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Background: A genotype-by-environment (G × E) interaction is defined as genotypes responding differently to different environments. In salmonids, G × E interactions can occur in different rearing conditions, including changes in salinity or temperature. However, water flow, an important variable that can influence metabolism, has yet to be considered for potential G × E interactions, although water flows differ across production stages. The salmonid industry is now manipulating flow in tanks to improve welfare and production performance, and expanding sea pen farming offshore, where flow dynamics are substantially greater. Therefore, there is a need to test whether G × E interactions occur under low and higher flow regimes to determine if industry should consider modifying their performance evaluation and selection criteria to account for different flow environments. Here, we used genotype-by-sequencing to create a genomic-relationship matrix of 37 Chinook salmon, Oncorhynchus tshawytscha, families to assess possible G × E interactions for production performance under two flow environments: a low flow regime (0.3 body lengths per second; bl s -1 ) and a moderate flow regime (0.8 bl s -1 )., Results: Genetic correlations for the same production performance trait between flow regimes suggest there is minimal evidence of a G × E interaction between the low and moderate flow regimes tested in this study, for Chinook salmon reared from 82.9 ± 16.8 g ( x ¯  ± s.d.) to 583.2 ± 117.1 g ( x ¯  ± s.d.). Estimates of genetic and phenotypic correlations between traits did not reveal any unfavorable trait correlations for size- (weight and condition factor) and growth-related traits, regardless of the flow regime, but did suggest measuring feed intake would be the preferred approach to improve feed efficiency because of the strong correlations between feed intake and feed efficiency, consistent with previous studies., Conclusion: This new information suggests that Chinook salmon families do not need to be selected separately for performance across different flow regimes. However, further studies are needed to confirm this across a wider range of fish sizes and flows. This information is key for breeding programs to determine if separate evaluation groups are required for different flow regimes that are used for production (e.g., hatchery, post smolt recirculating aquaculture system, or offshore)., (© 2024. The Author(s).)

Background: Past empirical evidence on the longitudinal relations between emotional mental health symptoms and parent-child close relationships has produced mixed and inconclusive results. Some studies suggest a unidirectional relation, whereas other studies point toward a bidirectional association. Additionally, most of the past research has been carried out with adolescent samples, rather than children. Hence, this study aimed to estimate the longitudinal relations between children's trait emotional difficulties and trait parent-child closeness, accounting for the time-invariant and time-varying state components of each factor., Methods: Participants were 7,507 children (ages 3 years, 5 years, 7 years, and 9 years) from the Growing Up in Ireland cohort. Α bivariate stable trait, autoregressive trait, and state (STARTS) model was estimated using Bayesian structural equation modelling., Results: The STARTS model revealed that children's emotional difficulties and parent-child closeness were relatively stable across time, and these overarching traits were strongly negatively correlated. Children's earlier trait emotional difficulties predicted later trait parent-child closeness and vice versa between 3 years and 5 years, and between 5 years and 7 years, but these effects disappeared between 7 years and 9 years. At all pairs of time points, state emotional difficulties and state parent-child closeness were weakly negatively correlated., Conclusions: Overall, the results suggest that early and middle childhood are critical stages for improving parent-child relationships and reducing children's emotional difficulties. Developing close parent-child relationships in childhood appears to be a key factor in reducing children's subsequent emotional difficulties. Children who face greater than usual emotional difficulties tend to be more withdrawn and less receptive to close parent-child relationships and this could serve as an important screening indicator., (© 2024. The Author(s).)

Chinook salmon (Oncorhynchus tshawytscha) farmed in New Zealand are known to develop abnormal spinal curvature late in seawater production. Its cause is presently unknown, but there is evidence to suggest a neuromuscular pathology. Using magnetic resonance imaging (MRI), we evaluated the relationship between soft tissue pathology and spinal curvature in farmed Chinook salmon. Regions of interest (ROIs) presenting as pathologic MRI signal hyper-intensity were identified from scans of 24 harvest-sized individuals: 13 with radiographically-detectable spinal curvature and 11 without. ROIs were excised from individuals using anatomical landmarks as reference points and histologically analysed. Pathologic MRI signal was observed more frequently in individuals with radiographic curvature (92%, n = 12) than those without (18%, n = 2), was localized to the peri-vertebral connective tissues and musculature, and presented as three forms: inflammation, fibrosis, or both. These pathologies are consistent with a chronic inflammatory process, such as that observed during recovery from a soft tissue injury, and suggest spinal curvature in farmed Chinook salmon may be associated with damage to and/or compromised integrity of the peri-vertebral soft tissues. Future research to ascertain the contributing factors is required., (© 2023 The Authors. Journal of Fish Diseases published by John Wiley & Sons Ltd.)

Fed aquaculture is one of the fastest-growing and most valuable food production industries in the world. The efficiency with which farmed fish convert feed into biomass influences both environmental impact and economic revenue. Salmonid species, such as king salmon (Oncorhynchus tshawytscha), exhibit high levels of plasticity in vital rates such as feed intake and growth rates. Accurate estimations of individual variability in vital rates are important for production management. The use of mean trait values to evaluate feeding and growth performance can mask individual-level differences that potentially contribute to inefficiencies. Here, the authors apply a cohort integral projection model (IPM) framework to investigate individual variation in growth performance of 1625 individually tagged king salmon fed one of three distinct rations of 60%, 80%, and 100% satiation and tracked over a duration of 276 days. To capture the observed sigmoidal growth of individuals, they compared a nonlinear mixed-effects (logistic) model to a linear model used within the IPM framework. Ration significantly influenced several aspects of growth, both at the individual and at the cohort level. Mean final body mass and mean growth rate increased with ration; however, variance in body mass and feed intake also increased significantly over time. Trends in mean body mass and individual body mass variation were captured by both logistic and linear models, suggesting the linear model to be suitable for use in the IPM. The authors also observed that higher rations resulted in a decreasing proportion of individuals reaching the cohort's mean body mass or larger by the end of the experiment. This suggests that, in the present experiment, feeding to satiation did not produce the desired effects of efficient, fast, and uniform growth in juvenile king salmon. Although monitoring individuals through time is challenging in commercial aquaculture settings, recent technological advances combined with an IPM approach could provide new scope for tracking growth performance in experimental and farmed populations. Using the IPM framework might allow the exploration of other size-dependent processes affecting vital rate functions, such as competition and mortality., (© 2023 The Authors. Journal of Fish Biology published by John Wiley & Sons Ltd on behalf of Fisheries Society of the British Isles.)

