Periodic Reporting for period 1 - SURFInG (StructURal and Functional dynamics of BrassIca napus polyploid Genome)
Reporting period: 2018-05-19 to 2020-05-18
The aim of the SURFInG project was to provide a unique interdisciplinary overview of the effects of interspecific hybridization and whole genome doubling (or polyploidy) in a major crop species Brassica napus (or oilseed rape). This polyploid is an excellent model to unravel the functional and structural consequences of both ancient and recent polyploidization events. I proposed to achieve a novel approach combining different ‘omics’ datasets with thorough phenotyping on original biological material created in the host lab. Methods and outcomes of the proposal allowed pushing further our knowledge on the molecular drivers of polyploid adaptation and success in order to improve current breeding strategies. More specifically, I determined the effects of structural and functional dynamics on B. napus (1) meiotic behavior and fertility, (2) gene expression variation and (3) phenotypic diversity.
Using comparative analyses of resynthesized and natural B. napus varieties, I determined for the first time how genome stabilization occurs in oilseed rape and identify genomic regions impacting meiotic behaviour and fertility (WP1). Second, I also investigated the intertwined role of genomic, transcriptomic and epigenetic dynamics in phenotypic plasticity, focusing on agronomically important traits in three independent experimental studies (WP2). Besides successfully achieving the scientific objectives of SURFInG, I also acquired managerial skills and reached my career objectives. Finally, I transferred important conceptual and technical knowledge in terms of gene expression evolution in polyploids and networking opportunities to the host organisation.
Using comparative analyses of resynthesized and natural B. napus varieties, I determined for the first time how genome stabilization occurs in oilseed rape and identify genomic regions impacting meiotic behaviour and fertility (WP1). Second, I also investigated the intertwined role of genomic, transcriptomic and epigenetic dynamics in phenotypic plasticity, focusing on agronomically important traits in three independent experimental studies (WP2). Besides successfully achieving the scientific objectives of SURFInG, I also acquired managerial skills and reached my career objectives. Finally, I transferred important conceptual and technical knowledge in terms of gene expression evolution in polyploids and networking opportunities to the host organisation.
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).
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).
I deeply benefited from this MSCA grant, both personally and professionally. I gained maturity and management skills, which allowed me to become an independent researcher while being able to collaborate within a multidisciplinary community. For instance, only in my close vicinity in the institute, I collaborated with mathematicians, modellers, microbiologists, bioinformatician and quantitative geneticists. Thus, I am now applying for a permanent position within my host laboratory, my project is highly innovative and transdisciplinary thanks to the knowledge and collaborative skills I was able to acquire during my fellowship.
Overall, my work brought innovative questions and strengthened the competitiveness of the host team as well as the institute at the international level. The results of this work is highly relevant in addressing current challenges facing modern agriculture. My mobility to INRAE and a more applied environment was extremely fulfilling and I envision keeping this line of research in the future.
Overall, my work brought innovative questions and strengthened the competitiveness of the host team as well as the institute at the international level. The results of this work is highly relevant in addressing current challenges facing modern agriculture. My mobility to INRAE and a more applied environment was extremely fulfilling and I envision keeping this line of research in the future.