Plant & Animal Genomes XVII Conference

January 10-14, 2009
Town & Country Convention Center
San Diego, CA

Functional Genomic Research On Atlantic Cod Immune Responses

Matthew L. Rise¹ , Stewart C. Johnson² , Charles Y. Feng¹ , Tiago S. Hori¹ , Jennifer R. Hall¹ , A. Kurt Gamperl¹ , Marlies Rise¹ , Sophie Hubert³ , Jennifer Kimball⁴ , Sharen Bowman^3,5

¹  Ocean Sciences Centre, Memorial University of Newfoundland, St. John’s, NL, Canada, A1C 5S7

²  Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC, Canada, V9T 6N7

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

⁴  Institute for Marine Biosciences, National Research Council of Canada, Halifax, NS, Canada, B3H 3Z1

⁵  Department of Process Engineering and Applied Science, Dalhousie University, Halifax, NS, Canada, B3J 1Z1

Atlantic cod (Gadus morhua) is an important species for the global fisheries and aquaculture industries. The Atlantic Cod Genomics and Broodstock Development Project (CGP web site: www.codgene.ca) has used genomic tools and techniques (e.g. normalized and reciprocal suppression subtractive hybridization cDNA library construction and characterization, expressed sequence tag assembly, identification, and functional annotation, and quantitative reverse transcription – polymerase chain reaction assay development and application) to identify and study the expression of cod genes involved in responses to immunogenic stimuli such as bacterial antigens and the viral mimic polyriboinosinic polyribocytidylic acid (poly[I:C]). Out of the ~ 158,000 expressed sequence tags (ESTs) generated by the CGP, approximately 27,000 ESTs were from immune-relevant tissues and cDNA libraries (e.g. immune-stimulated hematopoietic kidney, spleen, blood, and brain). This research has dramatically improved the characterization of the Atlantic cod immunome (i.e. all immune-responsive genes). For example, we have identified many interferon pathway genes (e.g. viperin, interferon regulatory factors 1, 7, and 10), and revealed that Atlantic cod has a RIG-I-like RNA helicase viral recognition pathway. We are currently building a 20,000-gene (20K) oligonucleotide microarray that will be a valuable resource for continuing functional genomic research on cod responses to pathogens (e.g. viral, bacterial, fungal, protozoan) and other stressors (e.g. environmental stress). A complete understanding of the genes and molecular pathways involved in cod defense responses will lead to the development of new strategies for combating disease in farmed cod, and new methods for studying the impact of pathogens and other stressors on wild cod populations.