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Background Atlantic salmon (Salmo Salar) is a key aquaculture species in several countries. Since its critical role in economic sector and scientific research, this species has been relatively extensively investigated, in comparison with other farmed and wild aquatic species. However, the genetic components associated with growth and fillet-related traits are lack consistency, and the issue of sea louse disease in both wild and famed salmon is still unsolved. Objectives Overall aim of this project was to understand the genetic basis of growth-related traits and host resistance to sea lice using three large commercial farmed salmon populations. Specifically, the method of quantitative trait loci (QTL) mapping, genome-wide association study (GWAS), and genomic prediction (GS) were utilized to dissect the genetic architectures associated with traits of interest in our experimental populations. Prior to this, linkage mapping was performed to construct a high-density linkage map for Atlantic salmon. Results Linkage map A linkage map was firstly constructed underlying a SNP array containing 132 K validated SNPs. 96,396 SNPs were successfully assigned to 29 chromosomes that correspond to the linkage group number of European Atlantic salmon. 6.5 % of unassigned contigs, which was equal to 1 % of recent whole genome reference assembly (GCA_000233375.4) anchored to exist chromosomes by referring to linkage mapping result. Genetic components associated with growth traits Heritabilities of growth-related traits were about 0.5 to 0.6 in adult and juvenile farmed salmon. The QTL mapping and GWAS suggested the growth-related traits are likely a polygenic genetic architecture with no major QTL segregating. The prediction accuracy estimated by genomic prediction showed that approximately 5,000 SNP markers could achieve the highest accuracy in body weight and length in juvenile salmon within population. Genetic components associated with lice resistance The heritability of lice resistance was 0.22 to 0.33 using pedigree and genetic relationship matrices respectively. GWAS indicated that the host resistance to sea lice was likely polygenic with no individual SNP surpassed the genome-wide significance threshold. Genomic prediction showed that about 5 to 10 K SNPs was able to achieve the asymptote of accuracy in closely related animals, while the greatest advantage of genomic prediction was observed in non-sibling test within population. Conclusions As the growth-related traits and lice resistance are both likely polygenic and population-specific, the genomic prediction is an efficient approach to capture the genetic variances of the traits in selection candidates in experimental population, especially for traits with low heritability such as flesh colour and lice resistance. Family-based selection method is the better choice than mass selection to accumulate the genetic effects in corresponding SNP platform. Given the high cost of genotyping and field data collection, the genotyping-by-sequencing and genotype imputation are likely the way to make significant improvements in relevant research.

The intestine and associated bacterial microbiota have a central role the physiology and homoeostasis of the host. The understanding of how farming conditions affect the intestine and associated microbiota of fish is the high importance to counteract the potential threats to health and welfare. Thus, this thesis aims to understand the role of stressful husbandry conditions on the intestine and associated microbiota of rainbow trout and Atlantic salmon. Within this context, the role of Pediococcus acidilactici as health promoter was also investigated Chapter 3 investigated the replacement of fishmeal by different plant protein ingredients in rainbow trout. The results of this chapter revealed that the effect of P. acidilactici on the microbiota of distal intestine in rainbow trout was dependent on the ingredients of the diet. The results also showed that the FM substitution induced major changes in the intestinal microbiota. Moreover, the modulation induced by plant-based diets on the microbiota varied according to the ingredients used. Chapter 4 studied the effect of dietary oxytetracycline in the distal intestinal microbiota of rainbow trout and the role of P. acidilactici to ameliorate the impact of antibiotic therapy. Experimental groups fed the diets with oxytetracycline had substantial changes in the distal intestinal microbiota including a decrease in the bacterial diversity. P. acidilactici did not ameliorate the effect of antibiotic therapy in the intestinal microbiota. Chapter 5 used Atlantic salmon during smoltification to study the changes in the microbiota of distal intestine and the role of P. acidilactici to promote intestinal health. The results showed that bacterial communities in the mucosa differed from the digesta. Seawater transfer and P. acidilactici had significant changes in the intestinal microbiota of both mucosa and digesta. However, the modulatory effect of both factors evaluated was larger in the mucosa-associated microbiota than in the digesta-associated microbiota. Furthermore, P. acidilactici induced a significant increase in antiviral-related genes. Chapter 6 investigated the replacement of fish oil by rapeseed oil alone or combined with P. acidilactici on the intestinal health and microbiota of two intestinal regions in Atlantic salmon. Replacement of fish oil by rapeseed oil alone or in combination with P. acidilactici supplementation did not induce major changes in the intestinal health and microbiota. The bacterial communities found were significantly different between the pyloric caeca and mid-intestine. In conclusion, this thesis contributes to new knowledge regarding the effect of dietary supplementation of P. acidilactici and the impact of different potential challenging factors in the health and intestinal microbiota of farmed salmonid species.

