Scientific Goal: « What genomic mechanisms drive the adaptation of modern species in the short (i.e. selection, domestication) but also medium and long (i.e. millions of years) evolutionary term from their extinct ancestors, i.e. Paleogenomics.
It is now clearly established that plant genomes have notably evolved through numerous series or rounds of partial (Segmental Duplication, i.e. SD) or total (Whole Genome Duplication, i.e. WGD) duplications of their genomes. Consequently, modern diploid species are all paleopolyploids. We formulate the working scientific hypothesis that, in line with recent knowledge acquired in mammals, these duplications (by doubling the gene content) induce structural and functional modifications of the genomes through genetic and epigenetic mechanisms, respectively. These duplication-mediated structural and functional genome modifications ultimately participated into the phenotypic or even physiological variability (or even adaptability) currently exploited during breeding, notably through the dissection and in fine improvement of QTL (Quantitative Trait Loci). Few precise scientific data are available at present time on the different stages of this model regarding the evolution of plant genomes, and more specifically on the impact of genome duplications (polyploidy) on the structure and function of the genes and the elaboration of complex traits of agronomic interest. Our research aims to characterise and precisely validate each stage in this model.
The first part of this research is aiming at gaining a clearer understanding of the organisation and evolutionary history of the plant (monocots and eudicots) and animal genomes from their founder ancestors. Recently, our data has enabled us to (i) propose a precise inventory of the evolutionary founding events of plant genomes (including the duplications) and (ii) gain a better understanding of their impact on gene structures, expression profiles and functions. The second part of the research focuses on the bread wheat genome which we consider to be a pertinent model to understand the impact of the structural evolutionary events (such as polyploidy, either shared by different plant species or specific to the bread wheat genome), with respect to gene expression and regulation as well as the elaboration of complex quantitative traits (QTL), with a view to their improvement in fine.
The biological questions that will be considered are therefore the following:
- What are the evolutionary events that have shaped the current genomic structure of modern plants and animals? [Task Evolution].
- What impact have these evolutionary events onto the genome organization? [Task Organization].
- What impact have these evolutionary events onto the genome regulation? [Task Regulation].
- What impact have these evolutionary events onto the development and adaptation of present-day species? [Volet Translation].
Our model, structured in 4 tasks, suggests that plant and animal species worked at INRA are paleopolyploïds (genome doubling) that were diploidized (loss of duplicates redundancy) during their evolution (task 1 'Evolution '). This diploidization took place preferentially on one of the post-duplication subgenome in defining a structural intra-genomic dominance (task 2 'Organization'). This differential plasticity of the subgenomes, probably inherited by a preferential flooding of the duplicated compartments by transposable elements, may have driven the neo-/sub-functionalization of genes (task 3 'Regulation') and ultimately mediated the adaptation to environmental constraints (task 4 'Translation').