Magnetic resonance imaging shows spinal curvature in Chinook salmon (Oncorhynchus tshawytscha) is associated with chronic inflammation of peri-vertebral soft tissues.

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.

Characterising the Physiological Responses of Chinook Salmon (Oncorhynchus tshawytscha) Subjected to Heat and Oxygen Stress.

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.

Prediction of Feed Efficiency and Performance-Based Traits in Fish via Integration of Multiple Omics and Clinical Covariates.

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.

Modeling the effects of ration on individual growth of Oncorhynchus tshawytscha under controlled conditions.

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.

Molecular evidence for stress, inflammation and structural changes in non-specific ulcers in skin of farmed Chinook salmon (Oncorhynchus tshawytscha).

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.

The influence of temperature on performance, biological indices, composition, and nutrient retention of juvenile Chinook salmon (Oncorhynchus tshawytscha) reared in freshwater.

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.

Relationship between gut microbiota and Chinook salmon (Oncorhynchus tshawytscha) health and growth performance in freshwater recirculating aquaculture systems.

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.

The relationships between specific dynamic action, nutrient retention and feed conversion ratio in farmed freshwater Chinook salmon (Oncorhynchus tshawytscha).

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.

An Efficient Tetraplex Surveillance Tool for Salmonid Pathogens.

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.

Effects of Harmful Algal Blooms on Fish and Shellfish Species: A Case Study of New Zealand in a Changing Environment.

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.

Protein metabolism in the liver and white muscle is associated with feed efficiency in Chinook salmon (Oncorhynchus tshawytscha) reared in seawater: Evidence from proteomic analysis.

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.

Transcriptomic characterisation of a common skin lesion in farmed chinook salmon.

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 1ß 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.

Effects of fasting and temperature on the biological parameters, proximal composition, and fatty acid profile of Chinook salmon (Oncorhynchus tshawytscha) at different life stages.

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.

Uncoupling Thermotolerance and Growth Performance in Chinook Salmon: Blood Biochemistry and Immune Capacity.

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.

Vertebral fusions in farmed Chinook salmon (Oncorhynchus tshawytscha) in New Zealand.

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.

Developing Successful Breeding Programs for New Zealand Aquaculture: A Perspective on Progress and Future Genomic Opportunities.

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 GreenshellTM 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.

Effects of neuropeptides and sex steroids on the pituitary-gonadal axis of pre-pubertal F1 wreckfish (hapuku) Polyprion oxygeneios in vivo: Evidence of inhibitory effects of androgens.

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 'hapuku' (Polyprion oxygeneios), a candidate for commercialization in aquaculture, were subjected to treatment for 8weeks with two implants, one containing steroid (blank; estradiol-17ß, 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 ß-subunit, fshb; luteinizing hormone ß-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 hapuku, 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.

Ovarian development of captive F1 wreckfish (hapuku) Polyprion oxygeneios under constant and varying temperature regimes - Implications for broodstock management.

In order to better understand how photo-thermal conditions affect oogenesis in captive-bred F1 hapuku, 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-17ß; 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 hapuku first mature as five-year-olds and that exposure to a decreased temperature is important for appropriate progression of oogenesis.

Unilateral perivertebral fibrosis associated with lordosis, kyphosis and scoliosis (LKS) in farmed Chinook salmon in New Zealand.

Vertebral column lordosis, kyphosis and scoliosis (LKS) can result in downgrading of farmed Chinook salmon Oncorhynchus tshawytscha in New Zealand. No cause of LKS has been identified. Radiography and histology were used to quantify LKS and perivertebral fibrosis in 27 fish with LKS visible at harvest and 30 visually normal fish from 3 New Zealand farms. Radiographic LKS was present in all 27 fish with LKS and in 18 of 30 fish without visible LKS. Quantification of the radiographic severity revealed significantly higher radiographic severity scores in fish with visible LKS (mean ± SD = 5.89 ± 2.41) than in fish with no visible, but radiographic LKS (1.44 ± 0.86, p < 0.001). The most frequent histological finding was unilateral perivertebral fibrosis that often extended into the horizontal septum and adjacent myomeres resulting in separation or loss of myocytes. Fibrosis was visible in all fish with LKS and in 12 of 30 fish without visible LKS. Fibrosis scores were higher in fish with visible LKS (3.32 ± 1.71) than in fish without visible LKS (0.35 ± 0.57, p < 0.001). The radiographic LKS severity scores were significantly correlated to the fibrosis scores (R2 = 0.59 p < 0.001) in the fish. Histology of other tissues revealed multifocal inflammation within muscle, peripheral connective tissues and myocardium which were considered most likely incidental in these fish. In this study, LKS was consistently and significantly associated with perivertebral fibrosis, suggesting that perivertebral fibrosis is an important process in the development of LKS. Further research to determine the cause of the fibrosis is required.

Mapping the sex determination locus in the hapuku (Polyprion oxygeneios) using ddRAD sequencing.

BACKGROUND: Hapuku (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 hapuku as a food fish.