Genetic bases of gene expression in brook charr (Salvelinus fontinalis): comparative study of hybrids and their parental strains

Louis Bernatchez (director) ; Céline Audet (co-director)

My project consists in understanding the mechanisms and genomic regulatory networks responsible for the observed phenotypes in brook charr (Salvelinus fontinalis) using different genomic techniques. To understand genome action and elucidate the resulting phenotype, we can study the complete genome, from gene sequences to their expression, and correlate this result with the phenotype. Within a genome, the first expression control point is its transcription regulation. We know that the mutations in structural genes maintain genetic diversity for natural selection to act upon, although mutations in regulatory genes and sequences play a more important role. Moreover, species or population hybrids allow us to study co-evolved genes and to identify possible gene interactions.

In order to study gene interactions in a non-model species, brook charr, and correlate these interactions with their growth phenotype, we created F1 hybrids from pure-bred parents (Laval, Rupert and Domestic). The brook charr were bred at the LARSA (Laboratoire Régional des Sciences Aquatiques), an aquatic facility at Laval University. The first part of my project consists of comparing 16006 gene transcriptions between parental strains and hybrids using microarrays. The observed transcription differences will be correlated to their growth phenotypes in order to identify the genes implicated in growth. These transcription results will be validated using qRT-PCR. Secondly, by using microarrays, I will identify how the parental genomes and maternal effects are implicated in genome expression, identify their contribution to the growth phenotype, and attempt to elucidate their progression of transcriptional changes during development. The last part of this project consists of determining the major control region (cis and trans regulation) of growth genes, using the pyrosequencing technique.