Fluorescent protein transgenesis has varied effects on behaviour and cold tolerance in a tropical fish (Gymnocorymbus ternetzi): implications for risk assessment.

Fluorescent protein (FP) transgenesis is used in the ornamental aquarium trade to produce new colour morphs in tropical fish. Understanding whether such genetic modification could alter ability to survive temperate waters, or interactions with native fish, should such fish be released to natural systems is critical in developing policy on their commercial use. We examined the competitive foraging ability and cold tolerance of unrelated pet-trade sourced adult green FP transgenic tetra and non-transgenic white tetra (Gymnocorymbus ternetzi), as well as white non-transgenic and green FP transgenic juvenile progeny of these groups. FP transgenesis did not affect the foraging success or aggressive behaviour in either adult or juvenile fish, indicating FP transgenesis may not influence potential hazards through this pathway. During a cold temperature tolerance trial, adult green tetras had greatly diminished cold tolerance relative to unrelated adult white fish, while sibling juvenile offspring of these groups had intermediate cold tolerance between adult fish groups that were not affected by FP transgenesis. This data suggests background genetics, rearing history and/or life stage may play larger roles in cold tolerance than FP transgenesis in this species. Unexpectedly, both adult and juvenile white tetras were 3.8 times more likely to take refuge in shelters when temperature declined than green tetras. These data indicate FP transgenic fish may pose equal or lesser risk than non-transgenic fish, should they be released to natural environments. Results also demonstrate that unrelated pet-trade sourced fish may not always be appropriate models for examining effects of FP transgenesis.

Insights from a chum salmon (Oncorhynchus keta) genome assembly regarding whole-genome duplication and nucleotide variation influencing gene function.

Chum salmon are ecologically important to Pacific Ocean ecosystems and commercially important to fisheries. To improve the genetic resources available for this species, we sequenced and assembled the genome of a male chum salmon using Oxford Nanopore read technology and the Flye genome assembly software (contig N50: ∼2 Mbp, complete BUSCOs: ∼98.1%). We also resequenced the genomes of 59 chum salmon from hatchery sources to better characterize the genome assembly and the diversity of nucleotide variants impacting phenotype variation. With genomic sequences from a doubled haploid individual, we were able to identify regions of the genome assembly that have been collapsed due to high sequence similarity between homeologous (duplicated) chromosomes. The homeologous chromosomes are relics of an ancient salmonid-specific genome duplication. These regions were enriched with genes whose functions are related to the immune system and responses to toxins. From analyzing nucleotide variant annotations of the resequenced genomes, we were also able to identify genes that have increased levels of variants thought to moderately impact gene function. Genes related to the immune system and the detection of chemical stimuli (olfaction) had increased levels of these variants based on a gene ontology enrichment analysis. The tandem organization of many of the enriched genes raises the question of why they have this organization.

The pink salmon genome: Uncovering the genomic consequences of a two-year life cycle.

Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to the western Pacific Ocean. Pink salmon are also the most abundant of these species and account for a large proportion of the commercial value of the salmon fishery worldwide. A two-year life history of pink salmon generates temporally isolated populations that spawn either in even-years or odd-years. To uncover the influence of this genetic isolation, reference genome assemblies were generated for each year-class and whole genome re-sequencing data was collected from salmon of both year-classes. The salmon were sampled from six Canadian rivers and one Japanese river. At multiple centromeres we identified peaks of Fst between year-classes that were millions of base-pairs long. The largest Fst peak was also associated with a million base-pair chromosomal polymorphism found in the odd-year genome near a centromere. These Fst peaks may be the result of a centromere drive or a combination of reduced recombination and genetic drift, and they could influence speciation. Other regions of the genome influenced by odd-year and even-year temporal isolation and tentatively under selection were mostly associated with genes related to immune function, organ development/maintenance, and behaviour.

Using problem formulation for fit-for-purpose pre-market environmental risk assessments of regulated stressors.

Pre-market/prospective environmental risk assessments (ERAs) contribute to risk analyses performed to facilitate decisions about the market introduction of regulated stressors. Robust ERAs begin with an explicit problem formulation, which involves among other steps: (1) formally devising plausible pathways to harm that describe how the deployment of a regulated stressor could be harmful; (2) formulating risk hypotheses about the likelihood and severity of such events; (3) identifying the information that will be useful to test the risk hypotheses; and (4) developing a plan to acquire new data for hypothesis testing should tests with existing information be insufficient for decision-making. Here, we apply problem formulation to the assessment of possible adverse effects of RNA interference-based insecticidal genetically modified (GM) plants, GM growth hormone coho salmon, gene drive-modified mosquitoes and classical biological weed control agents on non-target organisms in a prospective manner, and of neonicotinoid insecticides on bees in a retrospective manner. In addition, specific considerations for the problem formulation for the ERA of nanomaterials and for landscape-scale population-level ERAs are given. We argue that applying problem formulation to ERA maximises the usefulness of ERA studies for decision-making, through an iterative process, because: (1) harm is defined explicitly from the start; (2) the construction of risk hypotheses is guided by policy rather than an exhaustive attempt to address any possible differences; (3) existing information is used effectively; (4) new data are collected with a clear purpose; (5) risk is characterised against well-defined criteria of hypothesis corroboration or falsification; and (6) risk assessment conclusions can be communicated clearly. However, problem formulation is still often hindered by the absence of clear policy goals and decision-making criteria (e.g. definition of protection goals and what constitutes harm) that are needed to guide the interpretation of scientific information. We therefore advocate further dialogue between risk assessors and risk managers to clarify how ERAs can address policy goals and decision-making criteria. Ideally, this dialogue should take place for all classes of regulated stressors, as this can promote alignment and consistency on the desired level of protection and maximum tolerable impacts across regulated stressors.