Abstract The aims of this thesis included identifying ways to mitigate the economic losses of the commercial fishery in the Gulf of Bothnia resulting from fishery regulation enforced to protect wild Atlantic salmon stocks, the recent decline in survival of hatchery-reared salmon, and the dramatically increased seal-induced catch and gear damage. In addition, these solutions should facilitate safeguarding the recently-recovered wild salmon stocks and seal populations. Other goals included adding to and updating basic knowledge on the effects of increased seal populations, migrating salmon stocks, the coastal trap-net fishery, and their interactions. Seal-induced damage to the commercial fishery was found to be a significant problem throughout the Gulf of Bothnia. Catch and gear damage varied considerably among regions, fishing periods, target species and trap-net models. The regional patterns in seal-induced damage depended on the number of seals in the region and the type of gear, which is strongly associated with the netting materials. Strong and thick materials are more resistant to the attacks of hunting seals. Finer materials and larger mesh sizes that entangle fish are most prone to seal damage. Besides careful selection of the netting material it is also possible to markedly reduce damage by appropriate gear modifications. Three modified trap-net models showed promising results in terms of seal protection, with the pontoon trap being the most successful design. The total size of the spawning salmon population in the Gulf of Bothnia was c. 230 000 in the first two years of the 2000s. The proportions of wild salmon and hatchery-reared salmon, however, appeared to markedly change between years. The survival rate of cultured smolts seems to be considerably lower than that of wild smolts. Large variation in the returning migration patterns and run timing of salmon was found between sea age groups, stock components, and among and within regions. Run timing estimates revealed that the temporal regulation effectively safeguards the wild salmon, but, at the same time, a substantial proportion of the reared salmon escape the coastal fisheries in different regions. The likelihood of survival of wild salmon captured with trap-nets and then released was high, and the cumulative mortality even after several capture-and-release events was estimated to below. Trap-net capture and release did not lead to considerable changes in the normal migration behaviour of Atlantic salmon. This result suggests the potential for a selective harvesting strategy; a system where exploitable (e.g. hatchery-reared fish) and safeguarded (e.g. wild vulnerable stocks) fractions of a fish population complex could be separated in a mixed-stock fishery. However, before introducing a practical and successful selective trap-net fishery, several preconditions should be fulfilled.

