Transformational climate adaptation requires coordinated action across sectors and scales, enabled by governance arrangements that can address systemic barriers. Public-private partnerships (PPPs) may provide such a mechanism by aligning incentives, pooling resources and fostering collaboration between government and industry. In this paper, we evaluate a national PPP, The Aotearoa Circle (The Circle), and how it has catalysed climate adaptation in Aotearoa New Zealand’s seafood sector. Commissioned by The Circle, we conducted adaptation pathways planning, a decision-support process that identifies and sequences adaptation strategies and actions to reduce future climate risk, for two fisheries and two aquaculture industries. The process engaged company, government, research and civil society stakeholders to design suites of incremental and transformational strategies to reach long-term industry goals, and actions to implement them. We analysed these outputs to assess the PPP’s relevance in enabling implementation. Amongst the transformational pathways, 48% of actions required collaboration by public and private entities. Strategies were also identified to address systemic adaptation barriers across the sector (agile regulation, climate forecasting, fleet decarbonisation, oceans research). For these, the majority of actions required leadership by The Circle or public-private collaborations. Key informant interviews revealed challenges in implementation of immediate actions. While some were underway, shifts in national government policies had resulted in uneven progress amongst the industries. Interviewees emphasised the necessity for The Circle to convene stakeholders and sustain momentum, but resourcing was a constraint. Our results highlight The Circle’s core role in enabling transformational adaptation within industries and across the sector. Yet the PPP remains vulnerable to political cycles, variable public sector commitment and risk aversion. Strengthening PPP resourcing arrangements is necessary to action long-term adaptation, and to ensure ongoing, iterative pathways planning.

Antimicrobial peptides (AMPs) are key components of the innate immune system in fish, providing rapid protection against microbial pathogens. Among these, the liver-expressed antimicrobial peptides (LEAPs), comprising LEAP-1 (hepcidin; HAMP) and LEAP-2, play central roles in host defence and iron regulation. In this study, we present an integrated characterisation of the genomic organisation, tissue expression and dietary responsiveness of HAMP and LEAP2 paralogues in Chinook salmon (Oncorhynchus tshawytscha), and assess their modulation by a phytobiotic functional feed under commercial farming conditions. Genome mining identified three functional HAMP and three LEAP2 paralogues in Chinook salmon, all retaining conserved features typical of their respective peptide families and arising from salmonid-specific genome duplication events. Constitutive expression analysis revealed liver-dominant expression of HAMP, whereas LEAP2 paralogues exhibited distinct tissue-specific profiles, with LEAP2.1 and LEAP2.2 expressed predominantly in the liver and skin, and LEAP2.3 largely restricted to gills and skin. A six-month feeding trial using a functional diet supplemented with the phytobiotic NatControl™ resulted in marked tissue- and paralogue-specific upregulation of AMP gene expression. HAMP expression was upregulated across multiple immune-relevant tissues, including head kidney, skin, spleen, liver and gills. LEAP2 paralogues also showed clear dietary responsiveness, with LEAP2.1 and LEAP2.2 upregulated in the liver and kidney, and LEAP2.3 showing strong upregulation in gills. Despite these molecular responses, no significant differences in growth or survival were observed between diet groups. Together, these findings provide the first integrated characterisation of HAMP and LEAP2 systems in Chinook salmon, demonstrate their sensitivity to dietary immunomodulation and support their use as molecular biomarkers of functional immune priming. The results further indicate that NatControl™ acts as an effective immunostimulant, enhancing innate immune readiness without compromising growth performance under non-challenging conditions.

