Crosses were made between a stock of summer steelhead (Salmo gairdneri) known to be resistant to infection by Ceratomyxa shasta and stocks of summer steelhead known to be susceptible. Ceratomyxosis, the disease caused by C. shasta was initiated by exposure to Willamette River water. I found that the crosses were intermediate in susceptibility to ceratomyxosis relative to the parental stocks. There was no difference in susceptibility to ceratomyxosis between reciprocal crosses of the same stocks. Persistence of moderate susceptibility in the F₂ generation of experimental stock crosses and examples from both wild and hatchery stocks of mixed ancestry indicate long term disease problems may result from introductions of less adapted, foreign stocks. / Graduation date: 1987

Life history within a single species can vary significantly. Many of these differences are associated with varying environmental conditions. Understanding what environmental conditions cue alternate life histories within a single species has been researched extensively. In salmonid fishes, more than almost any other group, varying environmental conditions give rise to individuals within species that take markedly different life history trajectories. Oncorhynchus mykissis a species of salmonid native to the Pacific Northwest region of North America. This species has two life history forms, anadromous and resident. The anadromous form spends a portion of its life in ocean while the resident life history form completes its entire life history in freshwater. Until the decision to migrate and morphological changes associated with smoltification occur, the two life history variants of this species are indistinguishable from each other. This ambiguity in juvenile O. mykiss morphology presents challenges for conservation managers charged with protecting and increasing threatened O. mykiss populations around the Pacific Northwest because conservation efforts cannot be evaluated until juvenile fish make the decision to migrate. Microarray gene expression analysis was used to profile gene expression in juvenile populations of wild and hatchery O. mykiss to identify gene expression variation associated with alternate life history variants. This analysis identified 8 DNA sequences present in both brain and gill tissues that differ in expression in rainbow trout and steelhead hatchery stocks. Differential expression as quantified by microarrays was validated with quantitative real-time PCR. Lastly, the expression of these putative life history markers was preliminarily evaluated in a wild population of O. mykiss at sample locations in the South Fork John Day River Basin, Oregon with known ratios of juvenile anadromous and resident fish.

Gene expression profiles of tissues and cell-lines can be powerful tools for documenting the genetic response to a particular treatment, such as stressors. However, there is a paucity of information on the genetic stress response in the brain. Therefore, we attempted to profile gene expression in the brain of juvenile steelhead trout (Oncorhynchus mykiss) in response to stressors commonly encountered in aquaculture settings and similar to those encountered in hydropower dam mitigation efforts. We subjected fish to a combined out-of-water and low-water stressor totaling three hours. Plasma stress response factors indicate that fish were undergoing a physiological stress response after 3 hours of continuous stressor. We utilized suppression subtractive hybridization to identify cDNA fragments up- or down-regulated in the brain upon completion of the stressor. Forward and reverse subtractions, and sub-cloning of the purified PCR products yielded 59 clones all of which were sequenced. Sequenced cDNA fragments were subjected to BLASTn and BLASTx searches over the course of one year. Fragments fell into the following functional categories: those associated with ATP generation, signal transduction, ion transport, translational machinery, DNA packaging and mobilization, cell structure, and cDNA fragments with cryptic function. Of the 59, 12 were selected for further analysis, and 5 were confirmed to be differentially expressed by northern hybridization. The differentially expressed genes included cytochrome b, NADH dehydrogenase subunit 2, ATPsynthase subunit 6, a cDNA fragment with unknown function, and neuron specific gene 1. Our results present a first attempt to profile gene expression in the brain of fish and demonstrate the power of molecular tools at capturing large amounts of biological information without having to target any one particular gene. A gene expression profile of the brain consequent to stress provides a catalog of responses at a given time point. This catalog can then be used to isolate full-length cDNAs, localize mRNAs in the brain or other tissue, as probes to determine expression patterns and time courses of gene expression in other tissues, and for the quantification of cDNA molecules with real time PCR. / Graduation date: 2003

Transcriptomics and gene expression profiling enables the elucidation of the genetic response of an organism to various environmental cues. Transcriptomics enables the deciphering of differences between two closely related organisms to the same environment and in contrast, enables the elucidation of genetic responses of the same organism to different environmental cues. Two major methods are utilized for the study of transcriptomes, high-throughput sequencing and microarray analysis. High-throughput sequencing technologies such as the Illumina platform are relatively new and protocols must be developed for the analyses of transcriptomes (RNA-sequencing). A RNA-seq protocol was developed and refined for the Illumina sequencing platform. This protocol was then utilized for the de novo sequencing of the steelhead salmon transcriptome. Hatchery steelhead exhibit a reduced fitness compared to wild steelhead that has been shown to be genetically based. Consequently, the steelhead transcriptome was assembled, annotated, and used to identify gene expression differences between hatchery and wild fish. We uncovered many differentially expressed genes involved in metabolic processes and growth and development. This work has created a better understanding of the genetic differences between hatchery and wild steelhead salmon. Brachypodium distachyon is a monocot grass important as a model for cereal crops and potential biofuels feedstocks. To better understand the genetic response of this plant to different environmental cues, a comprehensive assessment of the transcriptomic response was conducted under a variety of conditions including diurnal/circadian light/dark/temperature environments and different abiotic stress conditions. Using a whole-genome tiling DNA microarray, we identified that the majority of transcripts in Brachypodium exhibit a daily rhythm in their abundance that is conserved between rice and Brachypodium. We also identified numerous cis-regulatory elements dictating these rhythmic expression patterns. We also identified the genetic response to abiotic stresses such as salinity, drought, cold, heat, and high light. We uncovered a core set of genes which responds to all stresses, indicating a core stress response. A large number of transcription factors were uncovered as potential nodes for regulating the abiotic stress response in Brachypodium. Moreover, promoter elements that drive specific responses to discrete abiotic stresses were uncovered. Altogether, the transcriptome analyses in this work furthers our understandings of how particular organisms respond to environmental cues and better elucidates the relationship between genes and the environment. / Graduation date: 2012 / Access restricted to the OSU Community at author's request from Oct. 5, 2011 - April 5, 2012.