Fin Tissue Research Articles

Development of a Novel Stress and Immune Gene Panel for the Australasian Snapper (Chrysophrys auratus)

Background: Snapper (Chrysophrys auratus) is a commercially, recreationally and culturally important teleost species in New Zealand and has been selected as a potential new species for aquaculture. Selective breeding to enhance stress tolerance, survival and growth are major breeding targets, yet research into snapper immune and stress responses has been limited. Methods: We explored a set of candidate genes in the fin, head kidney and liver tissues of 50 individuals by exposing 20 fish to increasing temperature (up to 31 °C) and 20 fish to decreasing temperature (down to 7 °C) for up to 33 h. Of these, we analysed 10 temperature-sensitive and 10 temperature-tolerant fish, along with 10 fish kept at 18 °C (acclimation temperature) as a control group. Results: Expression analyses of candidate stress genes in the three tissue types via NanoString Technologies, Inc., Seattle, WA, USA. showed that 22 out of 25 genes significantly changed in each experiment, demonstrating the significant impact of temperature on stress and immune responses. We further document that 10 key gene biomarkers can be used to predict genotypes that are tolerant to extreme temperatures. Conclusions: Taken together, our novel NanoString method can be used to monitor stress in snapper rapidly, and applications of this tool in this and potentially closely related teleost species can provide insights into stress resilience of wild stocks and inform the selection of grow-out locations for aquaculture.

Efficiency Evaluation of DNA Isolation Techniques in Fins of Channa marulius Using PCR Amplification and NanoDrop

Highly pure and good-quality extracted DNA is vital for PCR amplification, gene sequencing, and species identification. Seven genomic DNA isolation techniques were used to isolate the DNA from the fins of Channa marulius. The concentration and purity of isolated DNA were assessed with PCR amplification of the mitochondrial COI gene and NanoDrop. The phenol-chloroform method was found significantly (P<0.05) higher in concentration (1001 ng.ul-1) as compared to all other six evaluated DNA isolation methods. In terms of purity of isolated DNA GeneJET, the Genomic DNA Purification Kit was found significantly (P<0.05) higher among all analyzed methods. Both the Phenol chloroform method and GeneJET Genomic DNA Purification Kit were successfully used in PCR amplification. Concluding that the Phenol chloroform method and GeneJET Genomic DNA Purification Kit may be successfully used in PCR amplification. The phenol-chloroform method and GeneJET Genomic DNA Purification Kit proved the best in the extraction of DNA in high concentration with maximum yield and purity from fins of C. marulius and can be helpful to isolate DNA from fish species because a small quantity of fin tissues is required for DNA isolation without harm to fish. Moreover, data reported from this study about DNA isolation techniques may be used for molecular approaches like PCR amplification and gene sequencing of fishes.

CUT&Tag applied to zebrafish adult tail fins reveals a return of embryonic H3K4me3 patterns during regeneration

Regenerative potential is governed by a complex process of transcriptional reprogramming, involving chromatin reorganization and dynamics in transcription factor binding patterns throughout the genome. The degree to which chromatin and epigenetic changes contribute to this process remains only partially understood. Here we provide a modified CUT&Tag protocol suitable for improved characterization and interrogation of changes in chromatin modifications during adult fin regeneration in zebrafish. Our protocol generates data that recapitulates results from previously published ChIP-Seq methods, requires far fewer cells as input, and significantly improves signal to noise ratios. We deliver high-resolution enrichment maps for H3K4me3 of uninjured and regenerating fin tissues. During regeneration, we find that H3K4me3 levels increase over gene promoters which become transcriptionally active and genes which lose H3K4me3 become silenced. Interestingly, these reprogramming events recapitulate the H3K4me3 patterns observed in developing fin folds of 24-h old zebrafish embryos. Our results indicate that changes in genomic H3K4me3 patterns during fin regeneration occur in a manner consistent with reactivation of developmental programs, demonstrating CUT&Tag to be an effective tool for profiling chromatin landscapes in regenerating tissues.