The bacterial skin disease tenacibaculosis, caused by Tenacibaculum species, affects numerous economically important marine fish, including salmonids. This study reports the ability of three Tenacibaculum maritimum strains, belonging to different molecular O-AGC types, and a single Tenacibaculum dicentrarchi strain to induce tenacibaculosis in farmed Chinook salmon (Oncorhynchus tshawytscha, Walbaum 1792) in Aotearoa New Zealand. Naïve Chinook salmon were exposed to T. maritimum (2 × 108 cells/mL) and T. dicentrarchi (2 × 107 cells/mL) by immersion using natural seawater. Clinical signs of tenacibaculosis were apparent in all T. maritimum strains used in the challenged fish. Of these, 100% of the fish challenged with O-AGC Type 2-1 and Type 3-2 strains became moribund, whereas only 60% of the O-AGC Type 3-0 challenged fish became moribund. Fish exposed to T. dicentrarchi showed more severe symptoms, exposing musculature in 51% of the challenged population, with 28% of fish becoming moribund. Gross pathological signs of fin rot, scale loss, skin ulcers and haemorrhagic skin spots were observed for both Tenacibaculum species and were consistent with those observed on farmed fish. Pure T. maritimum and T. dicentrarchi cultures were reisolated from epidermal damage of challenged fish. Tenacibaculum species was not isolated from the anterior kidney of affected fish, which indicates no systemic infection in Chinook salmon.

Automated health assessment is important for efficiently managing spinal deformities, such as lordosis-kyphosisscoliosis (LKS) and vertebral compression, in farmed salmon. In this study, we present a multi-stage deep learning pipeline for vertebral detection and severity classification in salmon X-ray images. Following initial image preprocessing and segmentation via a U-Net model, vertebrae are detected and localized using an enhanced YOLOv12 object detection framework. YOLOv12 has high accuracy, stable convergence, and a faster inference compared to the prior YOLOv10 version. LKS severity is then assessed through a rule-based strategy using Cobb angle measurements derived from the detected vertebrae, enabling objective anatomical characterization across different regions of the vertebral column. For compressions, statistical and morphological features are extracted and classified using a suite of machine learning models, with performance optimized by feature selection and class balancing techniques. The proposed system achieves robust detection and disease classification across both normal and pathological regions, showing reliable performance even in anatomically challenging cases. Designed for integration into industrial aquaculture workflows, the pipeline enables highthroughput, automated screening of large fish populations to support timely, data-driven health management at scale. This integrated approach enhances the scalability and accuracy of disease monitoring in aquaculture, and thus fish welfare and farm productivity.

Blood biochemistry and haematological parameters are an integral part of evaluating the health status of fish. Accordingly, these parameters are useful indicators of fish health, welfare and nutritional status. This study examines 33 blood biochemistry and haematological parameters to compare presumed healthy Chinook salmon, Oncorhynchus tshawytscha, reared in commercial pens with research fish reared under controlled conditions in a land based recirculating aquaculture system (RAS). This study also examines the influence of weight and environmental factors, including water type (freshwater and seawater), on these parameters. Significant differences between the aquaculture rearing systems were found for the majority of the parameters, for example triglyceride, cholesterol, and alanine aminotransferase. Subsequently, reference ranges for the parameters were calculated separately for each rearing system. These differences were most likely due to the different stressors experienced by the fish in the open water farms versus the RAS research tanks, particularly the single handling of each on-farm fish versus the cumulative effect of multiple handlings on the trial fish prior to sampling. Significant differences were also identified for the other environmental factors examined. The parameters that exhibited the most significant differences or interactions were calcium, creatinine, and glucose. The parameters that exhibited the least significant differences or interactions were lipase, lactate, and monocytes. The results show that with many significant differences and interactions, it is more appropriate to use multiple reference intervals rather than a single reference interval that does not consider environmental factors, especially for the factors to which the parameters were most sensitive. Careful interpretation is needed in terms of the history of a given fish to provide accurate assessment of blood biomarker values.

