Development of single nucleotide polymorphism markers for Atlantic cod (Gadus morhua) using expressed sequences

Atlantic cod (Gadus morhua) is a species with economic significance both to the capture fishery and to the aquaculture industry. Until recently, however, molecular markers available for genetic analysis in this species were limited to a few microsatellite sequences used in population studies. Here we describe the development of low and high throughput pipelines for the identification of single nucleotide polymorphisms (SNPs) in expressed sequences generated from Atlantic cod. A subset of these SNPs (47) were selected based on their observed frequency in sequence data, and, in a preliminary study, thirty-three of these have been experimentally validated and tested for variability in fish from two Atlantic Canadian populations, Bay Bulls (Newfoundland) and Cape Sable (Nova Scotia). A significant proportion of the SNPs (30) tested were polymorphic in a panel of 22 wild-caught fish. Variable SNPs were also tested to determine their patterns of inheritance in families generated from Cape Sable parents. Mendelian inheritance was observed for most SNPs tested. However, a minority of predicted SNPs (7) did not segregate as expected. For these SNPs, it appears that the predicted SNP actually represents variation between two (or more) genes having a high degree of sequence identity that assemble together after clustering. Twenty three SNPs were validated as true SNPs for Atlantic cod.