Genetic health and diversity assessment of Sturgeon species in Kazakhstan's aquaculture and natural habitats

Sturgeon species hold significant commercial and ecological value, with many listed as endangered. Understanding their genetic structure is crucial for developing effective conservation strategies. The main aim of this study is to examine the genetic structure of sturgeon, which can provide a foundation for creating strategies to conserve these species. A total of 121 sturgeon individuals were analyzed using microsatellite molecular markers (STR) to conduct the study on the genetic structure of sturgeon fish species. DNA was extracted from fin tissues using a commercial kit, and genotyping was conducted using seven microsatellite loci. Cluster analysis and principal coordinates analysis (PCoA) were performed to identify genetic differentiation among populations. The analysis showed differences in genetic diversity between the Siberian sturgeon, Russian sturgeon, and beluga samples. A deficiency of heterozygotes was discovered in artificial samples of sturgeon, indicating possible inbreeding. Genetic analysis has also revealed genetic differentiation between populations, possibly due to geographic structure or other factors. The study allows us to recommend increasing genetic diversity by introducing individuals from natural environments into sturgeon populations in aquaculture. Regular monitoring of genetic parameters in aquaculture populations and monitoring diversity dynamics are also crucial for the conservation and sustainability of sturgeon populations. The findings could help shape conservation strategies, especially in managing genetic diversity in aquaculture and reducing the risks associated with inbreeding and genetic drift.

Dynamics of actinotrichia, fibrous collagen structures in zebrafish fin tissues, unveiled by novel fluorescent probes

Abstract Collagen fibers provide physical support to animal tissues by orienting in the correct position and at optimal density. Actinotrichia are thick collagen fibers that are present at the tips of fish fins and serve as scaffolds for bone formation. The arrangement and density of actinotrichia must be constantly maintained with a high degree of regularity to form spatial patterns in the fin bones, but the mechanisms of this process are largely unknown. To address this issue, we first identified two fluorescent probes that can stain actinotrichia clearly in vivo. Using these probes and time-lapse observation of actinotrichia synthesized at different growth stages, we revealed the following previously unknown dynamics of actinotrichia. (i) Actinotrichia do not stay stationary at the place where they are produced; instead, they move towards the dorsal area during the notochord bending and (ii) move towards the distal tip during the fin growth. (iii) Actinotrichia elongate asymmetrically as new collagen is added at the proximal side. (iv) Density is maintained by the insertion of new actinotrichia. (v) Actinotrichia are selectively degraded by osteoclasts. These findings suggest that the regular arrangement of actinotrichia is the outcome of multiple dynamic processes.

A New Investigation to Discriminate Sexes in Alive Nile Tilapia (Oreochromis niloticus) Using Cyp19a1a and Dmrt1 Gene Expression in Tail Fin Tissues

The Nile Tilapia (Oreochromis niloticus), a gonochoristic teleost fish with a XX/XY sex-determination system, is an ideal model for investigating gonadal sex differentiation. During gonadal differentiation, the expression of cyp19a1a in XX gonads and dmrt1 in XY gonads are required for undifferentiated tissues to develop into ovary or testis. In this study, quantitative real-time RT-PCR assessed the expression of cyp19a1a and dmrt1 genes in gonads and tail fin tissues. Differences in gene expression mean among sexually differentiated fish were analyzed using two-way analysis of variance (ANOVA) and validation of mixed model using discriminant analysis (DA) for morphometric traits and the gene expression in gonads and tail fin tissues used to validate and utilize them in discriminating sexes in sex-differentiated Nile Tilapia fish. The results revealed that, cyp19a1a gene expression in female ovaries was more significant than dmrt1 in male testis. In the other hand, the dmrt1 gene expression in the tail fin was higher in males than females. Both, cyp19a1a and dmrt1 genes, can discriminate fish sexes by 100% by using their expression in tail fin tissues. In conclusion, the cyp19a1a and dmrt1 genes could be used as a genetic marker to discriminate between the Nile Tilapia sexes, whereas used as an indicator for ovarian or testis differentiation in sexually differentiated Nile Tilapia using tail fin tissues. It is worth mentioning that this is the first investigation for using cyp19a1a and dmrt1 genes from Nile Tilapia tail fin tissues in sex determination.

