Mapping quantitative trait loci (QTL) for traits under consideration for genetic improvement is becoming more common for many aquatic species, including Atlantic salmon. The objective of the study was to map QTL associated with length, weight, shape, parr mark number and contrast in three F2 hybrid families of European and North American strains of Atlantic salmon using single nucleotide polymorphisms. GridQTL software was used to perform separate analyses for male and female linkage maps. Numerous highly significant QTL were detected for every trait. Locations of QTL differed based on age and map used. Some QTL locations for the analyzed traits were similar to those of other studies on purebred and backcross Atlantic salmon populations; however, many more QTL were detected in the hybrid F2’s. The amount of genetic variation in skin colour and pattern displayed within the transAtlantic F2 families greatly exceeded the ranges seen in nature. / NSERC Strategic Grant

Diss. (sammanfattning) Umeå : Sveriges lantbruksuniv., 2007. / Härtill 6 uppsatser.

Diss. (sammanfattning) Umeå : Sveriges lantbruksuniv., 2003. / Härtill 5 uppsatser.

En général, le métabolisme des poissons est estimé à des valeurs de température constantes, mais les effets de fluctuations journalières de température similaires à celles retrouvées en milieu naturel semblent peu connus. Les objectifs du présent mémoire sont de quantifier les effets de la température moyenne d’acclimatation et d’évaluer les effets de l’historique thermique des individus, sur les réponses métaboliques de tacons de saumon Atlantique (Salmo salar) aux fluctuations journalières de la température. Des tacons provenant de deux rivières, une fraîche et une chaude, ont été acclimatés à un maximum de quatre régimes thermiques (constant 15 °C ou 20 °C, fluctuant 15 °C ± 2.5 °C ou 20 °C ± 2.5 °C) et leur taux métabolique standard estimés par respirométrie par débit-intermittent. Les fluctuations journalières de température (15 °C ± 2.5 °C) près de l’optimum thermique pour cette espèce (16 °C) n’affectent pas le taux métabolique standard. À l’opposé, les fluctuations journalières de température plus chaudes (20 °C ± 2.5 °C) augmentent de 35.4% le taux métabolique standard des tacons de la rivière plus chaude, mais pas ceux des poissons de la rivière fraîche. Ainsi, la température moyenne à laquelle sont acclimatés les poissons peut affecter leur réponse métabolique aux fluctuations journalières de température, mais cette réponse peut varier entre populations provenant de rivières présentant des régimes thermiques différents. Enfin, grâce aux données de métabolisme précédemment estimées, un modèle de métabolisme standard a été développé pour des tacons de saumon Atlantique soumis à des fluctuations journalières de température. / Usually, fish metabolism is evaluated under constant values of temperature, but the effects of daily temperature fluctuations similar to those found in natural environment on metabolism seems to be much less understood. The goals of this study are to quantify the effects of the mean acclimation temperature and to assess the effects of the thermal history on the metabolic response of Atlantic salmon (Salmo salar) parr to daily fluctuations of water temperature. Atlantic salmon parr originating from two rivers, one cool and one relatively warm, were acclimated to up to four thermal regimes (constant 15 °C or 20 °C, daily fluctuating 15 °C ± 2.5 °C or 20 °C ± 2.5 °C) and their standard metabolic rate was estimated using intermittent-flow respirometry. Daily temperature fluctuations (15 °C ± 2.5 °C) near this species’ thermal optimum (16 °C) do not influence standard metabolic rate. In contrast, daily fluctuations of higher temperature (20 °C ± 2.5 °C) do increase standard metabolic rate by 35.4% for fish from the warmer river, but not for fish from the cooler river. Therefore, the mean temperature to which fish are acclimated may affect their responses to daily fluctuations of water temperature, but this response may vary between populations originating from rivers having different thermal regimes. Using standard metabolic rates previously estimated, a standard metabolic rate model was developed for Atlantic salmon parr exposed to daily fluctuations of temperature.