In New Zealand, during the hottest periods of the year, some salmon farms in the Marlborough Sounds reach water temperatures above the optimal range for Chinook salmon. High levels of mortality are recorded during these periods, emphasising the importance of understanding thermal stress in this species. In this study, the responses of Chinook salmon ( Oncorhynchus tshawytscha ) to chronic, long-term changes in temperature and dissolved oxygen were investigated. This is a unique investigation due to the duration of the stress events the fish were exposed to. Health and haematological parameters were analysed alongside gene expression results to determine the effects of thermal stress on Chinook salmon. Six copies of heat shock protein 90 (HSP90) were discovered and characterised: HSP90AA1.1a, HSP90AA1.2a, HSP90AA1.1b, HSP90AA1.2b, HSP90AB1a and HSP90AB1b, as well as two copies of SOD1, named SOD1a and SOD1b. The amino acid sequences contained features similar to those found in other vertebrate HSP90 and SOD1 sequences, and the phylogenetic tree and synteny analysis provided conclusive evidence of their relationship to other vertebrate HSP90 and SOD1 genes. Primers were designed for qPCR to enable the expression of all copies of HSP90 and SOD1 to be analysed. The expression studies showed that HSP90 and SOD1 were downregulated in the liver and spleen in response to longer term exposure to high temperatures and lower dissolved oxygen. HSP90 was also downregulated in the gill; however, the results for SOD1 expression in the gill were not conclusive. This study provides important insights into the physiological and genetic responses of Chinook salmon to temperature and oxygen stress, which are critical for developing sustainable fish aquaculture in an era of changing global climates.

Fish aquaculture is a rapidly expanding global industry, set to support growing demands for sources of marine protein. Enhancing feed efficiency (FE) in farmed fish is required to reduce production costs and improve sector sustainability. Recognising that organisms are complex systems whose emerging phenotypes are the product of multiple interacting molecular processes, systems-based approaches are expected to deliver new biological insights into FE and growth performance. Here, we establish 14 diverse layers of multi-omics and clinical covariates to assess their capacities to predict FE and associated performance traits in a fish model ( Oncorhynchus tshawytscha ) and uncover the influential variables. Inter-omic relatedness between the different layers revealed several significant concordances, particularly between datasets originating from similar material/tissue and between blood indicators and some of the proteomic (liver), metabolomic (liver), and microbiomic layers. Single- and multi-layer random forest (RF) regression models showed that integration of all data layers provide greater FE prediction power than any single-layer model alone. Although FE was among the most challenging of the traits we attempted to predict, the mean accuracy of 40 different FE models in terms of root-mean square errors normalized to percentage was 30.4%, supporting RF as a feature selection tool and approach for complex trait prediction. Major contributions to the integrated FE models were derived from layers of proteomic and metabolomic data, with substantial influence also provided by the lipid composition layer. A correlation matrix of the top 27 variables in the models highlighted FE trait-associations with faecal bacteria ( Serratia spp.), palmitic and nervonic acid moieties in whole body lipids, levels of free glycerol in muscle, and N-acetylglutamic acid content in liver. In summary, we identified subsets of molecular characteristics for the assessment of commercially relevant performance-based metrics in farmed Chinook salmon.