Growth-Enhanced Transgenic Coho Salmon (Oncorhynchus kisutch) Strains Have Varied Success in Simulated Streams: Implications for Risk Assessment.

Growth hormone (GH) transgenic fish have accelerated growth and could improve production efficiency in aquaculture. However, concern exists regarding potential environmental risks of GH transgenic fish should they escape rearing facilities. While environmental effects have been examined in some GH transgenic models, there is a lack of information on whether effects differ among different constructs or strains of transgenic fish. We compared growth and survival of wild-type coho salmon (Oncorhynchus kisutch) fry, a fast-growing GH transgenic strain containing a metallothionein promoter (TMT), and three lines/strains containing a reportedly weaker histone-3 promoter (TH3) in hatchery conditions and semi-natural stream tanks with varying levels of natural food and predators. Rank order of genotype size and survival differed with varying environmental conditions, both within and among experiments. Despite accelerated growth in hatchery conditions, TMT fry gained little or no growth enhancement in stream conditions, had enhanced survival when food was limiting, and inconsistent survival under other conditions. Rank growth was inconsistent in TH3 strains, with one strain having highest, and two strains having the lowest growth in stream conditions, although all TH3 strains had consistently poor survival. These studies demonstrate the importance of determining risk estimates for each unique transgenic model independent of other models.

Alternate Directed Anthropogenic Shifts in Genotype Result in Different Ecological Outcomes in Coho Salmon Oncorhynchus kisutch Fry.

Domesticated and growth hormone (GH) transgenic salmon provide an interesting model to compare effects of selected versus engineered phenotypic change on relative fitness in an ecological context. Phenotype in domestication is altered via polygenic selection of traits over multiple generations, whereas in transgenesis is altered by a single locus in one generation. These established and emerging technologies both result in elevated growth rates in culture, and are associated with similar secondary effects such as increased foraging, decreased predator avoidance, and similar endocrine and gene expression profiles. As such, there is concern regarding ecological consequences should fish that have been genetically altered escape to natural ecosystems. To determine if the type of genetic change influences fitness components associated with ecological success outside of the culture environments they were produced for, we examined growth and survival of domesticated, transgenic, and wild-type coho salmon fry under different environmental conditions. In simple conditions (i.e. culture) with unlimited food, transgenic fish had the greatest growth, while in naturalized stream tanks (limited natural food, with or without predators) domesticated fish had greatest growth and survival of the three fish groups. As such, the largest growth in culture conditions may not translate to the greatest ecological effects in natural conditions, and shifts in phenotype over multiple rather than one loci may result in greater success in a wider range of conditions. These differences may arise from very different historical opportunities of transgenic and domesticated strains to select for multiple growth pathways or counter-select against negative secondary changes arising from elevated capacity for growth, with domesticated fish potentially obtaining or retaining adaptive responses to multiple environmental conditions not yet acquired in recently generated transgenic strains.

Effects of chronic growth hormone overexpression on appetite-regulating brain gene expression in coho salmon.

Organisms must carefully regulate energy intake and expenditure to balance growth and trade-offs with other physiological processes. This regulation is influenced by key pathways controlling appetite, feeding behaviour and energy homeostasis. Growth hormone (GH) transgenesis provides a model where food intake can be elevated, and is associated with dramatic modifications of growth, metabolism, and feeding behaviour, particularly in fish. RNA-Seq and qPCR analyses were used to compare the expression of multiple genes important in appetite regulation within brain regions and the pituitary gland (PIT) of GH transgenic (fed fully to satiation or restricted to a wild-type ration throughout their lifetime) and wild-type coho salmon (Oncorhynchus kisutch). RNA-Seq results showed that differences in both genotype and ration levels resulted in differentially expressed genes associated with appetite regulation in transgenic fish, including elevated Agrp1 in hypothalamus (HYP) and reduced Mch in PIT. Altered mRNA levels for Agrp1, Npy, Gh, Ghr, Igf1, Mch and Pomc were also assessed using qPCR analysis. Levels of mRNA for Agrp1, Gh, and Ghr were higher in transgenic than wild-type fish in HYP and in the preoptic area (POA), with Agrp1 more than 7-fold higher in POA and 12-fold higher in HYP of transgenic salmon compared to wild-type fish. These data are consistent with the known roles of orexigenic factors on foraging behaviour acting via GH and through MC4R receptor-mediated signalling. Igf1 mRNA was elevated in fully-fed transgenic fish in HYP and POA, but not in ration-restricted fish, yet both of these types of transgenic animals have very pronounced feeding behaviour relative to wild-type fish, suggesting IGF1 is not playing a direct role in appetite stimulation acting via paracrine or autocrine mechanisms. The present findings provide new insights on mechanisms ruling altered appetite regulation in response to chronically elevated GH, and on potential pathways by which elevated feeding response is controlled, independently of food availability and growth.

