Plant & Animal Genomes XVII Conference

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

Large Scale Marker Identification And Validation In Expressed Sequences From Atlantic Cod (Gadus morhua).

Sophie Hubert¹ , Brent Higgins¹ , Garry Simpson¹ , Sharen Bowman^{1, 2}

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

²  Department of Process Engineering and Applied Science, Dalhousie University, Halifax, NS, B3J 1Z1, Canada

Atlantic cod (Gadus morhua) is a species with increasing economic significance for aquaculture. In support of the aquaculture industry in Atlantic Canada, the Atlantic Cod Genomics and Broodstock Development Project (CGP) has been established (http://www.codgene.ca) with the aim of producing large-scale genomic resources for Atlantic cod and to accelerate marker identification. From the CGP collection of 158328 expressed sequence tags (ESTs), we have identified a large number of markers, including single nucleotide polymorphisms (SNPs) and microsatellites. We have developed assays for 155 novel microsatellite markers. A subset of these markers, together with previously published cod microsatellites, were used to create a linkage map. The map currently has 166 unique markers in 22 linkage groups, with an average length of 1126 cM. High throughput identification of SNPs within our collection of ESTs has lead to the detection of 4781 predicted “good quality” SNPs. We selected 3072 SNPs to be tested using the GoldenGate assay system®(Illumina). Two panels of 1536 SNPs have been tested against 2 reference families (for mapping purposes) and against different populations (Canadian and European populations). A large number of SNPs amplified successfully, with 75 % of assays validated. From these, 74.12 % of SNPs were polymorphic in the individuals tested, with 4% representing possible genome duplications. The best polymorphic SNPs will be selected to build a third array for detection of quantitative trait loci (QTL). This large collection of markers is a first step to identifying QTL and enabling marker assisted selection for Gadus morhua.