This study investigated the effects of different temperatures on the performance, composition, and nutrient retention of Chinook salmon reared in freshwater. Individuals (187.6 ± 27.1 g) were distributed into twelve tanks of 8000 L each (155 to 157 fish per tank) at a temperature of 14 °C. The tanks were transitioned from 14 °C (hatchery temperature) to 8, 12, 16, and 20 °C over seven days. Three fish assessments were performed, the first (initial) when the fish were distributed in the tanks, a second (interim) between days 9 and 16 at the start of the experiment, and a third (final) after 41 to 49 days at the target temperature. At the end of the trial, performance parameters, proximate composition, amino acid, and fatty acid composition, and nutrient retention were evaluated. Better growth performance was observed in fish at 16 °C and 20 °C compared to the lower temperatures. Fish at higher temperatures had higher levels of saturated fatty acids (SFA), while at lower temperatures fish had higher levels of n-3 and n-6 polyunsaturated fatty acids (PUFA), especially eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA). A polynomial relationship between nutrient retention and temperature showed that fish from all treatments retained more lipids than proteins, with higher retention of MUFA compared to the other fatty acid classes. Additionally, DHA retention was approximately three times higher than EPA retention. The results showed that 16 to 20 °C was the optimum temperature range for Chinook salmon, and the performance differences were mainly modulated by lipid retention/catabolism., Competing Interests: Declaration of Competing Interest The authors report no conflicts of interest., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Fish skin is critical to physical defence against pathogens and there is a need to understand the physiological processes impacting ulcers and their healing. Ulcers have been reported in farmed Chinook salmon in New Zealand. This study investigated stress, immune and structural gene expression in farmed Chinook salmon skin with and without ulcers from two sites in New Zealand sampled from February (higher temperature, late summer) to May (lower temperature, late autumn). Skin samples taken adjacent to non-specific ulcers in May and control fish in February demonstrated upregulation of heat shock protein 70 relative to control fish in May. Anterior gradient 2 expression was upregulated in fish with ulcers relative to control fish (both February and May), suggesting increased mucous cell activity. Based on the results of this study, fish with non-specific ulcers showed evidence of stress, inflammation, re-epithelisation, and delayed healing near the ulcer site, elucidating the importance of these processes in the pathogenesis of non-specific ulcers in farmed chinook salmon., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Aims: Multiple studies have connected parenting styles to children's internalising and externalising mental health symptoms (MHS). However, it is not clear how different parenting styles are jointly influencing the development of children's MHS over the course of childhood. Hence, the differential effects of parenting style on population heterogeneity in the joint developmental trajectories of children's internalising and externalising MHS were examined., Method: A community sample of 7507 young children (ages 3, 5 and 9) from the Growing Up in Ireland cohort study was derived for further analyses. Parallel-process linear growth curve and latent growth mixture modelling were deployed., Results: The results indicated that the linear growth model was a good approximation of children's MHS development (CFI = 0.99, RMSEA = 0.03). The growth mixture modelling revealed three classes of joint internalising and externalising MHS trajectories (VLMR = 92.51, p < 0.01; LMR = 682.19, p < 0.01; E = 0.86). The majority of the children (83.49%) belonged to a low-risk class best described by a decreasing trajectory of externalising symptoms and a flat low trajectory of internalising MHS. In total, 10.07% of the children belonged to a high-risk class described by high internalising and externalising MHS trajectories, whereas 6.43% of the children were probable members of a mild-risk class with slightly improving yet still elevated trajectories of MHS. Adjusting for socio-demographics, child and parental health, multinomial logistic regressions indicated that hostile parenting was a risk factor for membership in the high-risk (OR = 1.47, 95% CI 1.18-1.85) and mild-risk (OR = 1.57, 95% CI 1.21-2.04) classes. Consistent (OR = 0.75, 95% CI 0.62-0.90) parenting style was a protective factor only against membership in the mild-risk class., Conclusions: In short, the findings suggest that a non-negligible proportion of the child population is susceptible to being at high risk for developing MHS. Moreover, a smaller proportion of children was improving but still displayed high symptoms of MHS (mild-risk). Furthermore, hostile parenting style is a substantial risk factor for increments in child MHS, whereas consistent parenting can serve as a protective factor in cases of mild-risk. Evidence-based parent training/management programmes may be needed to reduce the risk of developing MHS.

Improving the feed conversion ratio (FCR; the amount of feed consumed relative to the amount of weight gain) can reduce both production costs and environmental impacts of farmed fish. The aim of this study was to investigate what drives FCR to understand how nutrients are retained, as well as the amount of oxygen consumed for digestion, absorption and assimilation (a metabolic process known as specific dynamic action, SDA). Feed-efficient and inefficient Chinook salmon (Oncorhynchus tshawytscha) in fresh water were identified using ballotini beads and X-radiography that tracked individual feed intake across three assessment periods under satiated feeding. This allowed a comparison of physiological traits and body composition between the two FCR phenotypes over two time points as Chinook salmon grew from 305 to 620 g. Fish with higher daily feed intake (DFI) had higher daily weight gain (DWG) as expected. Nonetheless, the relationship between FCR and DFI as well as FCR and DWG was variable between time points. FCR and DWG were not correlated at the first time point and were negatively correlated at the second time point. In contrast, FCR and DFI were positively correlated at the first time point but not the second. Despite this, efficient fish ate smaller meals and retained more protein, lipid and energy in their body tissues. There was no detectable difference in metabolism between the two FCR phenotypes with respect to minimal resting metabolic rate, maximum metabolic rate, aerobic scope, or SDA parameters. In conclusion, FCR is not consistently associated with growth and metabolic differences in freshwater Chinook salmon, but FCR-efficient fish retain more nutrients and consume smaller meals., (© 2022 The Authors. Journal of Fish Biology published by John Wiley & Sons Ltd on behalf of Fisheries Society of the British Isles.)

School engagement in adolescence is often associated with better academic performance at school, but what are the longitudinal associations between school engagement and adult educational and employment status? The current study explored these longitudinal associations using data spanning 40-years of life, from the 1970 British Cohort Study. School engagement at age 16-years was used to predict highest educational level at age 34-years, and socioeconomic status and income at ages 34- and 46-years, controlling for childhood socioeconomic status, cognitive ability, gender, and ethnic minority status, collected at ages 5- or 10-years. The 13,135 individuals in the sample were born in 1970, were mainly White (96%), and were identified at age 5-years as being 48% female. Longitudinal structural equation models revealed that adolescent school engagement had a persistent, positive impact on adult educational and employment outcomes after individual differences were controlled for. The results are interpreted using the perspective that school engagement can channel resources which are important for later educational and occupational success. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

Gut microbiota play important roles in fish health and growth performance and the microbiome in fish has been shown to be a biomarker for stress. In this study, we surveyed the change of Chinook salmon ( Oncorhynchus tshawytscha ) gut and water microbiota in freshwater recirculating aquaculture systems (RAS) for 7 months and evaluated how gut microbial communities were influenced by fish health and growth performance. The gut microbial diversity significantly increased in parallel with the growth of the fish. The dominant gut microbiota shifted from a predominance of Firmicutes to Proteobacteria, while Proteobacteria constantly dominated the water microbiota. Photobacterium sp. was persistently the major gut microbial community member during the whole experiment and was identified as the core gut microbiota for freshwater farmed Chinook salmon. No significant variation in gut microbial diversity and composition was observed among fish with different growth performance. At the end of the trial, 36 out of 78 fish had fluid in their swim bladders. These fish had gut microbiomes containing elevated proportions of Enterococcus, Stenotrophomonas , Aeromonas, and Raoultella . Our study supports the growing body of knowledge about the beneficial microbiota associated with modern salmon aquaculture systems and provides additional information on possible links between dysbiosis and gut microbiota for Chinook salmon., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Zhao, Symonds, Walker, Steiner, Carter, Bowman and Nowak.)