Efficient control of sea lice is a major challenge for the sustainable production of farmed Atlantic salmon (Salmo salar (Linnaeus, 1758)). These marine ectoparasites feed on mucus, skin and blood of their hosts, thereby reducing the salmon’s growth rate and overall health. In the northern hemisphere, the most prevalent species is Lepeophtheirus salmonis (Krøyer, 1837). In 2006, global costs of sea lice infections are estimated to have exceeded €300 million, with the majority spent on a limited number of chemical delousing agents. Emamectin benzoate (EMB; SLICE®), an avermectin, has been widely used since its introduction in 2000, due to its convenient administration as an in-feed medication and its high efficacy against all parasitic stages of L. salmonis. However, over-reliance on a single or limited range of medicines favours the emergence of drug resistance and, as a result, the efficacy of this compound in treating L. salmonis has decreased in recent years, as reported from e.g. Chile, Norway, Scotland and Canada. Declining efficacy underlines the need for an improved understanding of the molecular mechanisms underlying EMB drug resistance in L. salmonis. Elucidation of these mechanisms would allow for improved monitoring tools, earlier detection of developing resistance, extended usability of current delousing agents and development of new parasiticides. The work described in this thesis sets out to examine the molecular mechanisms underlying EMB resistance in L. salmonis. In earlier studies, research in nematodes and arthropods has linked drug efflux transporters belonging to the family of ATP-binding cassette (ABC) transporters to ivermectin (IVM) resistance, a parasiticide with high chemical similarity to EMB. ABC transporters such as permeability glycoprotein (P-gp), transport a wide range of substrates, including drugs, and have been suggested to provide a potential molecular mechanism through which EMB resistance might be mediated in sea lice. As an example of such mechanisms, increased expression of P-gp is one of the causative factors for drug resistance in human cancer cells and avermectin resistance in nematode parasites such as Caenorhabditis elegans or Haemonchus contortus. Initial research involved screening for novel salmon lice P-gps that might contribute to EMB resistance. A novel P-gp, SL-PGY1, was discovered using a combined bioinformatic and molecular biological approach. The expression was compared in two well-characterised L. salmonis strains differing in their susceptibility to EMB (S = susceptible, R = resistant). Prior to EMB exposure, mRNA levels did not differ from each other, while, after 24 h exposure, a 2.9-fold increase in SL-PGY1 mRNA expression was observed in the R strain. SL-PGY1 appears not to be a major factor contributing to reduced EMB susceptibility, although it could play a role, as expression levels increased upon exposure to EMB. A further four additional drug transporters (ABC C subfamily) were also discovered showing high homology to multidrug-resistance proteins (MRP). The relative expression levels of each MRP was compared in the strains S and R, before and after exposure to EMB. No significant changes were found in their expression patterns. If ABC drug transporters mediate the efflux of EMB and thereby reduce the intracellular concentrations of the drug in exposed animals, the inhibition of those ABC drug transporters was expected to lead to higher intracellular levels of EMB. This could result in an enhanced toxic effect when EMB is co-administered with an inhibitor. Two known inhibitors of human P-gps and MRPs, cyclosporin A (CSA) and verapamil (VER), were co-administered with EMB. CSA increased the toxic effect of EMB in both tested strains, implying that the targets of CSA are expressed at comparable levels and that they may be part of the mechanism conferring EMB resistance. VER increased the toxic effect of EMB in the R strain, but had no significant effects on the S strain. This implies that the expression of factors inhibited by VER differs between the two L. salmonis strains. It is hypothesised that a number of ABC transporters with distinct, yet overlapping patterns of inhibitor specificity are affected by those inhibitors. The search for drug-resistance conferring genes was complemented with a systematic, genome-wide survey of ABC transporters in L. salmonis to find additional members of this important gene family. Next-generation high-throughput RNA sequencing (RNA-seq) was employed to assemble a reference transcriptome from pooled total RNA of salmon lice at different development stages. The transcriptome was assembled against the L. salmonis genome and annotated. Thirty-nine putative ABC transporters were found. Of further interest were transcripts of the subfamily B, C and G, as they contain drug-transporting ABC proteins. For the ABC B subfamily, one full (SL-PGY1) and three half transporter transcripts were found. Only full transporters are known to transport drugs and SL-PGY1 is apparently not a major factor contributing to EMB resistance. Fourteen ABCC sequences were found – 11 MRPs and 3 homologues to sulfonylurea receptors. Of interest are MRPs, as they contribute to drug detoxification in humans and invertebrates. Four MRPs had been identified previously and their expression ratios did not differ between S and R strain parasites. Seven sequences belonging to ABCG subfamily were found. However, none of the L. salmonis ABCG transcripts identified showed sufficient homology to known drug transporters in other species. With the currently limited understanding of the mechanisms conferring EMB resistance, monitoring the susceptibility of L. salmonis subpopulations is essential. Dose-response bioassays are currently widely used. Tests with pre-adult II or adult parasites requires relatively large numbers of parasites (~150) to conduct this type of bioassay, which may not always be available. Addressing this issue, we tested the feasibility of a single-dose bioassay (requiring fewer test animals than dose-response bioassays) to discriminate between L. salmonis strains with differing EMB susceptibility. This alternative approach uses time-course toxicity analysis, where the toxic effect of EMB is monitored over time. After clearly defining the effect criteria, we found that it is possible to discriminate between those L. salmonis strains. However, while requiring fewer test animals, time course toxicity analysis is more labour-intensive, but the alternative design can be suitable under certain circumstances. The work reported here has provided new knowledge concerning the mechanisms of EMB resistance in sea lice. Several novel putative drug transporters have been identified, an important first step toward unravelling the complex interactions of genes involved in EMB resistance in this commercially important parasite.

