Date of Award


Publication Type

Master Thesis

Degree Name



Great Lakes Institute for Environmental Research


additive genetics, chinook salmon, fish, maternal effects, microbiome, population effects


Daniel D. Heath


Subba Rao Chaganti




A critical emerging factor in the fitness of individuals is their microbiome, defined as the community of microorganisms found in and on the body of an individual. Despite the rapidly accumulating evidence of the significant role of the microbiome to host health and disease, there is a lack of studies partitioning microbiome variation into explanatory source components in fish, especially those relating to host genetics. To address this knowledge gap, this thesis made several contributions to estimate the transgenerational effects on the microbiome of an ecologically, economically and culturally important salmonid – Chinook salmon (Oncorhynchus tshawytscha). To achieve this goal, breeding designs were utilized to estimate various genetic architecture components, including additive among- population variance, additive genetic variance and maternal effects. DNA was extracted from hindgut contents of saltwater juveniles, the surface of eyed eggs, and maternally sourced gut content and ovarian fluids. Polymerase chain reactions (PCRs) were conducted to amplify and metabarcode the 16S rRNA encoding gene, and high throughput sequencing was then used to generate millions of sequences based on amplified PCR products. Taxonomic operational units (OTUs) were generated to measure microbiome diversity and allow for microbial community profiling. Using a combination of parametric and non-parametric modelling, significant hybrid-cross and sire were found on the gut microbiome at the juvenile saltwater stage, respectively indicative of population and additive genetic effects. Further, significant maternal effects were found on the surface of eyed eggs. Although no correlations were found between the ovarian fluid and the eyed eggs, a surprising and significant similarity was found between the microbiomes of the dam-sourced ovarian fluid and hindgut samples. Together, the findings presented in this thesis contribute to the characterization of the genetic architecture underlying microbiome variation in Chinook salmon and to its adaptive potential. The results presented in this thesis will have critical consequences for fisheries and conservation efforts and lead the way to exciting microbiome research with the ultimate goal of selecting for microbiomes associated with improved survivability and performance.