Understanding the molecular mechanisms that underlie differences in feed efficiency (FE) is an important step toward optimising growth and achieving sustainable salmonid aquaculture. In this study, the liver and white muscle proteomes of feed efficient (EFF) and inefficient (INEFF) Chinook salmon (Oncorhynchus tshawytscha) reared in seawater were investigated by liquid chromatography-tandem mass spectrometry (LC-MS/MS). In total, 2746 liver and 702 white muscle proteins were quantified and compared between 21 EFF and 22 INEFF fish. GSEA showed that gene sets related to protein synthesis were enriched in the liver and white muscle of the EFF group, while conversely, pathways related to protein degradation (amino acid catabolism and proteolysis, respectively) were the most affected processes in the liver and white muscle of INEFF fish. Estimates of individual daily feed intake and share of the meal within tank were significantly higher in the INEFF than the EFF fish showing INEFF fish were likely more dominant during feeding and overfed. Overeating by the INEFF fish was associated with an increase in protein catabolism. This study found that fish with different FE values had expression differences in the gene sets related to protein turnover, and this result supports the hypothesis that protein metabolism plays a role in FE., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Harmful algal blooms (HABs) have wide-ranging environmental impacts, including on aquatic species of social and commercial importance. In New Zealand (NZ), strategic growth of the aquaculture industry could be adversely affected by the occurrence of HABs. This review examines HAB species which are known to bloom both globally and in NZ and their effects on commercially important shellfish and fish species. Blooms of Karenia spp. have frequently been associated with mortalities of both fish and shellfish in NZ and the sub-lethal effects of other genera, notably Alexandrium spp., on shellfish (which includes paralysis, a lack of byssus production, and reduced growth) are also of concern. Climate change and anthropogenic impacts may alter HAB population structure and dynamics, as well as the physiological responses of fish and shellfish, potentially further compromising aquatic species. Those HAB species which have been detected in NZ and have the potential to bloom and harm marine life in the future are also discussed. The use of environmental DNA (eDNA) and relevant bioassays are practical tools which enable early detection of novel, problem HAB species and rapid toxin/HAB screening, and new data from HAB monitoring of aquaculture production sites using eDNA are presented. As aquaculture grows to supply a sizable proportion of the world's protein, the effects of HABs in reducing productivity is of increasing significance. Research into the multiple stressor effects of climate change and HABs on cultured species and using local, recent, HAB strains is needed to accurately assess effects and inform stock management strategies.

Little is known about host responses of farmed Chinook salmon with skin lesions, despite the lesions being associated with increased water temperatures and elevated mortality rates. To address this shortfall, a transcriptomic approach was used to characterise the molecular landscape of spot lesions, the most commonly reported lesion type in New Zealand Chinook salmon, versus healthy appearing skin in fish with and without spot lesions. Many biological (gene ontology) pathways were enriched in lesion adjacent tissue, relative to control skin tissue, including proteolysis, fin regeneration, calcium ion binding, mitochondrial transport, actin cytoskeleton organisation, epithelium development, and tissue development. In terms of specific transcripts of interest, pro-inflammatory cytokines (interleukin 1β and tumour necrosis factor), annexin A1, mucin 2, and calreticulin were upregulated, while cathepsin H, mucin 5AC, and perforin 1 were downregulated in lesion tissue. In some instances, changes in gene expression were consistent between lesion and healthy appearing skin from the same fish relative to lesion free fish, suggesting that host responses weren't limited to the site of the lesion. Goblet cell density in skin histological sections was not different between skin sample types. Collectively, these results provide insights into the physiological changes associated with common spot lesions in farmed Chinook salmon., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Fish disease surveillance methods can be complicated and time consuming, which limits their value for timely intervention strategies on aquaculture farms. Novel molecular-based assays using droplet digital Polymerase Chain Reaction (ddPCR) can produce immediate results and enable high sample throughput with the ability to multiplex several targets using different fluorescent dyes. A ddPCR tetraplex assay was developed for priority salmon diseases for farmers in New Zealand including New Zealand Rickettsia -like organism 1 (NZ-RLO1), NZ-RLO2, Tenacibaculum maritimum , and Yersinia ruckeri . The limit of detection in singleplex and tetraplex assays was reached for most targets at 10 -9  ng/μl with, respectively, NZ-RLO1 = 0.931 and 0.14 copies/μl, NZ-RLO2 = 0.162 and 0.21 copies/μl, T. maritimum = 0.345 and 0.93 copies/μl, while the limit of detection for Y. ruckeri was 10 -8 with 1.0 copies/μl and 0.7 copies/μl. While specificity of primers was demonstrated in previous studies, we detected cross-reactivity of T. maritimum with some strains of Tenacibaculum dicentrarchi and Y. ruckeri with Serratia liquefaciens , respectively. The tetraplex assay was applied as part of a commercial fish disease surveillance program in New Zealand for 1 year to demonstrate the applicability of tetraplex tools for the salmonid aquaculture industry., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 von Ammon, Averink, Kumanan, Brosnahan, Pochon, Hutson and Symonds.)