Considering the response of organisms to their environment is difficult; it is made more so if population numbers cannot be closely monitored. In such cases different methods of population assessment are required. This thesis uses lipids as a measure of Atlantic salmon (Salmo salar L.) quality and investigates its usefulness in indicating fish condition. The first study examines the relationship between fish total lipid content and W[sub]R condition factor; this study clearly demonstrates that there is a significant positive relationship between the condition factor of a fish and its total lipid content. In the following study the lipid storage between the different tissues of the Atlantic salmon is considered. This indicates that the red muscle and the adipose tissues hold higher concentrations of lipid than the white muscle. However, the white muscle makes up the majority of lipid tissue mass in the Atlantic salmon so contains the bulk of stored lipid in a fish, at low concentration. The next study investigates the effect of spawning on Atlantic salmon condition. Salmon can be seen preferentially conserving lipid in their musculature and drawing down the lipid stored in their adipose tissues. The following study looked at one key lipid group, triacylglycerides, in salmon. Triacylglycerides are energetically important in fish and this study found that the spawning process depleted triacylglyceride reserves, but that the red muscle conserves triacylglycerides even after spawning. The final study considers the relationship between maternal quality and egg quality, identifying that longer Atlantic salmon produce eggs with more lipid after spawning migration. Egg lipid concentrations were comparably maintained between fish. Monitoring quality in this way is a useful tool to determine population wellbeing and help indicate where populations are compromised.

Les poissons vivant au sein d’une rivière sont soumis à des variations circadiennes de température pouvant influencer la croissance, la digestion et le métabolisme standard. Les modèles bioénergétiques utilisant les fonctions métaboliques pour déterminer la croissance d’un poisson ont souvent été élaborés avec des poissons acclimatés à des températures constantes. Ces modèles pourraient sous-estimer l’énergie dépensée par un poisson soumis à des températures fluctuantes. En utilisant la respirométrie par débit intermittent, les objectifs de ce travail étaient : (1) de quantifier les différences entre les taux métaboliques standards de poissons acclimatés à une température constante (20.2 oC ± 0.5 oC) et à des fluctuations circadiennes de température (19.8 oC ± 2.0 oC; 19.5 oC ± 3.0 oC) et (2) comparer deux méthodologies pour calculer les taux métaboliques standards de poissons sujets aux fluctuations circadiennes de températures : respirométrie (a) en température constante ou (b) en température fluctuante. Les poissons acclimatés à des fluctuations circadiennes de température ont des taux métaboliques standards plus élevés que des poissons acclimatés à une température constante. À 20.2 oC ± 0.5 oC, les taux métabolique standards ont été de 25% à 32% plus bas pour des poissons maintenus à une température constante que pour des poissons gardés sous des fluctuations circadiennes de température. Les méthodologies utilisées pour estimer les taux métaboliques standards de poissons sujets aux fluctuations de température offrent des résultats similaires. / Fish that inhabits river are subjected to circadian fluctuations in water temperature. These fluctuations can influence growth, digestion and metabolic processes. Bioenergetic models are traditionally modeled using data recorded from fish kept at constant water temperatures. These models could underestimate the energy spent by fish subjected to fluctuating temperatures. Thus, with intermittent-flow respirometry, the objectives of this study were to: (1) quantify the differences between standard metabolic rates of fish acclimatized to a constant temperature (20.2 oC ± 0.5 oC) and two circadian fluctuating temperatures (19.8 oC ± 2.0 oC; 19.5 oC ± 3.0 oC) and (2) compare two methodology for calculate standard metabolic rates of fish subjected to circadian fluctuating temperatures: intermittent-flow respirometry with (a) constant temperature or (b) fluctuating temperatures. Fish held at circadian fluctuating temperatures have higher standard metabolic rates than fish acclimatized to a constant temperature. At 20.2 oC ± 0.5 oC, standard metabolic rates was 25% to 32% lower for fish held at constant temperature than for fish held under circadian fluctuations. However, results of the two different strategies used to calculate standard metabolic rates of fish subjected to circadian fluctuating temperatures did not differ.

