Development and application of molecular tools for the study of farmed and wild Atlantic cod (Gadus morhua) stocks

Atlantic cod (Gadus morhua) is a commercially and ecologically important fish inhabiting the shelf areas of the North Atlantic. Several genetic resources were developed for the study of cod in this thesis. Fifty-five new microsatellite loci in six multiplex panels were developed for characterising the wild Celtic Sea stock. The existing methodology for validation of novel microsatellite markers was improved by combining three-primer-PCR with multiplex reactions. In addition, the potential of microsatellite genotyping-by-sequencing (GBS) was investigated using a combinatorial barcoding method suitable for implementation in large-scale population genetics studies. The results confirmed a high correspondence between GBS and capillary/gel electrophoresis genotypes, but also revealed cases of homoplasy. Genetic structuring of local wild cod in waters surrounding Ireland was investigated and a baseline of genetic variation was recorded for wild cod from Celtic Sea, Irish Sea and West of Ireland using 53 microsatellite markers. The results showed that cod from the above areas likely form a genetically homogenous population. Genetic markers were employed to monitor the composition of an early phase breeding programme. Parentage analysis revealed large differences in survival between families during rearing for all three sampled year classes (2008, 2009 and 2010). These differences in survival resulted in large variation in family size which was a major contributing factor to a very low effective population size in the farmed stock for the sampled year classes. In addition, F1 broodstock fish contributing to mass spawning events were shown to have unequal reproductive contributions to the F2 cohort. These findings highlight the importance of genetic monitoring in early-phase breeding programs, shed light on the population structure of cod in Irish waters and provide new tools for both gadoid research and other research questions that can be addressed by means of microsatellite marker variation.2017-05-3