We investigated the effects of temperature and fasting on chinook salmon (Oncorhynchus tshawytscha) at different life stages. In the first stage, fish were reared at 13 °C (198.5 ± 34.6 g) or 17 °C (218.3 ± 47.6 g) and fasted for 27 and 26 days, respectively. In the second stage, fish reared at 13 °C (481.8 ± 54.3 g) and 17 °C (597.3 ± 64.3 g) were fasted for 42 and 41 days respectively. At the third stage, fish were reared only at 17 °C (1065.7 ± 190.9 g) and fasted for 42 days. At the end of each fasting period performance, fillet and whole-body proximal composition, and whole-body fatty acid profile were compared among fish before and after fasting. Additionally, fillet fatty acid daily loss was compared in fasted fish from different treatments. The results showed that body weight was not significantly impacted by fasting. However, at 17 °C fasting at all three stages had a negative impact on fillet weight and total fatty acid daily loss. With few exceptions, saturated (SFA), monounsaturated (MUFA) and polyunsaturated fatty acids from n-6 series (n-6 PUFA) were preserved in fillet of fish at 17 °C, while higher daily losses of docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and consequently polyunsaturated from n-3 series (n-3 PUFA) were observed in these same fish and in smaller fish at 13 °C. The results presented in this study provide important information regarding the influence of fasting and temperature on chinook salmon performance and metabolism, providing basis for future nutritional and compositional studies for this important commercial species., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Ocean warming and extreme sea surface temperature anomalies are threatening wild and domesticated fish stocks in various regions. Understanding mechanisms for thermotolerance and processes associated with divergent growth performance is key to the future success of aquaculture and fisheries management. Herein, we exposed Chinook salmon ( Oncorhynchus tshawytscha ) to environmentally relevant water temperatures (19-20 °C) approaching their upper physiological limit for three months and sought to identify blood biomarkers associated with thermal stress and resilience. In parallel, blood biochemical associations with growth performance were also investigated. Temperature stress-activated leukocyte apoptosis induced a minor immune response, and influenced blood ion profiles indicative of osmoregulatory perturbation, regardless of how well fish grew. Conversely, fish displaying poor growth performance irrespective of temperature exhibited numerous biomarker shifts including haematology indices, cellular-based enzyme activities, and blood clinical chemistries associated with malnutrition and disturbances in energy metabolism, endocrine functioning, immunocompetence, redox status, and osmoregulation. Findings provide insight into mechanisms of stress tolerance and compromised growth potential. Biochemical phenotypes associated with growth performance and health can potentially be used to improve selective breeding strategies.

Spinal anomalies are a recognised source of downgrading in finfish aquaculture, but identifying their cause(s) is difficult and often requires extensive knowledge of the underlying pathology. Late-onset spinal curvatures (lordosis, kyphosis, scoliosis) can affect up to 40% of farmed New Zealand Chinook (king) salmon (Oncorhynchus tshawytscha) at harvest, but little is known about their pathogenesis. Curvature development was radiographically documented in two related cohorts of commercially-farmed Chinook salmon throughout seawater production to determine (1) the timing of radiographic onset and relationships between (2) the curvature types, (3) the spinal regions in which they develop and (4) their associations with co-existing vertebral body anomalies (vertebral compression, fusion and vertical shift). Onset of curvature varied between individuals, but initially occurred eight months post-seawater transfer. There were strong associations between the three curvature types and the four recognised spinal regions: lordosis was predominantly observed in regions (R)1 and R3, kyphosis in R2 and R4, manifesting as a distinct pattern of alternating lordosis and kyphosis from head to tail. This was subsequently accompanied by scoliosis, which primarily manifested in spinal regions R2 and R3, where most of the anaerobic musculature is concentrated. Co-existing vertebral body anomalies, of which vertebral compression and vertical shift were most common, appeared to arise either independent of curvature development or as secondary effects. Our results suggest that spinal curvature in farmed New Zealand Chinook salmon constitutes a late-onset, rapidly-developing lordosis-kyphosis-scoliosis (LKS) curvature complex with a possible neuromuscular origin.

The recent development of Pacific oyster (Crassostrea gigas) SNP genotyping arrays has allowed detailed characterisation of genetic diversity and population structure within and between oyster populations. It also raises the potential of harnessing genomic selection for genetic improvement in oyster breeding programmes. The aim of this study was to characterise a breeding population of Australian oysters through genotyping and analysis of 18 027 SNPs, followed by comparison with genotypes of oyster sampled from Europe and Asia. This revealed that the Australian populations had similar population diversity (H E ) to oysters from New Zealand, the British Isles, France and Japan. Population divergence was assessed using PCA of genetic distance and revealed that Australian oysters were distinct from all other populations tested. Australian Pacific oysters originate from planned introductions sourced from three Japanese populations. Approximately 95% of these introductions were from geographically, and potentially genetically, distinct populations from the Nagasaki oysters assessed in this study. Finally, in preparation for the application of genomic selection in oyster breeding programmes, the strength of LD was evaluated and subsets of loci were tested for their ability to accurately infer relationships. Weak LD was observed on average; however, SNP subsets were shown to accurately reconstitute a genomic relationship matrix constructed using all loci. This suggests that low-density SNP panels may have utility in the Australian population tested, and the findings represent an important first step towards the design and implementation of genomic approaches for applied breeding in Pacific oysters., (© 2019 Stichting International Foundation for Animal Genetics.)

Vertebral fusions are an established economic concern in farmed Atlantic salmon, but have not been studied in detail in farmed Chinook salmon. Two radiographic studies of vertebral fusions were performed in farmed Chinook salmon. Sixteen of 1,301 (1.2%) smolt and 201 of 2,636 (7.6%) harvest fish had fusions. There were no significant differences in the number of fused vertebrae/fusion in smolt compared with harvest fish. Secondly, tagged fish were repeatedly radiographed to determine the progression of the fusions. Nineteen (4.4%), 23 (5.3%) and 39 (9.0%) fish had fusions as smolt, after 129 days in sea water, and at harvest, respectively. There were no significant differences in the average number of vertebra/fusion between the three time points. Of the fusions that were observed in smolt, additional vertebra did not become fused in 81% of the lesions. Within the rare fusions that did progress due to the involvement of adjacent vertebra, an average of 1.6 vertebrae were added per year. Fish with fusions were significantly lighter than non-affected fish at harvest. Fusions are common in farmed Chinook salmon; however, they are typically stable after development. As fish with fusions were lighter at harvest, reducing fusions may have an economic benefit., (© 2019 John Wiley & Sons Ltd.)

