I set out to identify candidate genes that can be used to develop genetic markers associated with Upper Temperature Tolerance (UTT) for use in a genomics-assisted broodstock program for Arctic charr (Salvelinus alpinus) and for examining wild populations at risk due to climate change. This was accomplished using genomic resources available for Atlantic salmon (Salmo salar), which allowed me to identify and examine genomic regions and specific genes of interest. In addition, I conducted expression profiling of Arctic charr exposed to acute and chronic thermal stress. Using comparative genomics, I identified several Atlantic salmon fingerprint scaffolds containing markers associated with UTT in Arctic charr and rainbow trout (Oncorhynchus mykiss). One of these was fully sequenced using 454 GS FLX next-generation sequencing and annotated, which identified nine genes in the putative Quantitative Trait Locus (QTL) region of the Atlantic salmon genome. This analysis also provided evidence that the 454 sequencing technology was suitable for partial assembly and gene annotation, but not for de novo whole genome sequencing of a complex salmonid genome. Next, I conducted expression profiling of phenotypically tolerant and intolerant Arctic charr. The differentially expressed genes were compared with those identified within the UTT QTL sequenced previously, which suggested COUP-TFII as a particularly interesting candidate gene. Heat shock proteins (Hsps) and hemoglobins were also significantly associated with acute thermal stress. Concurrently, I performed expression profiling of Arctic charr exposed to moderate, chronic temperature stress that mimicked a more realistic situation. Again, Hsps were identified in the thermal stress response, as well as ribosomal proteins, which were up-regulated throughout the exposure and the recovery period. Finally, I identified and fully annotated all of the hemoglobin genes in Atlantic salmon. This identified substantially more hemoglobin genes in this species than in any other fish analyzed to date, and included several non-Bohr beta hemoglobins, which may be used in emergency response situations. Combined, the findings of my research have substantial implications for developing a temperature tolerant Arctic charr broodstock and for examining wild populations of salmonids for responses to temperature stress brought by climate change.
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Thesis advisor: Davidson, William S.
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