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Family growth response to fishmeal and plant-based diets shows genotype x diet interaction in rainbow trout (Oncorhynchus mykiss)Lindsey R. Pierce (Abstract)The ability of rainbow trout to efficiently utilize plant-based diets for growth and the genetic variation for that trait have not been thoroughly examined. In this study, growth of a pedigreed population from the commercial Kamloop strain was assessed while feeding plant-based or traditional fishmeal-based diets. Both fish oil (5.00%) and soybean oil (8.43%) were included in the plant-based diet, and only fish oil was used in the fishmeal diet (10.10%). Ninety-five full-sib families nested within 47 half-sib families were reared in a common environment. Parentage assignment was performed on approximately 1,000 fish fed each diet using eight microsatellite markers chosen for nonduplication, a minimum of five alleles with no known null alleles, at least 50% heterozygosity, and unambiguous scoring. Progeny were assigned to parental pairs using two allocation programs, PAPA and FAP, to increase accuracy and to test assignment efficiency. The fish fed the fish meal/oil diet were approximately 8% larger than the fish fed the plant-based diet (P < 0.05). A significant genotype x diet effect accounted for 5% of the random variation. The genetic correlation for growth on the two diets was 73%, with a heritability of 30% across the diets. With this, I conclude that substantial genetic variation for utilizing plant-based diets containing soybean meal and oil exists in this widely used commercial rainbow trout strain. The genetic variation can be explored to detect and select for genes involved in improved utilization of plant-based diets containing soybean meal and oil if growth on plant-based meals becomes a long-term breeding goal in rainbow trout production.iii Acknowledgements My ability to relocate, complete research, perform class assignments, work as a teaching assistant, and study would have been impossible without the support and encouragement of close family, faculty, and friends. I have made several lasting connections throughout my master's studies and will continue collaborating with these individuals.

Viral Hemorrhagic Septicemia virus (VHSv) is an RNA rhabdovirus, which causes one of the world's most serious fish diseases, infecting >80 freshwater and marine species across the Northern Hemisphere. A new, novel, and especially virulent substrain—VHSv-IVb—first appeared in the Laurentian Great Lakes about a decade ago, resulting in massive fish kills. It rapidly spread and has genetically diversified. This study analyzes temporal and spatial mutational patterns of VHSv-IVb across the Great Lakes for the novel non-virion (Nv) gene that is unique to this group of novirhabdoviruses, in relation to its glycoprotein (G), phosphoprotein (P), and matrix (M) genes. Results show that the Nv-gene has been evolving the fastest (k = 2.0x10-3 substitutions/site/year), with the G-gene at ~1/7 that rate (k = 2.8x10-4). Most (all but one) of the 12 unique Nv- haplotypes identified encode different amino acids, totaling 26 changes. Among the 12 corresponding G-gene haplotypes, seven vary in amino acids with eight total changes. The P- and M- genes are more evolutionarily conserved, evolving at just ~1/15 (k = 1.2x10-4) of the Nv-gene’s rate. The 12 isolates contained four P-gene haplotypes with two amino acid changes, and six M-gene haplotypes with three amino acid differences. Patterns of evolutionary changes coincided among the genes for some of the isolates, but appeared independent in others. New viral variants were discovered following the large 2006 outbreak; such differentiation may have been in response to fish populations developing resistance, meriting further investigation. Two 2012 variants were isolated by us from central Lake Erie fish that lacked classic VHSv symptoms, having genetically distinctive Nv-, G-, and M-gene sequences (with one of them also differing in its P-gene); they differ from each other by a G-gene amino acid change and also differ from all other isolates by a shared Nv-gene amino acid change. Such rapid evolutionary differentiation may allow new viral variants to evade fish host recognition and immune responses, facilitating long-time persistence along with expansion to new geographic areas.

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