Over the past 40 years New Zealand (NZ) aquaculture has grown into a significant primary industry. Tonnage is small on a global scale, but the industry has built an international reputation for the supply of high quality seafood to many overseas markets. Since the early 1990s the industry has recognized the potential gains from selective breeding and the challenge has been to develop programs that can overcome biological obstacles (such as larval rearing and mortality) and operate cost-effectively on a relatively small scale while still providing significant gains in multiple traits of economic value. This paper provides an overview of the current status, and a perspective on genomic technology implementation, for the family based genetic improvement programs established for the two main species farmed in NZ: Chinook (king) salmon ( Oncorhynchus tshawytscha ) and Greenshell TM mussel ( Perna canaliculus ). These programs have provided significant benefit to the industry in which we are now developing genomic resources based on genotyping-by-sequencing to complement the breeding programs, enable evaluation of the genetic diversity and identify the potential benefits of genomic selection. This represents an opportunity to increase genetic gain and more effectively utilize the potential for within family selection.

Spinal abnormalities can be detected at harvest in around 40% of farmed Chinook salmon in New Zealand. However, whether these abnormalities are present in smolt is unknown. Radiographs of 3,736 smolt were taken immediately prior to transfer to sea water and evaluated for fusions, compressions, vertical shifts, and lordosis, kyphosis and/or scoliosis (LKS). The survey included smolt from two different chilling strategies that had been graded into slow- or fast-growing fish. Overall, 4.34% of Chinook salmon smolt had at least one spinal abnormality, similar to the rates of reported in Atlantic salmon smolt. The rate of abnormality was significantly higher in faster-growing fish. Fusions were most common with 2.68% of smolt affected. Smolt subjected to longer chilling times had lower rates of fusions. Compressions and vertical shifts were both observed in 1.31% of smolt. Although LKS is the most common abnormality of harvested fish, LKS was detected in just five smolt. The results suggest that some fusions in harvest fish have developed at the time of seawater transfer while LKS develops late in the production cycle. Overall, spinal abnormalities are uncommon in Chinook salmon smolt and may be influenced by chilling times and growth rates., (© 2018 John Wiley & Sons Ltd.)

In order to better understand how photo-thermal conditions affect oogenesis in captive-bred F1 hāpuku, a wreckfish considered for aquaculture in New Zealand, juvenile (pre-pubertal) fish were assigned to one of two regimes: exposed to a constant temperature of 17°C (CT group) or to seasonally varying temperatures (VT group range: 10-17°C), both under simulated ambient photoperiod, for nearly 2years. Development in females was monitored through repeated gonadal biopsies (histology; target gene mRNA levels) and blood sampling (plasma levels of estradiol-17β; E2). Very little evidence of advancing oogenesis was found in the first year of study, when fish were in their 4th year. In the subsequent year, a proportion of fish reached the pre-spawning stage (fully-grown ovarian follicles); the proportion of females reaching this stage was notably higher in the VT (62%) than the CT (28%) group. Of the few females that did reach maturity in the CT group, significantly lower levels of plasma E2 were observed relative to those in fish from the VT group possibly indicating a temperature-induced endocrine impairment during oogenesis. Interestingly, females that did not reach the pre-spawning stage presented with a small transient, but significant increase in oocyte diameters and plasma E2, suggestive of a dummy run. Clear seasonality was observed for fish under both photo-thermal regimes, and this was reflected in plasma E2 levels and transcript abundances of aromatase, fshr and luteinizing hormone receptor in the ovary; these end points all peaked in maturing females during the late or post-vitellogenic stage. We conclude that captive female F1 hāpuku first mature as five-year-olds and that exposure to a decreased temperature is important for appropriate progression of oogenesis., (Copyright © 2017 Elsevier Inc. All rights reserved.)

