Empreintes génomiques de la sélection et effet de la variation génétique sur les phénotypes de deux espèces d’arbres forestier (le chêne sessile) et fruitiers (l’abricotier) : focus sur les variants structuraux
- Encadrants de thèse : Véronique Decroocq (INRAE, BFP), Benjamin Linard (INRAE, MIAT)
- Début de thèse : 14 septembre 2023
- École doctorale : ED154 SVS
- Établissement : Université de Bordeaux
- Financement : Bourse ministèreille, MESR
Summary: Genetic diversity is a major determinant of the potential of organisms to adapt to environmental stresses. Domestication and selection of plant species over the last millennia have used only a small part of this diversity, so that a large part remains to be characterized and exploited. However, the characterization of this domesticated and wild genetic diversity has most often been limited to simple variations, such as nucleotide substitutions. In the framework of this thesis, the candidate will deepen the description of this genetic diversity to include variations that have a stronger impact on the structure and function of genes: structural variants, in two perennial models, apricot and sessile oak. Research:
- Pangenome constitution and structural variant (SV) detection - genome-wide. The first step of the project will be to build pangenomes from ‘complete genomes’. The necessary workflows (genome assembly and pangenome graph construction) are currently being developed in the laboratory.
- Importance of VS in the evolution of apricot and oak - population analysis. Once the VS have been detected in the pangenomes (step 1), the student will genotype them in the different apricot and oak populations presented above. The student will also look for links between genetic and environmental variations as well as signals of natural selection.
- Role of VS in adaptation and stress response - association genetics. The functional role of VS will be studied by (1) genetic association between VS and quantitative variation of the phenotypes studied (plum pox resistance and bud break in apricot, bud break and radial growth in oak) and (2) genetic-environmental correlation between VS and pedoclimatic variables.
