Genomic research on Atlantic cod

Atlantic cod (Gadus morhua) is an important species for the global fisheries and aquaculture industries. The Atlantic Cod Genomics and Broodstock Development Project (www.codgene.ca) aims to generate an extensive set of molecular tools for cod, including a database containing approximately 160,000 expressed sequence tags (ESTs). To date approximately 25,000 ESTs have been generated from normalized cDNA libraries representing various tissues (e.g. gonad, liver, heart, gill, brain), and suppression subtractive hybridization (SSH) libraries are being created for the purpose of identifying cod genes responsive to immunogens or environmental stress. The high-complexity cDNA libraries are being built from tissues collected in New Brunswick and Newfoundland, and individuals from the same populations have also been used to generate families for selective breeding. ESTs are being assembled, functionally annotated, and mined for marker development. Three methods are being used to generate markers within specific genes: 1) identification of gene-linked microsatellites, 2) development of exon-primed intron-flanking (EPIC) markers, and 3) analysis of single nucleotide polymorphisms (SNPs) within EST clusters. Ultimately, these markers will be used to generate a high resolution genetic map for Atlantic cod, for studies aimed at identifying production-relevant quantitative trait loci (QTL) within the cod breeding programs. A cod gene microarray will also be developed for use in functional genomic studies.