. The genetic diversity of its two (paleopolyploid) parental species, B. rapa and B. oleracea, both originating from the Mediterranean area and Europe, is an essential reservoir of diversity that can be used in oilseed rape breeding programs.

Recent evolutions of biotic constraints on oilseed rape cultures, and the desirable extension of agroecological practices have increased the need for varieties harbouring a higher diversity of genetic factors involved in the control of pests and diseases. In this perspective, a major strategy for oilseed rape relies on the introgression of genetic factors deriving from the diversity found in the parental or closely related species. This requires first to assess the genetic and functional diversity of biotic interactions on an enlarged taxonomic scale around the Brassica genus. This also requires to get a better understanding of the genomic impacts caused by interspecific hybridization, in particular the meiotic processes involved in the control of the frequency, localization and size of introgression. All those approaches not only give access to the identification and use of novel genetic factors, they also enable the understanding of the evolutionary processes involved in the diversification of traits and help for better introgression strategies to gain durable efficiency of varietal resistances. 

Objectives

The team Diversity, Evolution and genomics of Biotic Interactions was created in 2021 to 1/ study how genomic evolutionary processes in Brassicaceae can contribute to the diversification of (epi)genetics and metabolomic traits related to the control of biotic interactions, and 2/ investigate the meiotic processes specifically induced by interspecific hybridization shocks, to design new introgression strategies in cultivated Brassica

• Genome evolution in Brassicaceae and diversification of (epi)genetic and metabolomic traits associated to the control of biotic interactions.
  • The team DEBI works actively on the collect, conservation (through the Center for Biological Resources BrACySol: /About-IGEPP/Platforms/BrACySol), and genomic characterization of the diversity in B. oleracea and B. rapa (including landrace and wild accessions)
  • Based on the genetic diversity in Brassica species and in Arabidopsis thaliana, we study how structural variations (CNV, PAV), epigenetic and/or transcriptional regulations, the evolution of duplicated genes and recombination, have allowed the diversification of loci or metabolic pathways involved in resistances to pathogens. We currently work on the following interactions and pathosystems: clubroot, blackleg, broomrape (collaboration with the University of Nantes), phytophagous insects (collaboration with the team EGI, IGEPP) and microbial communities (collaboration with team PMB, IGEPP)
  • Further mechanistic characterisation is conducted for some candidate loci and metabolic pathways, and the evolution of these genes and metabolic functions is studied among Brassicaceae.
• Impact of interspecific hybridization (allotriploidy) in changing the strict control of recombination, and new strategies for the introgression of traits in cultivated Brassica
  • We study the role of (epi)genetic mechanisms in the regulation of the meiotic recombination in interspecific hybrids, as a major mechanism involved in the evolution of genomes
  • The understanding of those processes enables the creation of original genetic material, which facilitates the mapping and analysis of candidate genes underlying QTL (including in ‘cold’ regions, i.e. harbouring low recombination frequency), and that are interesting in breeding programs.

Skills and expertise

• Comparative and evolutionary genomics
• Quantitative (Epi)Genetics: disease or pathogen resistance
• Functional genomics (including Crispr-CAS9) and metabolomics
• Collect, create and maintain Brassica genetic resources

Molecular cytogenetics

Platforms

Several members of the team are in charge or belong to different regional or national platforms:

• Biological Resource Centre BrACySol (Brassica / Allium / Cynara / Solanum)
  /About-IGEPP/Platforms/BrACySol*
• Plant molecular cytogenetics platform (PFCMV)
  /About-IGEPP/Platforms/Molecular-Cytogenetics-Platform-PCMV
• Metabolic profiling and metabolomic platform (P2M2)
  /About-IGEPP/Platforms/P2M2-Platform
• GenOuest bioinformatic platform
  https://www.genouest.org/

Team leader Antoine Gravot Antoine.gravot@inrae.fr