Research involving exercise to optimise salmonid production performance has mostly focused on short exercise- training periods (< five months) with small size classes (< 500 g). There is urgency to understand the influence of sustained swimming on larger individuals and how to adequately scale exercise regimes for the larger smolt sizes that are now being transferred to sea. There is also a considerable knowledge gap in our understanding of using circular tanks to exercise salmonids and the impact that continuous circular swimming may have on muscle symmetry and physiology. This study aims to determine if exercise regimes optimised for small post-smolt salmonids can enhance production performance in larger post-smolts, while identifying possible muscle asymmetry resulting from exercise-training salmon in circular tanks. Post-smolt Chinook salmon were reared under low (LFR) or moderate (MFR) flow regimes for six months, to a larger size (1056 +/- 11 g and 374 +/- 1 mm) than typically studied in research. Several aspects of whole-animal performance were measured and matched with physical and biochemical responses on lower biological levels of organisation (i.e., tissue, cellular and molecular). Physical and biochemical responses of the skeletal muscle were further assessed with respect to the left and right fillets. Production performance (individual growth, tank level feed intake, growth and efficiency) was significantly better in Chinook salmon reared under LFR compared to MFR. Chemical composition (lipid and protein content) and muscle morphometrics did not differ between the flow regimes, even though genes involved in lipid metabolism and muscle repair and maintenance were upregulated in Chinook salmon reared under MFR. Lateral investigations of white muscle showed the right fillet (outward facing fillet) to have higher lipid content in the lateral and visceral regions, lower protein content across the entire fillet, and denser white muscle fibres. Genes involved in lipid metabolism and muscle development and contraction were also upregulate in the white muscle of the right fillet. This study shows that optimal exercise regimes for small post-smolt salmon are not necessarily suited to larger post-smolt salmon, and that exercise regimes for larger post-smolt salmonids may need to be optimised separately. Additionally, the results from this study suggest that continuous circular swimming may stimulate muscle blocks unevenly leading to muscle asymmetry and reveals a new set of questions associated with exercising salmonids in circular tanks. Further exploration is warranted to determine the relevance for commercial settings when larger rearing tanks are used.

Sampling bias was investigated in New Zealand farmed king salmon (Oncorhynchus tshawytscha) at the end of a feed trial. Two sampling techniques - a non-lethal manual assessment (MA) and a lethal hook and line (HL), were evaluated for the representativity of their samples, with regard to two performance indicators, weight and skin health. Both sampling techniques assessed (MA n = 60, HL n = 4) were biased when compared to the analysis of all the fish in each pen. However, MA samples were biased towards fish with better skin health and higher weight (+ 0.20 kg), while HL selected fish with poorer skin health than the pen population average and lower Fulton's Condition Factor (- 0.25) than MA samples. Our results emphasised the significance of understanding sampling bias so research interpretation is correct.

Production costs in finfish aquaculture can be reduced by improving feed conversion ratio (FCR, the ratio of feed intake to weight gain) but to improve FCR it is important to understand what influences it. As feed intake is one of the two main variables of FCR, analysing feeding behaviours of individuals during meals could explain differences in energy expenditure that influences individual FCR variation in Chinook salmon (Oncorhynchus tshawytscha). The aim of this study was to assess the influence of feeding behaviour on FCR. Feeding behaviours exhibited by feed efficient (FCRE), and inefficient (FCRI) Chinook salmon fed to satiation were characterised using video imaging across three separate meals, each a week apart. To quantify behaviour a scoring criterion was developed based on turning angles, distance travelled, acceptance/rejection of pellets, consumption/spitting of pellets as well as the time taken to make those decisions. Feeding behaviour was found to be consistent within the same group of individuals over a three-week period. FCRI fish exerted more effort during feeding, by carrying out more turns (P < 0.001) and covering more distance (P < 0.001) despite feed intake not differing to that of FCRE fish (P > 0.05). In addition, FCRI fish spat out more pellets rather than ingesting them (P = 0.02), thus further increasing their energy expenditure. These behaviours were recorded in fish fed to satiation as this is consistent with on-farm practices and it is hypothesised that this feeding practice allows for increased energy expenditure in FCRI fish, in particular spitting behaviours, which reduces feed efficiency.

Hāpuku (Polyprion oxygeneios) is a promising candidate for aquaculture production in New Zealand. Methods for spawning, juvenile production, and growout to harvest entirely on land, where water quality, pathogens, environmental impacts, and genetic “pollution” can be tightly controlled, have been developed, and genetic improvement to optimise land-based production is the obvious next step. However, estimates of genetic parameters are required to design a rigorous, disciplined, and effective selective breeding program. By using existing data consisting of irregularly spaced repeated measurements of fork length and live body weight collected on wild-collected founders and two generations of captively reared progeny, we evaluated the species’ genetic potential for improvement in growth. We first tested a range of univariate random regression models to identify the best-fitting models for these data. Subsequently, using a bivariate model, we estimated variance components for growth trajectories of fork length and whole body weight. With one to six records available per fish, the best-fitting univariate models included only a fixed effect for contemporary groups and fixed and random genetic third-order Legendre polynomials. More complex models that included full-sib family and/or permanent environmental effects produced unacceptable constrained and/or non-positive-definite solutions. Both traits are moderately heritable at all stages of the growout phase (~0.4–0.5), and the genetic correlation patterns between daily breeding values estimated via the covariance function are different for length and weight. Genetic correlations for length between all pairs of age-specific breeding values are positive and strong (>0.7) and change gradually and smoothly with increasing temporal separation. For weight, these correlations deteriorate more rapidly with increasing time lags between measurements and become negative for some age pairings. We conclude that random regression analyses are a valuable tool for extracting genetic information from irregularly spaced repeated measurements of fish size, speculate that emerging technologies for high-throughput genotyping and phenotyping will add to the value of this approach in the near future, and reason that a breeding strategy that rigorously takes into account the potentially unfavourable genetic correlations between breeding values for weight at some ages will further adapt hāpuku to land-based systems and enhance the profitability commercial-scale production.

