Date of Award


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Earth and Environmental Sciences


Additive genetic effects, Chinook salmon, Genetic architecture, Maternal effects, Non-additive genetic effects, Quantitative genetics, Oncorhynchus tshawytscha, Gut immune function, Bacterial community




Population divergence through selection can drive local adaptation, which has implications for effectively restoring declining and extirpated populations. Salmonid species provide an excellent model system to explore locally adapted traits as they are reproductively isolated and experience diverse environments. Here we focused on integrated immune function, which is affected by variation in host genetics and gene transcription as well as gut microbiome (bacterial community) variation. Furthermore, we explore interactions between host gut gene transcription levels and bacterial community composition to test co-adaptation of the host and its microbiome. In chapter 2, we utilized a factorial breeding design to determine the genetic architecture of gut gene transcription and microbiome. We discovered limited but significant gut microbiome maternal effects and transcriptional additive genetic effects. Significant correlations between gut gene transcription and gut bacterial community composition highlight important functional interactions. In chapter 3, we sampled four Chinook sample populations to explore selection and drift effects on population divergence in immune allele frequencies, gene transcription and gut microbiome composition. Chinook salmon populations exhibit divergent selection in immune function, which can drive local adaptation, although drift effects were more common. Overall, this thesis provides support for co-adaptation of host immune function and their gut microbiome composition. There is thus pressing need for the inclusion of immune function, including immune gene genotype and transcription as well as the associated gut microbiome composition for conservation and commercial rearing purposes.