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When unifying genomic resources among studies and comparing data between species, there is often no better resource than a genome sequence. Having a reference genome for the Chinook salmon (Oncorhynchus tshawytscha) will enable the extensive genomic resources available for Pacific salmon, Atlantic salmon, and rainbow trout to be leveraged when asking questions related to the Chinook salmon. The Chinook salmon’s wide distribution, long cultural impact, evolutionary history, substantial hatchery production, and recent wild-population decline make it an important research species. In this study, we sequenced and assembled the genome of a Chilliwack River Hatchery female Chinook salmon (gynogenetic and homozygous at all loci). With a reference genome sequence, new questions can be asked about the nature of this species, and its role in a rapidly changing world.

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In salmonids, growth hormone (GH) stimulates growth, appetite and the ability to compete for food. This study tested the hypothesis that increased GH levels in GH‐transgenic coho salmon Oncorhynchus kisutch (Walbaum) increase competitive ability through higher feeding motivation. The transgenic strain of salmon used contained a gene construct consisting of the sockeye metallothionein‐B promoter fused to the type 1 growth gene coding region. The transgenic animals (mean size = 250 g) were F1 individuals. In six consecutive feeding trials, the intake of contested food pellets by size‐matched pairs consisting of one control (1 year older non‐transgenic coho salmon) and one GH‐transgenic coho salmon was compared. Pellets were provided sequentially until neither fish took three consecutive pellets; the identity of the fish taking each pellet was noted. Calculated on the three first pellets offered at each feeding trial, the transgenic coho salmon consumed 2.5 times more contested pellets than the controls, supporting the hypothesis that GH transgenesis increases the ability to compete for food. Overall, the transgenic fish consumed 2.9 times more pellets that the non‐transgenic controls, indicating a high feeding motivation of the transgenic fish throughout the feeding trials. It appears that GH transgenesis and GH treatments can induce similar changes in the feeding behaviour of salmonids. Depending on how transgenic and wild individuals differ in other fitness‐related characters, escaped GH transgenic fish may compete successfully with native fish in the wild.

Environmental risk assessment of genetically modified organisms requires determination of their fitness and invasiveness relative to conspecifics and other ecosystem members. Cultured growth hormone transgenic coho salmon (Oncorhynchus kisutch) have enhanced feeding capacity and growth, which can result in large enhancements in body size (>7-fold) relative to nontransgenic salmon, but in nature, the ability to compete for available food is a key factor determining survival fitness and invasiveness of a genotype. When transgenic and nontransgenic salmon were cohabitated and competed for different levels of food, transgenic salmon consistently outgrew nontransgenic fish and could affect the growth of nontransgenic cohorts except when food availability was high. When food abundance was low, dominant individuals emerged, invariably transgenic, that directed strong agonistic and cannibalistic behavior to cohorts and dominated the acquisition of limited food resources. When food availability was low, all groups containing transgenic salmon experienced population crashes or complete extinctions, whereas groups containing only nontransgenic salmon had good (72.0 ؎ 4.3% SE) survival, and their population biomass continued to increase. Thus, effects of growth hormone transgenic salmon on experimental populations were primarily mediated by an interaction between food availability and population structure. These data, while indicative of forces which may act on natural populations, also underscore the importance of genotype by environment interactions in influencing risk assessment data for genetically modified organisms and suggest that, for species such as salmon which are derived from large complex ecosystems, considerable caution is warranted in applying data from individual studies.

Sockeye salmon ( Oncorhynchus nerka ) is a commercially and culturally important species to the people that live along the northern Pacific Ocean coast. There are two main sockeye salmon ecotypes—the ocean-going (anadromous) ecotype and the fresh-water ecotype known as kokanee. The goal of this study was to better understand the population structure of sockeye salmon and identify possible genomic differences among populations and between the two ecotypes. In pursuit of this goal, we generated the first reference sockeye salmon genome assembly and an RNA-seq transcriptome data set to better annotate features of the assembly. Resequenced whole-genomes of 140 sockeye salmon and kokanee were analyzed to understand population structure and identify genomic differences between ecotypes. Three distinct geographic and genetic groups were identified from analyses of the resequencing data. Nucleotide variants in an immunoglobulin heavy chain variable gene cluster on chromosome 26 were found to differentiate the northwestern group from the southern and upper Columbia River groups. Several candidate genes were found to be associated with the kokanee ecotype. Many of these genes were related to ammonia tolerance or vision. Finally, the sex chromosomes of this species were better characterized, and an alternative sex-determination mechanism was identified in a subset of upper Columbia River kokanee.

The reproductive performances of growth-enhanced transgenic, hatchery, and cultured nontransgenic coho salmon Oncorhynchus kisutch were examined to investigate the consequences of reproductive interaction between growth hormone (GH)-transgenic fish and wild fish that may occur if transgenic salmon escaped into the natural environment. We examined adult morphological phenotypes, gamete quantity and quality, in vitro offspring production, courtship and spawning behavior, male competitive behavior, and transgene transmission to offspring. Transgenic, hatchery, and cultured nontransgenic fish required 2, 3, and 3 or 4 years, respectively, to reach sexual maturation. No differences in male gamete quantity or in vitro offspring production were observed. Transgenic females were more fecund than hatchery females but had smaller eggs. Fewer transgenic females spawned than hatchery females under experimental conditions, and transgenic females displayed consistently low levels of courtship behavior. In noncompetitive trials, there were no differences in the courtship behavior of transgenic and hatchery males; during competition with hatchery males, however, transgenic males failed to spawn and displayed less courtship and competitive behavior. Cultured nontransgenic salmon also displayed reduced spawning capacity relative to hatchery salmon, indicating that the effects observed in transgenic salmon may arise in part from being reared in the culture environment and highlighting the difficulty in using laboratoryreared transgenic fish to assess reproductive fitness because of the strong genotype-environment interactions. As long as wild-reared transgenic fish are unavailable, exact determinations of reproductive fitness will be difficult. However, these studies have shown that in a simulated natural environment, growth-enhanced transgenic coho salmon do display courtship behavior and can spawn, producing viable transgenic offspring. The findings suggest some capacity exists for the natural transmission of transgenes to populations arising from reproductive interaction, which could occur during first contact between escaped cultured transgenic fish and wild conspecifics.