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INRA 24, chemin de Borde Rouge –Auzeville – CS52627 31326 Castanet Tolosan CEDEX - France
Since 2014: INRA Scientist (CR2) at INRA Rennes (France). Team « Biodiversity and Polyploidy » (Head: A-M Chèvre) 2012-2014: Post-doctoral fellow at University of Rennes 1 (France). Team « Mechanisms generating Biodiversity » (Head: M.L. Aïnouche) 2009-2012: ARC Post-doctoral fellow at University of Adelaide (Australia) on « Endosymbiosis and gene transfer from the organelles to the nucleus (Head: J. Timmis) 2004-2008: Ph.D. in Plant Genetics at INRA Bordeaux (France). Team « strawberry genetics and breeding » (Head: B. Denoyes-Rothan) 2004: Master of Sciences in Genetics, Adaptation and Plant Production (Plant Breeding) at the ENSAR and the University of Rennes 1 (France). 2003: Bachelor in Plant Biology and Physiology at the University of Rennes 1 (France)
My main interests are related to the structural and functional evolutionary dynamics of plant genomes (nuclear and chloroplast), especially in the B. napus polyploid species.
1) Brassica polyploid genome dynamics
Polyploidy (whole genome duplication) has played a major role in the evolutionary dynamic of plants, leading to an astonishing diversity of flowering plants. On this large topic, I specifically work on two aspects: a) the immediate and long-term evolution of duplicated genes and genomes; ii) the role of epigenetic variations in modifying the recombination rules in Brassica polyploids. To that purpose, we perform multidisciplinary approaches in the team, including comparative genomics (using NGS), molecular cytogenetics, functional genetics, molecular phylogeny, and genetic mapping. Results from this research is extremely important to identify the most efficient way to increase the genetically poorly diverse B. napus species and to facilitate the introduction of characters of agronomical interest.
a) Immediate and long term evolution of duplicated genes and genomes in Brassica species
Brassica diploid species have all been subjected to a whole genome triplication event, about 22 millions years ago, and are considered as paleopolyploids. Since this event, whereas some genes retained all duplicated copies, others lost their duplicated copy. Using available Brassica genomes and NGS sequences, we study the evolutionary dynamic of these old duplicated genes and the potential benefits of having multiple gene copies (i.e. subfunctionalisation, neo-functionalisation). More recently, about 7500 years ago, B. napus (oilseed rape) was formed through the hybridization and genome doubling of the diploid species B. rapa (turnip) and B. oleracea (cabbage), adding another layer of genome complexity. To better understand B. napus evolutionary dynamics and how it became a species, we resynthesized various B. napus and studied (using SNP arrays or NGS data) how allopolyploidy impacted both genome structure (identification of homoeologous exchanges) and gene expression. We also performed comparative genomics between resynthesized and cultivated B. napus to better understand the impact of human selection on B. napus evolution.
b) Role of epigenetics in modifying the recombination rules in Brassica polyploids
To improve the low B. napus genetic diversity, which have been severely eroded by human selection, breeders can only rely on recombination. However, this mechanism is strictly controlled, with only one and rarely three crossovers (COs) per homologous chromosomes formed during meiosis. Additionally, these crossovers mainly occur in chromosomal distal regions, preventing to introduce alleles of agronomical interest localized in other genomic regions. Recently, we demonstrated that allotriploidy can modify the crossover frequency (increased number of crossovers) and their distribution (all along the chromosomes). Using comparative genomics, cytogenetics, and genetic mapping, we are currently interested in deciphering the role of epigenetic changes in modifying the recombination rules in Brassica allotriploids, as well as the role of the ploidy level on the recombination pattern in Brassica species.
2) Chloroplast genome evolution
The cytoplasmic organelles of eukaryotes – mitochondria and chloroplasts – were once free-living prokaryotic organisms. From these ancestral prokaryotes, eukaryotes acquired the novel biochemistry of oxidative phosphorylation and photosynthesis. Since these events that occurred more than a billion of years ago, a deluge of DNA is transferred from the organelles to the nucleus, leading to the functional transfer of many organellar genes in the nucleus and the reduction of the organelle genome size. To date, almost all chloroplast proteins are encoded in the nucleus, but there still are chloroplast protein complexes that are encoded by both nuclear and chloroplast genes, at the origin of the nuclear and organellar genomes co-evolution. However, as the nuclear genome is biparentally inherited whereas the organellar genome is maternally inherited in almost all flowering plants, this fine tune co-evolution may be deeply affected in the context of interspecific hybridization or allopolyploidy, In this particular context, I am interested in deciphering how allopolyploidy immediately or in the longer term the nuclear genome at the genome or gene expression levels.
Present and former Ph.D. and Post-doc students
Franz Boideau (2018-2021) ‘Mechanisms involved in the modified recombination control in Brassica allotriploids’ (co-supervision with Dr A-M. Chèvre)
Dr. J. Ferreira de Carvalho (Marie-Curie Post-doctoral fellow: 2017-2020): ‘Immediate impact of polyploidy and of human selection on the evolutionary dynamic of B. napus’ (cosupervision with Dr A-M. Chèvre)
Dr. J. Boutte (Lecturer: 2018-2019): ‘Evolutionary dynamic of polyploid genomes’
Thanina Azibi (Ph. D. student: 2016-2019): ‘Study of the molecular mechanisms involved in the loss of self-incompatibility in Brassica species’ (cosupervision with Dr A-M. Chèvre and Dr. H. Hadj-Arab)
Hélène Rousseau (Ph. D. student: 2014-2018): ‘Evolution of polyploid genomes and phenotypic novelties: example of the Spartina genus’ (cosupervision with Pr. M. Ainouche and Pr. J. Wendel)
2018-2019: INRA Grant (29 k€): ‘Role of epigenetic modifications in modifying crossover frequency and distribution in Brassica species (PI: M. Rousseau-Gueutin)
2017-2019: small project (40 k€) in a Work Package of the Plan d’Investissement d’Avenir ‘Genius’: “Duplex: Tuning a ménage à 4: how to deal with duplicated gene expression”. (PI PIA project: P. Rogowski, ENS Lyon)
2016-2017: INRA Grant (28 k€): “Impacts of hybridization and polyploidy on the evolutionary dynamic of B. napus genome (PI: M. Rousseau-Gueutin)
2016-2017: ‘Promosol’ (Brassica breeding private companies) grant: ‘A better method to introgress variability into oilseed rape’. (PI: A-M. Chèvre)
2014-2017: European ERA-CAPS grant: “Evolution of genomes: structure-function relationships in the polyploid crop species Brassica napus” (PI: I. Bancroft, Unif. of York)
Since 2014: France Genomique project: “How a polyploid becomes a new species: Brassica model” (PI: A-M. Chèvre)