King salmon is important for aquaculture in New Zealand, contributing significant economic value. Fish health is a priority for the industry, and the change in the health status of king salmon needs to be accurately detected at the earliest possible stage. Many factors affect the health of king salmon, such as temperature. Identifying the key features that influence health prediction is a crucial step toward achieving this goal. This study utilizes trial data collected by the Cawthron Institute, which includes diverse information on king salmon, such as blood biochemistry and hematology. We explore the data by employing statistical methods and feature selection techniques in machine learning to identify the most relevant features for king salmon health prediction, aiming to classify individuals as healthy or unhealthy with a small number of features. The results show that although the most efficient feature selection techniques on different datasets vary, overall, feature selection approaches can successfully identify relevant and informative features for king salmon health classification. Through the incorporation of a few selected features, the learned classifiers could still achieve statistically equal or better classification performance. This study not only contributes to the understanding of the health indicators of king salmon but also provides crucial insights into health prediction, which will be beneficial to the improvement of the health of king salmon, leading to the development of more effective management strategies for aquaculture.

Fish feeding behaviour can be complicated and time consuming to observe, analyse and quantify. The conventional single ballotini X-radiography method was modified to determine the timing of feeding within a meal in farmed fish reared at commercial densities. Feed pellets containing two bead sizes were fed at different times during a single meal, either for the first half or second half of the meal. The two different ballotini sizes were differentiated on X-radiographs by human eye and semi-automated bead counting software was able to count the different bead sizes accurately. This dual ballotini method was used to assess whether fish ate earlier, later or during both halves of the meal and showed that individual fish feeding patterns were similar across two repeated meals. The method was applied to Chinook salmon (Oncorhynchus tshawytscha), a premium farmed salmonid, to determine the relationship between feed conversion ratio (FCR) and the timing of feeding. Results showed that fish that ate smaller amounts of feed ate most of their meal at the end of the meal. There was no significant difference in when feed efficient or feed inefficient fish ate within the meal but, at the first dual ballotini assessment, there was a relationship between FCR and the timing of feeding where more efficient fish ate later in the meal. However, this relationship was absent at the second time point. Despite this, the dual ballotini method is a promising and versatile alternative method for the characterisation of fish feeding behaviours and can be applied under a range of conditions including higher rearing densities.

A healthy skeletal system is fundamental to fish welfare and performance and a key physiological feature of a robust fish. The presence of skeletal deformities in farmed salmonids is a persistent welfare problem in aquaculture, and one which threatens to impede industry growth. Deformities of the fine bones of fish, such as ribs and intermuscular bones (IBs), have received less attention than vertebral body deformities, despite their potential to compromise fish welfare and product quality. IBs, commercially known as pin bones, are small spicule-like bones embedded in the muscle fillets of salmonids, cyprinids and other basal teleost species. In farmed basal teleosts, they impact fish processing, have negative effects on the economic value of fish and present a potential consumer health concern if ingested. Current understanding of IB development and function in teleosts has mostly relied on morphological research. More recently, advances in our understanding of molecular mechanisms of IB development in cyprinids have been made, largely due to the exploration of breeding IB-free fish for use in aquaculture. In this review, we explore the existing literature on IBs in teleosts, highlight the points of contention within this field of research and identify the significant knowledge gaps about the development and function of salmonid IBs. To our knowledge, there is no available research on the function of IBs and scarce research concerning IB development in salmonids. Future research on teleost IBs would benefit from the use of consistent terminology to facilitate interdisciplinary collaboration and identify research outputs in this field.