Atlantic salmon (Salmo salar L.) has been domesticated since the 1960s and has undergone over 10 generations of artificial selection for economically important traits. As a result, domesticated salmon have diverged with respect to a number of phenotypic, genotypic and behavioural traits from their wild counterparts. Since the selection pressures that are present in the wild differ greatly from the ones that shape salmon under culture conditions, domesticated salmon stocks are considered to be maladapted to natural conditions. Despite strict regulations, insoluble issues pertaining to large-scale cage rearing of farmed fish mean that there is a continuous presence of farm escapees in the wild. Gene flow from escapees has been perceived as a factor in the decline of wild populations, suggested to occur through disruption of local adaptation. This study aims to improve understanding of the genetic differences between wild and domesticated stocks by comparing the transcriptomes of Figgjo (wild) and Mowi (domesticated) strains. A series of common garden experiments have been performed, utilizing pure and reciprocal hybrid crosses of the wild and domesticated stocks, reared under two different conditions and sampled at four time points and three distinct life stages (embryo, sac-fry and feeding fry). Microarray interrogations were performed employing a 44K custom microarray design to identify genes and gene pathways that are differentially expressed between the stocks. KEGG-based functional analyses have been implemented using different gene set enrichment packages, and dominance and additive parameters were calculated from normalized expression values to predict the mode of heritability of the genes identified as differentially expressed between stocks. Most biological functions represented in wild and domesticated crosses were consistent across life stages and environments. The transcriptomic differences detected between stocks in multiple developmental stages likely reflected adaptations to selection pressures differing between natural and aquaculture environments. Down-regulated environmental information processing and immune and nervous system functions in domesticated vs. wild fish may be due to local adaptation to captivity. These included reduced information acquisition and processing systems, altered stress responsiveness and changes in feeding behaviour. In line with the resource allocation theory of production trait animals, reduced immune function was coupled with increased expression of growth and development related pathways in domesticated salmon, compared to wild counterparts. Although there is support for this trade-off in all life-stages, resource allocation showed a shift over time; possibly reflecting variation in the utilization of energy sources during the transition from endogenous to exogenous feeding. Differences in cell communication and signalling pathways between wild and domesticated stocks, associated with organogenesis during the embryo stage, reflect sampling time and are indicative of altered organ development in response to domestication. Stress responses common across stocks included the down-regulation of cellular processes, including cell cycle and meiosis, and genetic information processing, such as replication and repair, transcription and translation pathways, probably reflecting the reallocation of energy resources away from growth and towards the restoration of homeostasis. Moreover, the mobilization of energy to cover the increased demands of maintaining homeostasis was indicated by the up-regulation of some metabolic pathways, mostly involved in energy, lipid and carbohydrate metabolism in response to stress. The analysis also revealed cross-specific stress responses, including indicators of a non-additive stress response in hybrid crosses. Most differentially expressed transcripts exhibited additive (31-59%) or maternal dominant (19-33%) inheritance patterns, although maternal over-dominance (23-26%) was also significant in the embryo stage. The mode of heritability of some immune transcripts was suggestive of maternal environmental influence having been affected by aquaculture. This study has demonstrated that biological functions affected by domestication include those associated with allocation of resources, involve reduction of information acquisition and processing systems and may lead to loss of local adaptation to wild conditions. Since such changes may affect key systems, such as immunity and responsiveness to stress, they can potentially have serious negative consequences under natural conditions. Transcriptomic differences observed between wild and domesticated stocks primarily exhibited additive and maternal dominant inheritance modes. Since gene-flow from farmed fish can be frequent and primarily concerns farmed females, this suggests that introgression due to repeated large scale escape events has the capacity to significantly erode local adaptation.

Despite the controversy over environmental sustainability, salmon aquaculture in British Columbia is economically important for many coastal communities and is reported as being the largest agricultural export product for the province. This thesis examined the welfare status of commercially produced Atlantic salmon smolts during transport from freshwater farms to the saltwater net pens using physiology and behaviour to assess transport stress. Smolts were transported first by truck from the freshwater farm to the dock, and then in the flow-through cargo holds of a live-haul vessel to the saltwater net pens. Fish and water were sampled before and after truck transport, and several times aboard the vessel. Assessment of stress was based on measurement of plasma cortisol, glucose, lactate, potassium, sodium and chloride concentrations, as well as behavioural observations made on underwater video footage. Seven transports of fish originating from two different hatcheries were sampled; one was a land-based tank hatchery that required a 30-min drive to the dock, and the other a lake net pen facility that was 90 min to the dock. Analysis of plasma constituents supported previous studies that recovery from the stress accumulated during loading and truck transport can be quite rapid in a live-haul vessel. Underwater video footage, recorded at the freshwater farms and in the cargo holds of the Sterling Carrier, also suggested recovery onboard in that for the most part, behaviour onboard was similar to behaviour at the freshwater farms. There were some significant differences between fish from the two types of hatcheries, particularly in the original hatchery conditions and in their behavioural responses to transport conditions; however, post-transport growth and mortality rates reported by the saltwater farms showed no significant difference. Although fish were subjected to moderately stressful conditions during part of the process, smolt transport as currently carried out by our industry partners reflects good husbandry practices and fish welfare. / Land and Food Systems, Faculty of / Graduate

