Genomic and Behavioral Diversity in Rainbow Trout
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Genomic diversity between hatchery and wild salmonids is thought to underlie differential survival rates in the wild. Decreased survival may result from a hatchery fish's inability to properly respond to a predator. In this dissertation, behavioral and physiological responses to a predator are reviewed, followed by an analysis of behavioral differences between clonal rainbow trout with wild and hatchery origins. Genomic diversity of single nucleotide polymorphisms (SNPs) in rainbow trout and evidence at the sequence level for ancestral genome duplications are analyzed and discussed.Behavioral differences were observed between hatchery and wild-derived clonal lines of rainbow trout at multiple time points after swim-up. Genetic associations with behavioral characteristics were determined through Quantitative Trait Loci (QTL) analysis and loci associated with the behaviors were mapped. Some of the identified loci had similar map locations and potentially may influence boldness in rainbow trout. Thousands of possible single nucleotide polymorphisms (SNPs) were identified among five different clonal lines of rainbow trout using a novel transcriptome analysis. This method was developed for organisms with duplicated genomes to avoid mistaking paralogous sequence variants for allelic variation (i.e. SNPs) and was demonstrated to be superior to previously published strategies of SNP discovery in polyploids.In a final study, gene copy number variance was examined in rainbow trout and other organisms. Evidence for previously reported genome duplications in a variety of organisms was found using a new method of transcriptome analysis. This strategy offers advantages in cost and efficiency over existing methods of identifying whole genome duplications.