King (Chinook) salmon is the only salmon species farmed in Aotearoa New Zealand and accounts for over half of the world's production of king salmon. Determining the health status of king salmon effectively is important for farming. However, it is a challenging task due to the complex biotic and abiotic factors that influence health. Evolutionary machine learning algorithms have shown their superiority in learning models for challenging tasks. However, they have not been investigated for health prediction in king salmon farming. This paper focuses on data processing and machine learning algorithm design to develop king salmon health prediction models in Aotearoa New Zealand. Particularly, this paper proposes a king salmon health prediction method based on genetic programming which is an evolutionary machine learning algorithm. The results show that genetic programming achieves the best overall performance among all examined typical machine learning algorithms for most trials. Further analyses show that genetic programming can automatically detect important features for learning classifiers for king salmon health classification tasks effectively, and can also learn potentially interpretable models. Our results are an important step forward in developing health prediction tools to automatically assess health status of farmed king salmon in Aotearoa New Zealand.

AbstractThe bacterial skin disease tenacibaculosis, caused byTenacibaculumspecies, can compromise numerous species of economically important marine fish, including salmonids. While tenacibaculosis is a known threat to Atlantic salmon (Salmo salar) aquaculture, the pathogenesis ofTenacibaculum maritimumandTenacibaculum dicentrarchion Chinook salmon (Oncorhynchus tshawytscha) has not yet been investigated. In this study, three molecular O-AGC types ofT. maritimum(O-AGC Type 3-0, Type 2-1 and Type 3-2) andT. dicentrarchiisolated during a disease outbreak of farmed Chinook salmon in Aotearoa New Zealand were assessed for their ability to induce tenacibaculosis in salmon smolts under controlled conditions. Naive Chinook salmon were exposed toT. maritimumorT. dicentrarchiby immersion. Clinical signs of tenacibaculosis were apparent post-exposure and observed in 100% of all three molecular O-AGC types ofT.-maritimum-challenged fish, with 100% morbidity in O-AGC Type 2-1 and Type 3-2 and 60% in O-AGC Type 3-0. Chinook salmon exposed toT. dicentrarchishowed characteristic clinical signs of disease in 51% of the challenged population, with 28% morbidity. Common gross pathological signs observed for bothTenacibaculumspecies were congruent with observations on farmed fish in the field, including scale loss, erythematous skin lesion, skin ulcers, fin necrosis, mouth erosion and gill ulceration. Exophthalmia was observed only inT. maritimum-challenged fish, while skin ulcers appeared grossly more severe with exposed musculature inT. dicentrarchi-challenged fish. PureT. maritimumandT. dicentrarchicultures were reisolated from the skin and gills of the challenged fish and their identity was confirmed by species-specific PCR and molecular O-AGC typing. Challenge experiments and associated field surveillance (forT. maritimum) did not show the presence of culturableT. maritimumcells in the anterior kidney. This provides compelling evidence that tenacibaculosis in farmed Chinook salmon is an external infectious disease, and thatTenacibaculumis a marine obligate organism that is unable to survive in fish body fluids and does not cause septicaemia. This has repercussions for approaches to experimental challenges withTenacibaculumspecies, which must occur by immersion rather than intraperitoneal or intramuscular inoculation, to replicate the natural transmission pathway and to ensure a successful challenge model. This study fulfilled modernised Koch’s postulates for the three molecular O-AGC types ofT. maritimumand single strain ofT. dicentrarchias aetiological agents of tenacibaculosis in Chinook salmon that cause mortalities with considerable external abnormalities.Author summaryChinook salmon,Oncorhynchus tshawytscha, is the most significant species of Pacific salmon for its large size and nutritional content which makes it a premium choice for aquaculture. In Aotearoa|New Zealand, Chinook salmon is the only marine salmon species farmed. For a decade, the industry was impacted by an undiagnosed skin disease resulting in high mortalities. Disease susceptibility in Chinook salmon is scarcely studied and added to the challenge for a timely diagnosis. This novel research provides insight on disease susceptibility of Chinook salmon and confirmsTenacibaculumspecies identified in New Zealand pose a high threat to the aquaculture industry. This research has global implications and contributes valuable insights and approaches to disease management that can be applied in British Columbia and Canada where Chinook salmon populations are in decline.

