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Interspecific hybridization and genome doubling is a key factor of plant speciation and adaptation. These intriguing evolutionary processes entail extensive genome restructuring and reprogramming of functional regulatory pathways inherited from parental species. However, mechanisms responsible for genome stabilization and adaptation remain poorly understood. The aim of my project is to provide an interdisciplinary overview of the effects of polyploidy in a major crop. Brassica napus (oilseed rape) is an excellent system to unravel the immediate and long-term effects of polyploid speciation and adaptation under human selection. It has been made possible by the advent sequencing technologies and availability of Brassica complete genomes and transcriptomes. In my project, I will use a novel approach combining DNA Seq, RNA Seq and methylation variation levels in phenotypically contrasted polyploids. I will perform and implement in the host lab, cutting-edge methods to unravel the role of epigenetic regulation in genome stabilization. Altogether, my project will allow determining the effects of structural dynamic and epigenetic variation on (1) meiotic behaviour and fertility, (2) gene expression variation and (3) glucosinolate content. My expected findings will open a new avenue to better understand how to use genetic diversity and to modify agronomic traits through gene dosage and translocations in breeding programs.
Thanks to the rapidly evolving sequencing technologies, we are able only recently to address questions in evolutionary biology of major importance using genomic approaches (even for non-model systems). More specifically, I am interested in unravelling molecular processes (transcriptomic, genomic and epigenetic) and building an integrative understanding (from genes to eco-agrosystems) of the main molecular mechanisms involved in plant genome evolution and adaptation. These fundamental mechanisms can help us predict the faith of biodiversity in a changing environmental context and improve its management. Since 2009, I gained international experience in gene expression evolution in polyploid plant genomes (using RNA Seq), by characterising and understanding the role of transposable elements on genome evolution and gene expression, as well as on epigenetic inheritance and regulation in plants. In 2017 thanks to the AgreenSkills plus fellowship, I returned to my home country and integrated INRA and the research group IGEPP (Rennes). I am currently working on the structural and functional consequences of allopolyploid speciation with a special emphasis on the underlying molecular processes of oilseed rape adaptation. I will pursue my research at INRA with a Marie Curie Fellowship.
Ferreira de Carvalho J., Desnoues E., Zonner C., Renner S. and T. Crowthe, 2017. Nurture is more important than nature in determining leaf out timing across temperate tree species. Forest Ecosystems, 4,26. Doi: 10.1186/ s40663-017-0113-z
Morgado L., Preite V., Oplaat C., Anava S., Ferreira de Carvalho J., Rechavi O., Johannes F., and K.J.F. Verhoeven, 2017. Small RNAs reflect environment from grandparental generation in apomictic dandelions. Molecular Biology and Evolution, 34, 8, 2035-2040.
Ferreira de Carvalho J., Boutte J., Bourdau P., et al., 2017. Gene expression variation in natural populations of hexaploid (parents and hybrids) and allododecaploid Spartina species (Poaceae). Plant Systematics and Evolution, 303, 8, 1061-1079.
Ferreira de Carvalho J., de Jager V., van Gurp T., et al., 2016. Recent and dynamic transposable elements contribute to genomic divergence under asexuality. BMC Genomics 17, 884.
Ferreira de Carvalho J., Oplaat C., Pappas N., et al., 2016. Heritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants. BMC Genomics. 17: 203. Doi: 10.1186/s12864-016-2524-6.
2018 Travel award to the Evolution meeting (Montpellier, France) funded by the Society for the Study of Evolution.
2012 Travel Award to the Plant and Animal Genome Meetings (San Diego, USA) financed by the French Society of Genetics.
2010 Scholarship from VAS PhD School to attend the International European course on Comparative Genomics and Epigenomics at Ecole Normale Supérieure of Lyon, France
2010 1st prize for the best oral and poster presentation at the PhD school (VAS) meeting, Rennes, France.