Rearing in seawater mesocosms improves the spawning performance of growth hormone transgenic and wild-type coho salmon.

Growth hormone (GH) transgenes can significantly accelerate growth rates in fish and cause associated alterations to their physiology and behaviour. Concern exists regarding potential environmental risks of GH transgenic fish, should they enter natural ecosystems. In particular, whether they can reproduce and generate viable offspring under natural conditions is poorly understood. In previous studies, GH transgenic salmon grown under contained culture conditions had lower spawning behaviour and reproductive success relative to wild-type fish reared in nature. However, wild-type salmon cultured in equal conditions also had limited reproductive success. As such, whether decreased reproductive success of GH transgenic salmon is due to the action of the transgene or to secondary effects of culture (or a combination) has not been fully ascertained. Hence, salmon were reared in large (350,000 L), semi-natural, seawater tanks (termed mesocosms) designed to minimize effects of standard laboratory culture conditions, and the reproductive success of wild-type and GH transgenic coho salmon from mesocosms were compared with that of wild-type fish from nature. Mesocosm rearing partially restored spawning behaviour and success of wild-type fish relative to culture rearing, but remained lower overall than those reared in nature. GH transgenic salmon reared in the mesocosm had similar spawning behaviour and success as wild-type fish reared in the mesocosm when in full competition and without competition, but had lower success in male-only competition experiments. There was evidence of genotype×environmental interactions on spawning success, so that spawning success of transgenic fish, should they escape to natural systems in early life, cannot be predicted with low uncertainty. Under the present conditions, we found no evidence to support enhanced mating capabilities of GH transgenic coho salmon compared to wild-type salmon. However, it is clear that GH transgenic salmon are capable of successful spawning, and can reproduce with wild-type fish from natural systems.

Exogenous glutathione can increase glutathione levels in tissues of rainbow trout (Oncorhynchus mykiss) through extracellular breakdown and intracellular synthesis.

Glutathione (GSH) is an important intracellular antioxidant involved in numerous cellular pathways. However, little is known about the transport of GSH into fish tissues. To determine whether fish tissues took up GSH by extracellular breakdown and intracellular synthesis or by direct cellular transport, we injected rainbow trout (Oncorhynchus mykiss) with exogenous GSH along with blockers of GSH breakdown and synthesis. Exogenous GSH increased GSH levels to the greatest degree in the cells of the posterior kidney, followed by the liver. Exogenous GSH inconsistently increased liver GSH levels independent of GSH synthesis, although this may have been due to disruption of gradient-dependent GSH export, and not necessarily to intact uptake of GSH. The cells of the posterior kidney, liver and gill took up GSH by extracellular breakdown and intracellular synthesis. This indicates that, unlike mammalian tissues, normal cellular GSH levels in fish are not sufficient to inhibit additional GSH synthesis. This may lend flexibility to the GSH system in fish, where levels of GSH may rapidly increase in response to an increased supply of amino acids, or during times of high demand, without increasing synthesis enzymes.

The glutathione antioxidant system is enhanced in growth hormone transgenic coho salmon (Oncorhynchus kisutch).

Insertion of a growth hormone (GH) transgene in coho salmon results in accelerated growth, and increased feeding and metabolic rates. Whether other physiological systems within the fish are adjusted to this accelerated growth has not been well explored. We examined the effects of a GH transgene and feeding level on the antioxidant glutathione and its associated enzymes in various tissues of coho salmon. When transgenic and control salmon were fed to satiation, transgenic fish had increased tissue glutathione, increased hepatic glutathione reductase activity, decreased hepatic activity of the glutathione synthesis enzyme gamma-glutamylcysteine synthetase, and increased intestinal activity of the glutathione catabolic enzyme gamma-glutamyltranspeptidase. However, these differences were mostly abolished by ration restriction and fasting, indicating that upregulation of the glutathione antioxidant system was due to accelerated growth, and not to intrinsic effects of the transgene. Increased food intake and ability to digest potential dietary glutathione, and not increased activity of glutathione synthesis enzymes, likely contributed to the higher levels of glutathione in transgenic fish. Components of the glutathione antioxidant system are likely upregulated to combat potentially higher reactive oxygen species production from increased metabolic rates in GH transgenic salmon.