Exercise regimes provide a promising opportunity to enhance production performance during hatchery rearing, but exercise-enhanced traits are presently poorly understood in Chinook salmon. In addition, spinal health can be a concern in some farms in New Zealand and unfavourable correlations between higher condition factor and spinal curvature have been detected. Exercise regimes, in other salmonids, have improved bone mineralisation and lowered condition factor. Therefore, we hypothesise that sustained swimming could be used as a tool to improve spinal health. Here we tested the influence of low (0.3 bl s-1) and moderate (0.8 bl s-1) flow regimes on post -smolt (initial size: wet weight = 82.9 +/- 0.3 g, fork length = 174.6 +/- 0.2 mm) Chinook salmon feed efficiency and growth performance, as well as spinal health. We first measured the actual swimming speeds of Chinook salmon under low and moderate flow regimes to determine differences in exercise levels. Swimming speeds were not different between the flow regimes and were much higher than the set flow, because the Chinook salmon were advancing around the tank, swimming faster than the set flow at their own chosen swimming speed. Moderate flow regimes improved feed efficiency but did not influence other feed and growth metrics or spinal curvature and vertebral anomalies prevalence or severity. Production performance significantly differed between individuals with normal spinal health and those that developed spinal anomalies (vertebral compression, -fusion, and/or -vertical shift) or spinal curvature (lordosis, kyphosis, and/or scoliosis). Chinook salmon that developed spinal anomalies were smaller, grew slower, and exhibited poorer feed efficiency, whereas individuals that developed spinal curvature were significantly heavier, longer, and had higher condition factor. The probability of individuals developing spinal curvature increased with higher condition factor. These results provide critical information for industry to consider in their selective breeding objectives to curb the prevalence and severity of spinal curvature incidences.

The bacterial skin disease tenacibaculosis, caused by Tenacibaculum species, can compromise numerous species of economically important marine fish, including salmonids. While tenacibaculosis is a known threat to Atlantic salmon ( Salmo salar ) aquaculture, the pathogenesis of Tenacibaculum maritimum and Tenacibaculum dicentrarchi on Chinook salmon ( Oncorhynchus tshawytscha ) has not yet been investigated. In this study, three molecular O-AGC types of T. maritimum (O-AGC Type 3-0, Type 2-1 and Type 3-2) and T. dicentrarchi isolated during a disease outbreak of farmed Chinook salmon in Aotearoa New Zealand were assessed for their ability to induce tenacibaculosis in salmon smolts under controlled conditions. Naive Chinook salmon were exposed to T. maritimum or T. dicentrarchi by immersion. Clinical signs of tenacibaculosis were apparent post-exposure and observed in 100% of all three molecular O-AGC types of T.-maritimum -challenged fish, with 100% morbidity in O-AGC Type 2-1 and Type 3-2 and 60% in O-AGC Type 3-0. Chinook salmon exposed to T. dicentrarchi showed characteristic clinical signs of disease in 51% of the challenged population, with 28% morbidity. Common gross pathological signs observed for both Tenacibaculum species were congruent with observations on farmed fish in the field, including scale loss, erythematous skin lesion, skin ulcers, fin necrosis, mouth erosion and gill ulceration. Exophthalmia was observed only in T. maritimum -challenged fish, while skin ulcers appeared grossly more severe with exposed musculature in T. dicentrarchi -challenged fish. Pure T. maritimum and T. dicentrarchi cultures were reisolated from the skin and gills of the challenged fish and their identity was confirmed by species-specific PCR and molecular O-AGC typing. Challenge experiments and associated field surveillance (for T. maritimum ) did not show the presence of culturable T. maritimum cells in the anterior kidney. This provides compelling evidence that tenacibaculosis in farmed Chinook salmon is an external infectious disease, and that Tenacibaculum is a marine obligate organism that is unable to survive in fish body fluids and does not cause septicaemia. This has repercussions for approaches to experimental challenges with Tenacibaculum species, which must occur by immersion rather than intraperitoneal or intramuscular inoculation, to replicate the natural transmission pathway and to ensure a successful challenge model. This study fulfilled modernised Koch’s postulates for the three molecular O-AGC types of T. maritimum and single strain of T. dicentrarchi as aetiological agents of tenacibaculosis in Chinook salmon that cause mortalities with considerable external abnormalities. Author summary Chinook salmon, Oncorhynchus tshawytscha , is the most significant species of Pacific salmon for its large size and nutritional content which makes it a premium choice for aquaculture. In Aotearoa|New Zealand, Chinook salmon is the only marine salmon species farmed. For a decade, the industry was impacted by an undiagnosed skin disease resulting in high mortalities. Disease susceptibility in Chinook salmon is scarcely studied and added to the challenge for a timely diagnosis. This novel research provides insight on disease susceptibility of Chinook salmon and confirms Tenacibaculum species identified in New Zealand pose a high threat to the aquaculture industry. This research has global implications and contributes valuable insights and approaches to disease management that can be applied in British Columbia and Canada where Chinook salmon populations are in decline. ### Competing Interest Statement The authors have declared no competing interest.

