Plant & Animal Genomes XVI Conference

January 12-16, 2008
Town & Country Convention Center
San Diego, CA

Atlantic Cod ( Gadus morhua ) Genomics In Canada.

Sophie Hubert¹ , Stewart C. Johnson² , Matthew L. Rise³ , Cynthia Stone¹ , Jennifer Hall³ , Brent Higgins¹ , Jillian Tarrant Bussey¹ , Tiago Hori³ , Jennifer Kimball² , Charles Feng³ , Cathy Kozera¹ , Tudor Borza¹ , Sharen Bowman^1,4

¹  The Atlantic Genome Centre, Halifax, NS, B3H 3Z1, Canada

²   Institute for Marine Biosciences, National Research Council, Halifax, NS, B3H 3Z1, Canada

³  Ocean Sciences Centre, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada

⁴  Department of Process Engineering and Applied Science, Dalhousie University, Halifax, NS, B3J 1Z1

Atlantic cod (Gadus morhua) has become an important target species for aquaculture development. In order to improve cod farming in Canada, the Atlantic Cod Genomics and Broodstock Development Project (CGP) has initiated two programs in cod selective breeding, together with associated genomic research. The genomics component of the CGP will generate 160,000 expressed sequence tags (ESTs) from both normalized and Suppression Subtractive Hybridization (SSH) libraries. To date, 18 normalized cDNA libraries and 15 SSH libraries have been created using RNA prepared from different tissues and developmental stages. Several libraries have been constructed using tissues from fish stimulated with the viral mimic polyriboinosinic polyribocytidylic acid (pIC), killed Aeromonas salmonicida, thermal stress or handling/net stress. Currently, 98,856 ESTs have been obtained, and are accessible from our in-house database (http://ri.imb.nrc.ca/codgene). EST clustering of all available sequences generates 16,168 contigs and 15,804 singlets. An automated pipeline has been used to attach potential informative annotation to 30 % of ESTs. Unique sequences have been screened to identify microsatellites and contigs have been analysed to identify single nucleotide polymorphisms (SNPs). To date, we have identified 216 microsatellites and 2746 potential SNPs. Ultimately, genes of interest will be selected to create an oligonucleotide microarray with 10,000 elements, and markers will be used to generate a high density genetic map. These genomics tools will allow us to identify genes of potential importance in cod aquaculture.