The development of hydroelectric power production and the damming of water courses that ensues causes a threat to the migration patterns of Atlantic salmon (Salmo salar), by altering their habitat and compromising river connectivity. Because the species’ survival heavily depends on the completion of their migration between rivers and oceans, the design of guidance structures that promote successful passages around dams is a critical goal. Physical structures have been used to steer downwards-migrating smolts through safe fishways but they have not always proven effective, both from an ecological and economical perspective. In this study, the potential of bubbles in guiding salmon trajectories around a hydropower dam was tested as an alternative to existing guiding systems. Here the hypotheses were: i) bubbles guide downstream-migrating smolts around dams; ii) the reaction of smolts to a bubble barrier is linked to their individual boldness; iii) bubbles have varying effects on different school sizes. The first and third hypotheses were tested in the field, by recording sonar footage at the entrance of a fishway, downstream of a bubble barrier. The second hypothesis was evaluated by conducting a scototaxis experiment and an assessment of the reaction of young salmon to bubbles in the laboratory. My analysis of the fish abundance data collected in the river confirmed the first and third hypotheses. In the field, the presence of a predator (Esox lucius) was revealed to be a more influential factor than bubbles in regulating the number of smolts steered towards the fishway, indicating that predators generated a larger anxiety-like response in smolts than bubbles. In the controlled laboratory setting, there was no significant correlation between anxiety-like behaviour and reaction to bubbles and the second hypothesis did not appear to be valid. Therefore, the cause of avoidance of the barrier remains unclear, but bubble barriers seem to be an efficient and cost-effective structure for guiding downstream-migrating salmon smolts.

<p>Many salmonid populations are supported through captive breeding programs in which hatchery production supplies fish for reintroduction or supplementation efforts. In Lake Champlain, Atlantic salmon (Salmo salar) are the subject of a reintroduction effort that is complicated by the occurrence of thiamine (vitamin B1) deficiency in adult salmon returning to spawn. This deficiency results in high offspring mortality rates that must be mitigated by hatchery interventions (reviewed in Chapter 1). I used an experimental transcriptomics approach coupled with survival analyses to assess genetic variation in thiamine deficiency outcomes (i.e., survival at the family level) and identified candidate genes that may comprise a putatively adaptive response to selection imposed by thiamine deficiency (Chapter 2). Using sequence data from this study, I next compared patterns of genetic variation in the Lake Champlain population against two other populations to identify signatures of selection associated with hatchery rearing environment and differences in life history strategies (Chapter 3). Finally, I surveyed salmonid populations for density-dependent effects of adult spawning density on per capita fitness and found that in many cases, hatchery releases can contribute to decreased individual fitness. Using genotype data for returning adults in multiple populations, I also tested for reductions in effective population size (Ne) associated with hatchery supplementation and describe how increasing hatchery contribution to a population decreases Ne (Chapter 4). Together, my results demonstrate the powerful influences of hatchery supplementation on salmonid populations and suggest that specific modifications to hatchery practices can limit negative impacts of captive breeding on population genetic and demographic characteristics.</p>

Fragmentation of rivers due to the rapid expansion of hydropower plants is one of the major factors responsible for the decline in the Atlantic salmon (Salmo salar L.) in the Baltic Sea. Current methods to aid downstream migrating salmon smolt still struggle with effectively stopping the smolt from going through the hydropower turbines, by guiding them towards the available salmon ladders. A promising guiding method is using a barrier of bubbles which may serve as a non-intrusive alternative to conventional guiding structures. This study evaluated the risk of artificial selection caused using bubble barriers and compared the results with an earlier study.  The three hypotheses tested were: i) the salmon display a scototaxis behaviour related to their boldness, ii) temperature, and size of arena affect the scototaxis of the salmon, and iii) the salmons reaction to a bubble barrier is correlated to their boldness. The hypotheses were tested in a controlled laboratory setting by conducting three scototaxis tests and an experiment with several bubble barriers, where the reaction of salmon to bubbles could be assessed. There was significant positive correlation (r = 0,62 &amp; p = 0,012) between the boldness of an individual and the time it took to swim through the bubbles. Even though a significant difference in scototaxis as a result of lowered temperature were discovered, the difference was too small to have a noticeable effect on the overall results. A bubble barrier may therefore put artificial selection pressure on the salmon population.

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