Establishment and characterization of cell line from fin of Chinense bahaba (Bahaba taipingensis) and transcriptome analysis of its response to megalocytivirus SKIV-SD strain infection

The Chinese bahaba (Bahaba taipingensis) is an endangered fish species with high economic value, found in the southeastern sea of China. In this study, we established the first Chinese bahaba cell line, named BTF, derived from fin tissue. The primary cells were cultured for over 55 passages in L-15 medium with 15% FBS at 27 °C. These cells exhibited a fibroblast-like morphology with multipolar shapes. Karyotype testing revealed a chromosome number of 2n = 48. After thawing the cells that had been stored in liquid nitrogen for 10 months, their viability was >80%. The cell was separately transfected with EGFP-N3 plasmid and cy3 labeled scramble siRNA and clear fluorescence were observed. Moreover, the cells displayed sensitivity to megalocytivirus SKIV-SD strain, demonstrating a pronounced cytopathic effect (CPE) 24 h after infection. Transcriptome sequencing analysis of SKIV-SD infected cells revealed highly expressed genes significantly enriched in nucleic acid replication and protein translation-related pathways, such as Ribosome biogenesis, RNA polymerase, Nucleocytoplasmic transport, and DNA replication. In addition, the infected cells showed differential expression of immune-related genes such as cxcr4 and dr5, which are involved in virus infection. In conclusion, the BTF cell line, derived from the fin tissue of the Chinese bahaba, exhibits stable growth and can be stored in liquid nitrogen for extended periods. This cell line plays a crucial role in conserving the germplasm resources of Chinese bahaba and will serve as a valuable reference for establishing cell lines from other tissues of the Chinese bahaba. Furthermore, our findings suggest that this cell line holds significant potential for virology research, foreign protein expression, and in vitro biological studies of Chinese bahaba.

Genome wide association analysis reveals the genetic sites of heat resistance in largemouth bass (Micropterus salmoides)

Largemouth bass (Micropterus salmoides) is an important commercially cultured freshwater fish. High temperature is a common challenge encountered in the summer cultivation of largemouth bass. In this study, we conducted a genome-wide association study using general linear models and linear mixed models to identify significant single nucleotide polymorphisms (SNPs) and candidate genes associated with loss of equilibrium (LOE) and weight gain (WG) during high temperature challenge. We collected fin tissue from 353 individuals of largemouth bass exposed to high water temperature (37.5 °C) and performed whole-genome resequencing. Through association analysis, we successfully identified 10 SNPs and 38 candidate genes that were significantly associated with LOE, and four SNPs and 19 candidate genes that were significantly associated with WG. Using quantitative PCR and Western blot, we tested the expression of eight genes related to LOE in heat-sensitive and heat-tolerant individuals, and identified significant differences in the expression of the following five genes: Tmub2, Ngfr, Hgf, Hdac6, and Sypl. For WG, we assessed the expression of three candidate genes, among which Mrc2l displayed significant differences in expression between the high WG group and low WG group. We discuss the functions and potential biological processes of candidate genes for LOE and WG. Our results provide basic genetic information for breeding largemouth bass with high temperature tolerance.

A Novel Investigation for Early Sex Determination in Alive Adult European Seabass (Dicentrarchus labrax) Using cyp19a1a, dmrt1a, and dmrt1b Genes Expression in Tail Fin tissues

This study is the first investigation for using sex-related gene expression in tail fin tissues of seabass as early sex determination without killing the fish. The European seabass (Dicentrarchus labrax) is gonochoristic and lacks distinguishable sex chromosomes, so, sex determination is referred to molecular actions for some sex-related genes on autosomal chromosomes which are well known such as cyp19a1a, dmrt1a, and dmrt1b genes which play crucial role in gonads development and sex differentiation. cyp19a1a is expressed highly in females for ovarian development and dmrt1a and dmrt1b are for testis development in males. In this study, we evaluated the difference in the gene expression levels of studied genes by qPCR in tail fins and gonads. We then performed discriminant analysis (DA) using morphometric traits and studied gene expression parameters as predictor tools for fish sex. The results revealed that cyp19a1a gene expression was significantly higher in future females’ gonads and tail fins (p ≥ 0.05). Statistically, cyp19a1a gene expression was the best parameter to discriminate sex even the hit rate of any other variable by itself could not correctly classify 100% of the fish sex except when it was used in combination with cyp19a1a. In contrast, Dmrt1a gene expression was higher in males than females but there were difficulties in analyzing dmrt1a and dmrt1b expressions in the tail because levels were low. So, it could be used in future research to differentiate and determine the sex of adult fish using the cyp19a1a gene expression marker without killing or sacrificing fish.

