Wild and domesticated Atlantic salmon males display large variation for sea age at sexual maturation, which varies between 1–5 years. Previous studies have uncovered a genetic predisposition for variation of age at maturity with moderate heritability, thus suggesting a polygenic or complex nature of this trait. The aim of this study was to identify associated genetic loci, genes and ultimately specific sequence variants conferring sea age at maturity in salmon. We performed a genome wide association study (GWAS) using a pool sequencing approach (20 individuals per river and phenotype) of male salmon returning to rivers as sexually mature either after one sea winter (2009) or three sea winters (2011) in six rivers in Norway. The study revealed one major selective sweep, which covered 76 significant SNPs in which 74 were found in a 370 kb region of chromosome 25. Genotyping other smolt year classes of wild and domesticated salmon confirmed this finding. Genotyping domesticated fish narrowed the haplotype region to four SNPs covering 2386 bp, containing the vgll3 gene, including two missense mutations explaining 33–36% phenotypic variation. A single locus was found to have a highly significant role in governing sea age at maturation in this species. The SNPs identified may be both used as markers to guide breeding for late maturity in salmon aquaculture and in monitoring programs of wild salmon. Interestingly, a SNP in proximity of the VGLL3 gene in humans (Homo sapiens), has previously been linked to age at puberty suggesting a conserved mechanism for timing of puberty in vertebrates.

Introgression of farmed salmon escapees into wild stocks is a major threat to the genetic integrity of wild populations. Using germ cell-free fish in aquaculture may mitigate this problem. Our study investigated whether it is possible to produce germ cell-free salmon in F0 by using CRISPR-Cas9 to knock out dnd, a factor required for germ cell survival in vertebrates. To avoid studying mosaic animals, sgRNA targeting alb was simultaneously used as a visual tracer since the phenotype of alb KO is complete loss of pigmentation. Induced mutations for the tracer (alb) and the target (dnd) genes were highly correlated and produced germ cell-less fish lacking pigmentation, underlining the suitability of alb KO to serve as tracer for targeted double allelic mutations in F0 animals in species with prohibitively long generation times. This is also the first report describing dnd knockout in any fish species. Analyzing gene expression and histology of dnd KO fish revealed that sex differentiation of the somatic compartment does not depend on the presence of germ cells. However, the organization of the ovarian somatic compartment seems compromised in mutant fish.

Understanding the biological function behind key proteins is of great concern in Atlantic salmon, both due to a high commercial importance and an interesting life history. Until recently, functional studies in salmonids appeared to be difficult. However, the recent discovery of targeted mutagenesis using the CRISPR/Cas9 (clustered regularly interspaced palindromic repeats/CRISPR-associated) system enables performing functional studies in Atlantic salmon to a great extent. We used the CRISPR/Cas9 system to target two genes involved in pigmentation, tyrosinase (tyr) and solute carrier family 45, member 2 (slc45a2). Embryos were assayed for mutation rates at the 17 somite stage, where 40 and 22% of all injected embryos showed a high degree of mutation induction for slc45a2 and tyr, respectively. At hatching this mutation frequency was also visible for both targeted genes, displaying a graded phenotype ranging from complete lack of pigmentation to partial loss and normal pigmentation. CRISPRslc45a2/Cas9 injected embryos showing a complete lack of pigmentation or just a few spots of pigments also lacked wild type sequences when assaying more than 80 (slc45a2) sequence clones from whole embryos. This indicates that CRISPR/Cas9 can induce double-allelic knockout in the F0 generation. However, types and frequency of indels might affect the phenotype. Therefore, the variation of indels was assayed in the graded pigmentation phenotypes produced by CRISPR/Cas9-slc45a2. The results show a tendency for fewer types of indels formed in juveniles completely lacking pigmentation compared to juveniles displaying partial pigmentation. Another interesting observation was a high degree of the same indel type in different juveniles. This study shows for the first time successful use of the CRISPR/Cas9 technology in a marine cold water species. Targeted double-allelic mutations were obtained and, though the level of mosaicism has to be considered, we demonstrate that F0 fish can be used for functional studies in Atlantic salmon.

