In SURFInG, I proposed to explore structural, functional, and phenotypical consequences of allopolyploidy in oilseed rape through two objectives corresponding to different work packages (WP):
WP1. Understand processes of genome stabilization in B. napus and identify genomic regions impacting meiotic behaviour and fertility. This WP has been completely perform and all deliverables were achieved. The results of this WP have been communicated in international conferences (ESEB Montpellier France in 2018, at the Polyploidy meeting in Ghent Belgium in 2018 and at the Plant and Animal Genome conference in San Diego USA in 2020). A manuscript is being submitted to New Phytologist (I am first author of this publication).
WP2. Determine the intertwined role of genomic, transcriptomic and epigenetic dynamics in phenotypic plasticity, focusing on agronomically important traits. This WP has been divided in three main studies: (1) Association between repetitive sequences and methylation status with structural rearrangements in polyploids. To investigate this question, I used a new genome assembly published by the host laboratory (Belser et al. 2018) and performed comparative genomics to identify repetitive sequences (to this aim I supervised two Bioinformatics Master students and collaborated with researchers at the University of Rennes). These results were presented during the Polyploidy meeting in Ghent Belgium in 2018 and the manuscript is currently under review in the journal Frontiers in Plant Science (I am last author of this publication). (2) Evolution of duplicated gene expression and impact of structural variants. In tight collaboration with Mathieu Rousseau-Gueutin, Jérémy Lucas and Julien Boutte, we identified differentially expressed genes and duplicated copies (Deliverable 2.2a achieved). We also collaborated with Jérôme Salse (INRAE Clermont-Ferrand) to investigate the role of ancient polyploidy events in the diploid Brassica species and achieved Deliverable 2.2c. The results were presented in international conference and a publication is being finalized. Finally I investigated (3) genomic and transcriptomic control of an agronomically important trait. Photosynthetic pathways can be altered following allopolyploidy mainly because photosynthetic genes are encoded in both nucleus and cytoplasmic genomes. So far, only a couple studies investigated this phenomenon in allopolyploids and it was thus timely to resolve this research question that can impair development of these crops. This study has been accepted as oral presentations in two international conferences (Crucifer genetics Conference St Malo France in 2018 and ESEB Montpellier France 2018). We also published one scientific article in The Plant Journal (Ferreira de Carvalho et al. 2018) and one book chapter (Rousseau-Gueutin et al. 2018).