Mercury bioaccumulation and its relationship with trophic biomarkers in a Mediterranean elasmobranch mesopredator

Human activity has led to increased concentrations of mercury (Hg) in the world's oceans. Mercury can bioaccumulate and biomagnify in animal tissues via trophic transfer, thus, becoming most pronounced in larger and older predators. Here, we measured Hg concentrations and their relationship with stable isotopes-based proxies of trophic level (δ13C and δ15N values) in multiple tissues of Mustelus spp. from the Mediterranean Sea. We found higher Hg concentrations in muscle than in liver and fin tissues. The relationship between Hg concentrations and δ15N values in muscle suggested repeated foraging for low trophic level and Hg-poor prey, and biomagnification of Hg at higher trophic levels. Seasonal variations in δ13C values could indicate shifts in primary production sources and/or in local prey availability. The HBVSe index suggested no risk to human health, however the safe meal limit recommendations are 4.5 and 2.2 portions per month for adults and children, respectively.

Glyphosate- and aminomethylphosphonic acid (AMPA)-induced mortality and residues in juvenile brown trout (Salmo trutta f. fario) exposed at different temperatures

BackgroundGlyphosate is a broad-spectrum, non-selective systemic herbicide with a commonly assumed low potential for accumulation in biota. Nevertheless, glyphosate has been shown to bioaccumulate in the tissues of several organisms. To understand the bioconcentration dynamics of glyphosate in fish, brown trout (Salmo trutta forma fario) of different age were exposed to different concentrations of glyphosate, the formulation Roundup® LB Plus, and the major transformation product aminomethylphosphonic acid (AMPA) for two, three, or four weeks at different temperatures in the laboratory. Mortality rates were determined, and tissue samples were collected at the end of the experiment to ascertain concentrations of glyphosate and AMPA residues by liquid chromatography coupled to mass spectrometry (LC–MS/MS).ResultsBrown trout mortality during exposure to glyphosate or AMPA was considerably higher at 15 °C than at 7 °C. Also, a significant increase in glyphosate concentrations in samples containing muscle, head, backbone, and caudal fin tissue with increasing exposure concentrations and temperatures was observed. Six-month-old fish contained more glyphosate per kg wet weight after exposure than ten-month-old fish. The bioconcentration factors (BCFs) for glyphosate and AMPA were much higher at 15 °C than at 7 °C, but in both cases decreased with higher glyphosate concentrations. The BCF for glyphosate formulated in Roundup® was higher than the one for the parent compound. Approximately 30–42% of the organ-absorbed glyphosate and AMPA remained in the tissues even when the fish were kept in clean water lacking the test substances for three weeks after termination of exposure.ConclusionOur study demonstrated that there is an interaction between glyphosate and ambient temperature in terms of toxicity. Further it was shown that increasing concentrations of glyphosate and AMPA in the surrounding media lead to significantly increased concentrations of these substances in brown trout tissues, although neither bioconcentration nor bioaccumulation of glyphosate in animal tissues is expected due to the high water solubility of this chemical. As a consequence, the uptake of glyphosate by humans through the consumption of contaminated edible fish is very likely.