The ability to advance puberty in broodstock that have a long generation interval and mature at large size is a highly valuable tool in contemporary aquaculture enterprise. Juvenile male and female wreckfish 'hāpuku' (Polyprion oxygeneios), a candidate for commercialization in aquaculture, were subjected to treatment for 8weeks with two implants, one containing steroid (blank; estradiol-17β, E2; 11-ketotestosterone, KT; 17 α-methyltestosterone, MT), the other peptide (blank; gonadotropin-releasing hormone analog, GnRHa; kisspeptin, Kiss2-12). The expression of target genes (glycoprotein homone α-subunit, gpa; follicle stimulating-hormone β-subunit, fshb; luteinizing hormone β-subunit, lhb; GnRH receptor, gnrhr) in the pituitary was assayed by quantitative PCR. KT and MT decreased mRNA levels of all target genes in both male and female hāpuku, suggestive of a strong inhibitory tone by these steroid hormones. E2, GnRHa and Kiss2-12 were largely ineffective, regardless of whether they were administered alone or in combination with steroid implants. Clear differences in release and/or clearance rates between E2 and KT from implants were evident, in part explaining our observations. Advancement of puberty was not achieved, and we pose that different hormone doses and/or administration during more advanced stages of gonadogenesis need to be considered to move this field forward., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Background: Hāpuku (Polyprion oxygeneios) is a member of the wreckfish family (Polyprionidae) and is highly regarded as a food fish. Although adults grow relatively slowly, juveniles exhibit low feed conversion ratios and can reach market size in 1-2 years, making P. oxygeneios a strong candidate for aquaculture. However, they can take over 5 years to reach sexual maturity in captivity and are not externally sexually dimorphic, complicating many aspects of broodstock management. Understanding the sex determination system of P. oxygeneios and developing accurate assays to assign genetic sex will contribute significantly towards its full-scale commercialisation., Results: DNA from parents and sexed offspring (n = 57) from a single family of captive bred P. oxygeneios was used as a template for double digestion Restriction-site Associated DNA (ddRAD) sequencing. Two libraries were constructed using SbfI - SphI and SbfI - NcoI restriction enzyme combinations, respectively. Two runs on an Illumina MiSeq platform generated 70,266,464 raw reads, identifying 19,669 RAD loci. A combined sex linkage map (1367 cM) was constructed based on 1575 Single Nucleotide Polymorphism (SNP) markers that resolved into 35 linkage groups. Sex-specific linkage maps were of similar size (1132 and 1168 cM for male and female maps respectively). A single major sex-determining locus, found to be heterogametic in males, was mapped to linkage group 14. Several markers were found to be in strong linkage disequilibrium with the sex-determining locus. Allele-specific PCR assays were developed for two of these markers, SphI6331 and SphI8298, and demonstrated to accurately differentiate sex in progeny within the same pedigree. Comparative genomic analyses indicated that many of the linkage groups within the P. oxygeneios map share a relatively high degree of homology with those published for the European seabass (Dicentrarchus labrax)., Conclusion: P. oxygeneios has an XX/XY sex determination system. Evaluation of allele-specific PCR assays, based on the two SNP markers most closely associated with phenotypic sex, indicates that a simple molecular assay for sexing P. oxygeneios should be readily attainable. The high degree of synteny observed with D. labrax should aid further molecular genetic study and exploitation of hāpuku as a food fish.

In order to develop biomarkers that may help predict the egg quality of captive hapuku (Polyprion oxygeneios) and provide potential avenues for its manipulation, the present study (1) sequenced the proteome of early-stage embryos using isobaric tag for relative and absolute quantification analysis, and (2) aimed to establish the predictive value of the abundance of identified proteins with regard to egg quality through regression analysis. Egg quality was determined for eight different egg batches by blastomere symmetry scores. In total, 121 proteins were identified and assigned to one of nine major groups according to their function/pathway. A mixed-effects model analysis revealed a decrease in relative protein abundance that correlated with (decreasing) egg quality in one major group (heat-shock proteins). No differences were found in the other protein groups. Linear regression analysis, performed for each identified protein separately, revealed seven proteins that showed a significant decrease in relative abundance with reduced blastomere symmetry: two correlates that have been named in other studies (vitellogenin, heat-shock protein-70) and a further five new candidate proteins (78 kDa glucose-regulated protein, elongation factor-2, GTP-binding nuclear protein Ran, iduronate 2-sulfatase and 6-phosphogluconate dehydrogenase). Notwithstanding issues associated with multiple statistical testing, we conclude that these proteins, and especially iduronate 2-sulfatase and the generic heat-shock protein group, could serve as biomarkers of egg quality in hapuku.

The present study investigated, for the first time in a perciform teleost, the effects of in vivo 11-ketotestosterone (11-KT) treatment using slow-release implants on ovarian development and gonadotropin receptor mRNA levels in captive previtellogenic females of hapuku (Polyprion oxygeneios). At the cellular/functional level, ovarian development and ovarian and hepatic total lipid levels were examined. At the molecular level, transcript abundance of ovarian follicle-stimulating hormone receptor (FSH-R) and luteinizing hormone receptor (LH-R) was measured. Additionally, cyclic adenosine monophosphate (cAMP) levels in ovarian fragments from placebo and 11-KT implanted fish incubated with or without human chorionic gonadotropin (hCG) in vitro were compared between groups. There were no significant differences between treatments with regard to oocyte size and lipid contents of liver and ovary. Messenger RNA levels of FSH-R and LH-R were significantly lower in the treated females. Similarly, cAMP levels were significantly lower in the ovarian fragments of the 11-KT implanted females. These results suggest that 11-KT specifically, but possibly androgens in general, may not have an important function in regulating gonadal development of previtellogenic female hapuku; indeed, if anything, 11-KT appeared to have a detrimental effect and its use will not be beneficial in advancing sexual maturity of hapuku in aquaculture., (© 2013.)

The effectiveness of low cost breeding scheme designs for small aquaculture breeding programmes were assessed for their ability to achieve genetic gain while managing inbreeding using stochastic simulation. Individuals with trait data were simulated over 15 generations with selection on a single trait. Combinations of selection methods, mating strategies and genetic evaluation options were evaluated with and without the presence of common environmental effects. An Optimal Parent Selection (OPS) method using semi-definite programming was compared with a truncation selection (TS) method. OPS constrains the rate of inbreeding while maximising genetic gain. For either selection method, mating pairs were assigned from the selected parents by either random mating (RM) or Minimum Inbreeding Mating (MIM), which used integer programming to determine mating pairs. Offspring were simulated for each mating pair with equal numbers of offspring per pair and these offspring were the candidates for selection of parents of the next generation. Inbreeding and genetic gain for each generation were averaged over 25 replicates. Combined OPS and MIM led to a similar level of genetic gain to TS and RM, but inbreeding levels were around 75% lower than TS and RM after 15 generations. Results demonstrate that it would be possible to manage inbreeding over 15 generations within small breeding programmes comprised of 30 to 40 males and 30 to 40 females with the use of OPS and MIM. Selection on breeding values computed using Best Linear Unbiased Prediction (BLUP) with all individuals genotyped to obtain pedigree information resulted in an 11% increase in genetic merit and a 90% increase in the average inbreeding coefficient of progeny after 15 generations compared with selection on raw phenotype. Genetic evaluation strategies using BLUP wherein elite individuals by raw phenotype are genotyped to obtain parentage along with a range of different samples of remaining individuals did not increase genetic progress in comparison to selection on raw phenotype. When common environmental effects on full-sib families were simulated, performance of small breeding scheme designs was little affected. This was because the majority of selection must anyway be applied within family due to inbreeding constraints.

