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.

From gametogenesis to spawning: How climate-driven warming affects teleost reproductive biology.

Ambient temperature modulates reproductive processes, especially in poikilotherms such as teleosts. Consequently, global warming is expected to impact the reproductive function of fish, which has implications for wild population dynamics, fisheries and aquaculture. In this extensive review spanning tropical and cold-water environments, we examine the impact of higher-than-optimal temperatures on teleost reproductive development and physiology across reproductive stages, species, generations and sexes. In doing so, we demonstrate that warmer-than-optimal temperatures can affect every stage of reproductive development from puberty through to the act of spawning, and these responses are mediated by age at spawning and are associated with changes in physiology at multiple levels of the brain-pituitary-gonad axis. Response to temperature is often species-specific and changes with environmental history/transgenerational conditioning, and the amplitude, timing and duration of thermal exposure within a generation. Thermally driven changes to physiology, gamete development and maturation typically culminate in poor sperm and oocyte quality, and/or advancement/delay/inhibition of ovulation/spermiation and spawning. Although the field of teleost reproduction and temperature is advanced in many respects, we identify areas where research is lacking, especially for males and egg quality from "omics" perspectives. Climate-driven warming will continue to disturb teleost reproductive performance and therefore guide future research, especially in the emerging areas of transgenerational acclimation and epigenetic studies, which will help to understand and project climate change impacts on wild populations and could also have implications for aquaculture.

A transcriptomic investigation of appetite-regulation and digestive processes in giant grouper Epinephelus lanceolatus during early larval development.

The giant grouper Epinephelus lanceolatus is an ecologically vulnerable species with high market demand. However, efforts to improve larval husbandry are hindered by a lack of knowledge surrounding larval developmental physiology. To address this shortfall, a transcriptomic approach was applied to larvae between 1 and 14 days post hatch (dph) to characterise the molecular ontogenesis of genes that influence appetite and digestion. Appetite regulating factors were detected from 1 dph, including neuropeptide Y, nesfatin-1, cocaine and amphetamine regulated transcript, cholecystokinin and pituitary adenylate cyclase activating peptide and the expression level of several genes changed sharply with the onset of exogenous feeding. The level of expression for proteases, chitinases, lipases and amylases typically followed one of two expression patterns, a general increase as development progressed, or an inverted U-shape with maximal expression at c. 6 dph. Similarly, the tendency among both expression patterns was for the level of expression to increase around the time of mouth-opening. There was also evidence to suggest the presence of putative isoforms for several digestion-related genes. We have provided an insight into appetite-regulation and digestive processes in groupers during early larval development and have developed a transcriptomic database that will aid future efforts to rear this species in an aquaculture setting.

Development of a new 'ultrametric' method for assessing spawning progression in female teleost serial spawners.

The collection and presentation of accurate reproductive data from wild fish has historically been somewhat problematic, especially for serially spawning species. Therefore, the aim of the current study was to develop a novel method of assessing female spawning status that is robust to variation in oocyte dynamics between specimens. Atlantic cod (Barents Sea stock) were used to develop the new 'ultrametric' method, that is based on the progressive depletion of the vitellogenic oocyte pool relative to the rather constant previtellogenic oocyte (PVO) pool. Fish were subsequently partitioned into one of four categories that accurately reflected changes in their oocyte size frequency distribution characteristics and gonadosomatic index throughout spawning. The ultrametric method overcomes difficulties associated with presence of bimodal oocyte distributions, oocyte tails, lack of clear hiatus region, and presence of free ova, and can be implemented at a single sampling point. Much of the workflow is fully automated, and the technique may circumvent the need for histological analysis depending on the desired outcome. The ultrametric method differs from the traditional autodiametric method in that PVOs can be separated by ultrasonication and then enumerated, and ovarian homogeneity is not a mandatory requirement per se. The method is designed for determinate spawners but might be extended to include indeterminate spawners.

Hepatic reference gene selection in adult and juvenile female Atlantic salmon at normal and elevated temperatures.

BACKGROUND: The use of quantitative real-time polymerase chain reaction (qPCR) has become widespread due to its specificity, sensitivity and apparent ease of use. However, experimental error can be introduced at many stages during sample processing and analysis, and for this reason qPCR data are often normalised to an internal reference gene. The present study used three freely available algorithms (GeNorm, NormFinder and BestKeeper) to assess the stability of hepatically expressed candidate reference genes (Hprt1, Tbp, Ef1α and ß-tubulin) in two experiments. In the first, female Atlantic salmon (Salmo salar) broodstock of different ages were reared at either 14 or 22 °C for an entire reproductive season, therefore a reference gene that does not respond to thermal challenge or reproductive condition was sought. In the second, estrogen treated juvenile salmon were maintained at the same temperatures for 14 days and a reference gene that does not respond to temperature or estrogen was required. Additionally, we performed independent statistic analysis to validate the outputs obtained from the program based analysis. RESULTS: Based on the independent statistical analysis performed the stability of the genes tested was Tbp > Ef1α > Hprt1 > ß-tubulin for the temperature/reproductive development experiment and Ef1α > Hprt1 > Tbp for the estrogen administration experiment (ß-tubulin was not analysed). Results from the algorithms tested were quite ambiguous for both experiments; however all programs consistently identified the least stable candidate gene. BestKeeper provided rankings that were consistent with the independent analysis for both experiments. When an inappropriate candidate reference gene was used to normalise the expression of a hepatically expressed target gene, the ability to detect treatment-dependent changes in target gene expression was lost for multiple groups in both experiments. CONCLUSIONS: We have highlighted the need to independently validate the results of reference gene selection programs. In addition, we have provided a reference point for those wishing to study the effects of thermal challenge and/or hormonal treatment on gene stability in Atlantic salmon and other teleost species.