Lordosis-Kyphosis-Scoliosis (LKS) is a spinal deformity that affects salmon, leading to health and economic consequences in aquaculture. Early detection of LKS is critical for mitigating it effects and improving fish welfare. This paper presents an AI-driven system for detecting and classifying LKS in salmon using X-ray imaging and Cobb angle analysis. The proposed system incorporates image preprocessing, vertebra detection using the YOLOv10 model, and Cobb angle calculation to quantify spinal deformities. A dataset of 1,888 X-ray images was utilized to evaluate the performance of the system, achieving high accuracy in vertebra detection and real-time prediction with an average inference time of 3-5 seconds. Our results demonstrate that this system offers an efficient and scalable solution for integrating automated health monitoring in aquaculture environments, ultimately enhancing both productivity and fish welfare.

Abstract 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 ($${\overline{\text{x}}}$$ x ¯ ± s.d.) to 583.2 ± 117.1 g ($${\overline{\text{x}}}$$ 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).

The effect of feeding restricted rations was investigated in two different size classes of Chinook (King) salmon (Oncorhynchus tshawytscha). Smaller individuals (725 g initial mean weight) were fed with 100% (satiation, SR1), 90.4% (SR2), or 81.6% (SR3) feed rations for 64 days, while larger individuals (1689 g initial mean weight) were fed with 100% (LR1), 82.6% (LR2), or 76.1% (LR3) feed rations for 119 days. The growth performance was evaluated for both size classes, and for the larger individuals, the analysis also included spinal curvature inci-dence (lordosis???kyphosis???scoliosis (LKS)), whole-body and fillet proximate composition, and fatty acid profiles. In both size classes, the final weight, weight gain, specific growth rate (SGR), and condition factor (CF) were significantly higher in individuals fed to satiation (SR1 and LR1) compared to individuals fed restricted rations (SR2 and LR2, SR3 and LR3). However, no significant differences in FCR were observed among the different treatments. Although the incidence of spinal curvature and vertebral body anomalies (i.e., compressions, fusions, vertical shifts) in the larger individuals were higher for the groups fed to satiation (LR1) compared to the groups fed restricted rations (LR2 and LR3), only the differences in vertebral anomalies were statistically significant. No significant differences were observed in whole-body and fillet proximate composition, while several significant differences were observed in the fatty acid profiles (whole-body and fillet) of larger individuals fed different rations. Monounsaturated fatty acids (MUFA), especially oleic acid (OA, 18:1n-9), and n-6 polyunsaturated fatty acids (n-6 PUFA), especially linoleic acid (LA, 18:2n-6) levels, were higher in fish fed to satiation. In contrast, saturated (SFA), primarily palmitic acid (PA, 16:0), and n-3 polyunsaturated fatty acids (n-3 PUFA), primarily eicosapentaenoic acid (EPA, 20:5n-3), and docosahexaenoic acid (DHA, 22:6n-3), were lower in groups fed the higher rations. Despite the overall improved growth performance of the groups fed to satiation, our results suggest that feeding Chinook salmon restricted rations has the potential to decrease the incidence of spinal anomalies, particularly vertebral body anomalies, and improve product quality (based on n-3 PUFA levels), without compromising FCR.

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.