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Aquaculture is the fastest growing food production sector and is rapidly becoming the primary source of seafood for human diets. Selective breeding programs are enabling genetic improvement of production traits, such as disease resistance, but progress is limited by the heritability of the trait and generation interval of the species. New breeding technologies, such as genome editing using CRISPR/Cas9 have the potential to expedite sustainable genetic improvement in aquaculture. Genome editing can rapidly introduce favorable changes to the genome, such as fixing alleles at existing trait loci, creating de novo alleles, or introducing alleles from other strains or species. The high fecundity and external fertilization of most aquaculture species can facilitate genome editing for research and application at a scale that is not possible in farmed terrestrial animals. The Role of Aquaculture in Food SecurityFood security is a major and increasing global challenge, associated with a rapidly growing demand for high-quality animal protein. Competition for land use will present a serious limitation to the scope for increases in terrestrial crop and animal production [1,2]. Therefore, it is likely that aquaculture will have a growing role in meeting this rising food and nutrition demand. Fish production via aquaculture is now approximately equal to capture fishery production for the first time in history, will be the dominant source of seafood within a few decades [3], and is the fastest growing food production sector, predicted to grow by 31% over the next 10 years [4]. Fortunately, development potential is huge, with only~1% of suitable marine sites currently being used for aquaculture [5]. Furthermore, aquaculture production is considered efficient in terms of feed conversation and protein retention compared with most terrestrial livestock [6], and seafood is the major source of long-chain polyunsaturated fatty acids, which are considered essential for human health [7]. However, relative to many crop and livestock production systems, most aquaculture is at a formative stage and is typically a high-risk activity. Sustainability can be hindered by an initial lack of control of the reproduction cycles of species, and periodic collapses due to infectious diseases. Upscaling and improving the reliability of production will require disruptive innovation in engineering, health, nutrition, and genetic improvement technologies, the latter being the focus of this review. Genetic Improvement for Sustainable Aquaculture ProductionDomestication and genetic improvement of terrestrial livestock has occurred for several millennia, with organized breeding programs for most species in place for N50 years. The results have been striking; for example, selective breeding has led to a threefold increase in efficiency of milk production in cows, with similar gains for other target traits [8]. By contrast, relatively little aquaculture production is underpinned by modern selective breeding programs [9,10]. Most farmed aquatic species are eith...

Summary The present review sums up and discusses the current literature on occurrence, causation and pathology of vertebral deformities in farmed Atlantic salmon, and also gives a brief introduction into the normal ontogeny and anatomy of the vertebral column of Atlantic salmon. Skeletal development and growth are sensitive processes that can be affected by many factors. Many of these factors can be manipulated under farming conditions, and are thus regarded as risk factors. Several risk factors that relate to environmental conditions and to feed composition have been identified. Elevated temperatures and photoperiod manipulation to speed up growth are likely the most important environmental factors that cause skeletal deformities. Among the nutritional factors, optimal phosphorus nutrition during specific periods, for example after transfer to sea water, appears to be critical for development of deformity at later stages. More research is needed to understand the interdependency of genetics, development, aging, phosphorus nutrition, temperature and photoperiod, in order to establish the best practice procedures for salmon farming that improve fish welfare.

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In several terrestrial vertebrates, heat shock (HS) during somitogenesis causes vertebral deformities. To determine if vertebral deformities can occur due to sudden temperature changes during early development in fish, Atlantic salmon embryos were HS treated during somitogenesis. Ten months later these individuals displayed a high prevalence of caudal vertebral column condensations (27-34%). The defects were located caudally of the abdominal cavity, displaying an even distribution in this region independent of time of HS. To determine if HS disturbed vertebral development during somitogenesis, two genes coding for markers of skeletal development were identified, namely, the secreted protein Shh (Sashh) and the transcription factor Twist (Satwist). These proteins are involved in the proliferation and specification of presumptive skeletal cells (sclerotome) in vertebrates. The spatial expression pattern of sashh and satwist in salmon indicated a functional conservation of these proteins. Furthermore, HS embryos displayed expressional disturbance in both sashh and satwist, indicating an effect of HS on sclerotomal cell patterning. However, the HS-protecting ability in embryos seems to be individually regulated because reduction in gene expression was not detected at all stages; in addition, HS did not induce somitic disturbance and vertebral deformity in all embryos.