This study describes for the first time the normal development of New Zealand hapuku Polyprion oxygeneios embryos and larvae reared from fertilization to 11 days post-hatch (dph) at a constant temperature. Fertilized eggs were obtained from natural spawnings from communally reared captive wild broodstock. Eggs averaged 2 mm in diameter and had single or multiple oil globules. Embryos developed following the main fish embryological stages and required an average of 1859·50 degree hours post-fertilization (dhpf) to hatch. The newly hatched larvae (4·86 mm mean total length, L(T) ) were undifferentiated, with unpigmented eyes, a single and simple alimentary tube and a finfold that covered the entire body. Larvae relied on the energy from the yolk-sac reserves until 11 dph (7·33 mm mean L(T) ), when yolk-sac reabsorption was almost completed. Some of the major developmental stages from hatching to yolk-sac reabsorption were eye pigmentation (5 dph), upper jaw formation (7 dph), lower jaw formation (8 dph) and mouth opening (8-9 dph). By 9 dph, the digestive system consisted of pancreas, liver, primordial stomach, anterior and posterior gut; therefore, P. oxygeneios larvae would be capable of feeding on live prey. The developmental, morphological and histological data described constitutes essential baseline information on P. oxygeneios biology and normal development., (© 2012 NIWA. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.)

Uptake of exogenous DNA by electroporated salmon sperm for gene transfer is being investigated. Our studies show that electroporated salmon sperm cells were more efficient and more reliable than untreated sperm in picking up exogenous DNA and subsequently transferring the DNA into salmon embryos. Indirect evidence suggest that some of the exogenous DNA was internalized in the sperm nuclei. The taken up DNA retained its integrity as demonstrated by PCR. The foreign DNA was detected in 15-month-old fish, and had a mosaic pattern of distribution. Integration of the foreign DNA occurred infrequently, and the expression of the foreign genes was poor. The potential of sperm-mediated gene transfer as a routine protocol for mass gene transfer in salmon will be dependent on the improvement of integration and expression of the foreign gene.

The insertion of the blood retrotransposon into the untranslated region of exon 7 of the sn-glycerol-3-phosphate dehydrogenase-encoding gene (Gpdh) in Drosophila melanogaster induces a GPDH isozyme-GPDH-4-and alters the pattern of expression of the three normal isozymes-GPDH-1 to GPDH-3. The process of transcript terminus formation inside the retrotransposon insertion reduces the level of the Gpdh transcript that contains exon 8 and increases the level of the transcript that contains exons 1-7. The induced GPDH-4 isozyme is a translation product of the three transcripts that contain fragments of the blood retrotransposon. The mechanism of mutagenesis by the blood insertion is postulated to involve the pause or termination of transcription within the blood sequence, which in turn is caused by the interference of a DNA-binding protein with the RNA polymerase. Thus, we show the formation of a new functional GPDH protein by the insertion of a transposable element and discuss the evolutionary significance of this phenomenon.

A rare naturally occurring allele, GpdhACb62, at the sn-glycerol-3-phosphate dehydrogenase locus in Drosophila melanogaster, encodes an enzyme with an electrophoretic mobility that is more cathodal than that produced by the common slow electrophoretic allele. After electrophoresis and staining of extracts of single adult flies there is a single band of activity corresponding in position to GPDH-1, but, using highly concentrated extracts, a faint band corresponding to GPDH-3 is observed. In GpdhACb62 homozygotes there is about 26% of the normal level of activity in adults, and less than 6% in third instar larvae. The reduction in activity is significantly greater than the decrease in GPDH immunologically cross-reacting material (CRM). Northern analyses, and rapid amplification of the cDNA ends (RACE) of the 3' regions of the transcripts, show that the levels and structures of the poly(A)+RNAs are similar in homozygotes for GpdhACb62 and for a normal activity allele GpdhAC8. Hybridization to oligonucleotide probes specific for the GPDH-1 and GPDH-3 transcripts was of a similar intensity in GpdhACb62 and GpdhAC8 adult flies. In third instar larvae the main transcript is for GPDH-3 and again the hybridization signals were similar in each line. The activity of the enzyme produced by GpdhACb62 was unstable both at 50 degrees C and at 0 degrees C. The activity lost at 0 degrees C was recovered by incubation at 20 degrees C. The complete GpdhACb62 gene, and the partial Gpdh tandem duplication 3' to this gene, were cloned and sequenced. Comparisons with two normal activity GpdhF genes revealed 31 unique changes in the first copy of GpdhACb62. In exon 4, a T to G substitution changes cysteine to glycine and may disrupt a disulphide bond and be responsible for the distinctive properties of GPDH-ACb62.

Restriction site variation in a 25-kb region including the sn-glycerol-3-phosphate dehydrogenase (Gpdh) locus has been assessed in 29 single female D. melanogaster lines from the Cardwell (Australia, QLD) population. The Gpdh locus was duplicated in about one-third of the lines, although the duplication was incomplete and lacked exons 1 and 2. There was no restriction site variation in the duplicated region. Three insertions were found in the gene region but only one affected GPDH activity. The lines with the duplication had higher levels of GPDH activity and protein amount than did nonduplicated lines. This effect was also observed in lines extracted from two other Australian populations. The duplication is shown to have a similar structure in each population investigated and is also present in populations from China and Africa. It is suggested that the effect of the duplication on GPDH activity, which might be due to structural factors affecting transcription at the Gpdh locus, could account for the worldwide distribution of the duplication.