Julie Ferreira de Carvalho

**INRAE Researcher** **Currently @UMR IRHS : Research Institute in Horticulture and Seeds** ***Research interests*** - Studying the bases of phenotypic diversity and how plants cope with challenging and fluctuating environments is essential to improve resilience and sustainability of biological systems. Using complex polyploid plant models I investigate the functional and structural consequences of hybridisation and genome doubling on plant genomes in an evolutionary and ecological framework. As all Angiosperms have experienced at least one round of genome doubling and as most important crops have multiple sets of chromosomes, it is paramount to dive into their genomes in the light of this complex and redundant ecosystem. I have been interested in determining the molecular (genetic, epigenetic) bases of polyploid plant phenotypes and adaptation to various environmental cues (both abiotic and biotic). I utilize multidisciplinary approaches combining quantitative genetics, evolutionary biology, ecology, experimental and molecular biology, and bioinformatics to inform the genetic and epigenetic bases of polyploid speciation and tackle important questions in plant adaptation and evolution. In the last ten years, I pushed forward the knowledge frontier around three main questions: - What are the consequences of interspecific hybridization and polyploidy on genome organization, and how do these changes contribute to functional diversification and adaptation to the environment? - How important is epigenetics in fostering new functional traits and adapted phenotypes to contrasted environments and herbivory? - What is the extent of the unexplored diversity (structural variants, genetics and epigenetics) at the intraspecific and interspecific levels, and how much of this diversity could be harvested to enhance plant response to biotic and abiotic cues? ***Scientific Skills*** - Comparative genomics and transcriptomics: Bioinformatics analyses, assemblies, annotations, differential gene transcription, SNP calling and identification of promoter regions and Transposable Elements - **Phylogeny, Quantitative and Population Genetics**: Neighbor Joining, Maximum Likelihood and Maximum Parsimony, Population structure, Genome Wide Association Studies, Genotyping analyses (DNA-Seq and DNA microarrays) - **Bio-statistics and environments**: Experimental designs (RCBD), parametric and non-parametric tests, linear models, mixed models. R programming, Rstudio, Galaxy and Unix, knowledge in Python programming - **Molecular Biology**: DNA, RNA extractions, cDNA synthesis, PCR, real-time quantitative PCR and derived methods, cloning and sequencing, library preparation for different sequencing platforms - **Epigenomics**: Bisulfite treatment and sequencing (WGBS, Epi-GBS), differential methylation level analyses, smallRNA extraction and analyses