Apela promotes blood vessel regeneration and remodeling in zebrafish

In contrast to adult mammals, zebrafish display a high capacity to heal injuries and repair damage to various organs. One of the earliest responses to injury in adult zebrafish is revascularization, followed by tissue morphogenesis. Tissue vascularization entails the formation of a blood vessel plexus that remodels into arteries and veins. The mechanisms that coordinate these processes during vessel regeneration are poorly understood. Hence, investigating and identifying the factors that promote revascularization and vessel remodeling have great therapeutic potential. Here, we revealed that fin vessel remodeling critically depends on Apela peptide. We found that Apela selectively accumulated in newly formed zebrafish fin tissue and vessels. The temporal expression of Apela, Apln, and their receptor Aplnr is different during the regenerative process. While morpholino-mediated knockdown of Apela (Mo-Apela) prevented vessel remodeling, exogenous Apela peptide mediated plexus repression and the development of arteries in regenerated fins. In contrast, Apela enhanced subintestinal venous plexus formation (SIVP). The use of sunitinib completely inhibited vascular plexus formation in zebrafish, which was not prevented by exogenous application. Furthermore, Apela regulates the expression of vessel remolding-related genes including VWF, IGFPB3, ESM1, VEGFR2, Apln, and Aplnr, thereby linking Apela to the vascular plexus factor network as generated by the STRING online database. Together, our findings reveal a new role for Apela in vessel regeneration and remodeling in fin zebrafish and provide a framework for further understanding the cellular and molecular mechanisms involved in vessel regeneration.

A non-lethal stable isotope analysis of valued freshwater predatory fish using blood and fin tissues as alternatives to muscle tissue.

Stable isotope analysis (SIA) is widely used to study trophic ecology and food webs in aquatic ecosystems. In the case of fish, muscle tissue is generally preferred for SIA, and the method is lethal in most cases. We tested whether blood and fin clips can be used as non-lethal alternatives to muscle tissue for examining the isotopic composition of two freshwater predatory fish, European catfish (Silurus glanis) and Northern pike (Esox lucius), species of high value for many freshwater systems as well as invasive species in many others. Blood samples from the caudal vein, anal fin clips, and dorsal muscle obtained by biopsy punch were collected from four catfish and pike populations (14-18 individuals per population). Subsequently, these samples were analyzed for δ13C and δ15N. The effects of alternative tissues, study site, and fish body mass on the isotopic offset were investigated. Both species showed a correlation between the isotopic offset and the tissue type, as well as the study site, but no significant relationship with the body mass. The isotopic offsets between tissues were used to calculate the conversion equations. The results demonstrated that both blood and fin clips are suitable and less invasive alternative to muscle in SIA studies focused on European catfish and Northern pike. Blood provided better correspondence to muscle isotope values. However, our results clearly demonstrated that isotopic offsets between tissues vary significantly among populations of the same species. Therefore, obtaining a muscle biopsy from several individuals in any population is advisable to gain initial insights and establish a possible population-specific inter-tissue conversion.

Differential expression and alternative splicing analyses of multiple tissues reveal albinism-associated genes in the Wels catfish (Silurus glanis)

Albinism is a widespread departure from a typical body colouration due to altered melanin production. The Wels catfish (Silurus glanis) is among the largest freshwater fish species in the world, and albino individuals occur both in the wild and in aquaculture. Here, we performed transcriptome-wide analysis of albino and normally pigmented S. glanis using four tissues (skin, dorsal fin, whole eye and liver) to identify genes associated with albinism by exploring patterns of differential expression (DE) and differential alternative splicing (DAS). Multi-tissue analyses revealed a large number of genes in skin (n = 1355) and fin (n = 614) tissue associated with the albino phenotype in S. glanis, while the number of DE genes in eye and liver tissues was lower (n = 188, n = 189, respectively). Several DE genes across multiple tissues were detected as the most promising candidates (e.g., hsp4, hsp90b1, raph1, uqcrfs1, adcy-family and wnt-family) potentially causally linked to the albino phenotype in Wels catfish. Moreover, our findings supported earlier observations of physiological differences between albino and normally pigmented individuals, particularly in energy metabolism and immune response. In contrast, there were only a few pigmentation-related genes observed among DAS genes (4 in skin, 2 in fin), the overlap between DAS and DE genes was low (n = 25) and did not include known pigmentation-related genes. This suggests that DAS and DE in Wels catfish are, to a large extent, independent processes, and the observed alternative splicing cases are probably not causally linked with albinism in S. glanis. This work provides the first transcriptome-wide multi-tissue insights into the albinism of Wels catfish and serves as a valuable resource for further understanding the genetic mechanisms of pigmentation in fish.

Biocompatible recombinant type III collagen enhancing skin repair and anti-wrinkle effects.