The thesis combines laboratory experiments and field expeditions to study production, transfer and consumption of non-enzymatic antioxidants and thiamine in an aquatic food web. In particular, I (1) documented spatial and seasonal variation of tocopherols and carotenoids in the Baltic Sea pelagic food web, and (2) examined the effects of abiotic and biotic factors on tocopherol, carotenoid and thiamine concentrations in phytoplankton, zooplankton and fish. Moderate differences in temperature and salinity affected α-tocopherol, β-carotene and thiamine production in microalgae. Furthermore, the results suggest that acute stress favors the expression of non-enzymatic antioxidants rather than enzymatic antioxidants. Because production of α-tocopherol, β-carotene and thiamine differ markedly between microalgae, the availability of non-enzymatic antioxidants and thiamine is likely to be highly variable in the Baltic Sea and is difficult to predict. The transfer of non-enzymatic antioxidants from phytoplankton to zooplankton was biomass dependent. The field expeditions revealed that phytoplankton biomass was negatively associated with α-tocopherol concentration in mesozooplankton. Thus, increased eutrophication of the Baltic Sea followed by an increase in phytoplankton biomass could decrease the transfer of essential biochemicals to higher levels in the pelagic food web. This could lead to deficiency syndromes, of the kind already observed in the Baltic Sea. Astaxanthin is synthesized from precursors provided by the phytoplankton community. Thus biomass dependent transfer of astaxanthin precursors from phytoplankton to zooplankton could be responsible for astaxanthin deficiency in zooplanktivorous herring. Astaxanthin in herring consists mostly of all-Z-isomers, which are characterized by low bioavailability. Therefore, astaxanthin deficiency in salmon could be explained by the low concentration of this substance and its isomeric composition in herring.

Les poissons vivant au sein d’une rivière sont soumis à des variations circadiennes de température pouvant influencer la croissance, la digestion et le métabolisme standard. Les modèles bioénergétiques utilisant les fonctions métaboliques pour déterminer la croissance d’un poisson ont souvent été élaborés avec des poissons acclimatés à des températures constantes. Ces modèles pourraient sous-estimer l’énergie dépensée par un poisson soumis à des températures fluctuantes. En utilisant la respirométrie par débit intermittent, les objectifs de ce travail étaient : (1) de quantifier les différences entre les taux métaboliques standards de poissons acclimatés à une température constante (20.2 oC ± 0.5 oC) et à des fluctuations circadiennes de température (19.8 oC ± 2.0 oC; 19.5 oC ± 3.0 oC) et (2) comparer deux méthodologies pour calculer les taux métaboliques standards de poissons sujets aux fluctuations circadiennes de températures : respirométrie (a) en température constante ou (b) en température fluctuante. Les poissons acclimatés à des fluctuations circadiennes de température ont des taux métaboliques standards plus élevés que des poissons acclimatés à une température constante. À 20.2 oC ± 0.5 oC, les taux métabolique standards ont été de 25% à 32% plus bas pour des poissons maintenus à une température constante que pour des poissons gardés sous des fluctuations circadiennes de température. Les méthodologies utilisées pour estimer les taux métaboliques standards de poissons sujets aux fluctuations de température offrent des résultats similaires. / Fish that inhabits river are subjected to circadian fluctuations in water temperature. These fluctuations can influence growth, digestion and metabolic processes. Bioenergetic models are traditionally modeled using data recorded from fish kept at constant water temperatures. These models could underestimate the energy spent by fish subjected to fluctuating temperatures. Thus, with intermittent-flow respirometry, the objectives of this study were to: (1) quantify the differences between standard metabolic rates of fish acclimatized to a constant temperature (20.2 oC ± 0.5 oC) and two circadian fluctuating temperatures (19.8 oC ± 2.0 oC; 19.5 oC ± 3.0 oC) and (2) compare two methodology for calculate standard metabolic rates of fish subjected to circadian fluctuating temperatures: intermittent-flow respirometry with (a) constant temperature or (b) fluctuating temperatures. Fish held at circadian fluctuating temperatures have higher standard metabolic rates than fish acclimatized to a constant temperature. At 20.2 oC ± 0.5 oC, standard metabolic rates was 25% to 32% lower for fish held at constant temperature than for fish held under circadian fluctuations. However, results of the two different strategies used to calculate standard metabolic rates of fish subjected to circadian fluctuating temperatures did not differ.

Salmonids are a diverse group of fishes whose common ancestor experienced an evolutionarily important whole genome duplication (WGD) event approximately 90 MYA. This event has shaped the evolutionary trajectory of salmonids, and may have contributed to a proliferation of the repeated DNA sequences known as transposable elements (TEs). In this work I characterized repeated DNA in five salmonid genomes. I found that over half of the DNA within each of these genomes was derived from repeats, a value which is amongst the highest of all vertebrates. I investigated repeats of the most abundant TE superfamily, Tc1-Mariner, and found that large proliferative bursts of this element occurred shortly after the WGD and continued during salmonid speciation, where they have produced dramatic differences in TE content among extant salmonid lineages. This work provides important resources for future studies of salmonids, and advances the understanding of two important evolutionary forces: TEs and WGDs. / Graduate / 2019-04-19