Genetic and phenotypic diversity in sockeye salmon, Oncorhynchus nerka

Abstract

The work described here was motivated by a need for improved genetic tools for the management of sockeye salmon, specifically those populations inhabiting Bristol Bay, and a desire to better understand the process of senescence in Pacific Salmon. The first chapter details the development and evaluation of single nucleotide polymorphisms assays for sockeye salmon. With hundreds or thousands of SNPs potentially available, there is interest in comparing and developing methods for evaluating SNPs to create panels of high-throughput assays that are customized for performance, research questions, and resources. Here we use five different methods to rank 43 new SNPs and 71 previously published loci for sockeye salmon: FST, informativeness (In), average contribution to principal components (LC), and the locus-ranking programs BELS and WHICHLOCI. We then tested the performance of these different ranking methods by creating 48- and 96-SNP panels of the top-ranked loci for each method and used empirical and simulated data to obtain the probability of assigning individuals to the correct population using each panel. The second chapter details the development of five new gene expression assays to investigate the mechanisms driving senescence in Pacific salmon. We assessed five different physiological processes that might be involved in senescence (olfaction, immune response, reproduction, memory, and aging) using these new assays. While expression was higher in senescent fish for all five genes surveyed there were only significant differences in expression for two genes: Viperin (immune) and TERT (aging).