Treating sunburn and other UV-induced skin damage issues remains a significant challenge in the field of dermatology. In this study, we synthesized a highly bioactive recombinant type III collagen (rCol III) to accelerate the healing of UV-damaged skin. The high-purity rCol III demonstrated excellent biocompatibility and bioactivity, significantly promoting the adhesion, proliferation, and migration of HFF-1 cells. In a mouse UV-damage model, Combo evaluations demonstrated that rCol III contributed to restore transepidermal water loss (TEWL) values of UV-damaged skin to normal levels. Histological analysis further confirmed that rCol III substantially accelerated skin repair by enhancing collagen regeneration. Additionally, rCol III facilitated the regeneration of zebrafish tail fin tissue and alleviated shrinkage caused by excessive UV exposure. The biocompatible and bioactive rCol III offers a novel strategy for treating UV-induced skin damage, holding immense potential for applications in skin tissue engineering.

Unlocking the genomes of formalin‐fixed freshwater fish specimens: An assessment of factors influencing DNA extraction quantity and quality

AbstractObjectiveRecent technological developments may facilitate the description of evolutionary relationships and population genetic structure as well as other information relevant to fisheries management by using readily available natural history collections. Contemporary sequence capture and short‐read sequencing methods offer opportunities to analyze highly fragmented DNA from formalin‐fixed specimens so long as enough DNA of sufficient quality is recovered.MethodsWe compared two protocols developed to extract DNA from formalin‐fixed tissues using specimens of three freshwater fishes: the Southern Brook Lamprey Ichthyomyzon gagei, Slimy Sculpin Cottus cognatus, and Brown Trout Salmo trutta. Extractions were attempted using hot alkali digestion with and without buffer wash pretreatments to compare the DNA concentration, purity, and fragment length of DNA recovered between extraction protocols, tissue types (muscle and caudal fin tissue for Brown Trout and Slimy Sculpin), and preservation periods (5 or 7 years for Southern Brook Lamprey).ResultLikelihood models generally did not detect DNA quantity differences between extraction protocols nor tissue types; however, 6.0–8.7× more DNA was recovered from Slimy Sculpin caudal fins than from muscle tissue. Extraction protocol had mixed effects on DNA purity; the wash protocol outperformed the no‐wash protocol for Slimy Sculpin and Brown Trout, but the reverse was true for the lamprey. Purer DNA was recovered from the caudal fins; however, fragment lengths were generally greater from muscle tissue for both ray‐finned species.ConclusionOur results suggest that the best tissue for sampling may depend on the quality metric considered most important for a study's objectives and that omitting time‐consuming tissue wash steps can yield DNA of quantity and quality comparable to DNA from more complex methods. Regardless of species, the DNA extracted from most samples using both protocols met quantity and quality thresholds that are likely to result in short‐read sequencing success. These results provide optimism for unlocking the wealth of genetic information in natural history collections for use in fisheries management and conservation genomics.

Genome-wide association study (GWAS) analysis of black color trait in the leopard coral grouper (Plectropomus leopardus) using whole genome resequencing

The leopard coral grouper (Plectropomus leopardus) is a coral reef fish species that exhibits rapid and diverse color variation. However, the presence of melanoma and the high proportion of individuals displaying black color in artificial breeding have led to reduced economic and ornamental value. To pinpoint single nucleotide polymorphisms (SNPs) and potential genes linked to the black pigmentation characteristic in this particular species, This study gathered a cohort of 360 specimens from diverse origins and conducted a comprehensive genome-wide association analysis (GWAS) employing whole-genome resequencing. As a result, 57 SNPs related to the black skin trait were identified, and a grand total of 158 genes were annotated within 50 kb of these SNPs. Subsequently, GWAS was applied to three populations (LED, QHH, and QHL), and the corresponding results were compared with the analysis results of the total population. The results of the four GWAS models showed significant enrichment in Rap1 signaling pathway, melanin biosynthesis, metabolic pathways, tyrosine metabolism, cAMP signaling pathway, AMPK signaling pathway, PI3K-Akt signaling pathway, EGFR tyrosine kinase inhibitor resistance, HIF-1 signaling pathway, Ras signaling pathway, MAPK signaling pathway, etc. (p < 0.05), which were mainly associated with eleven genes (POL4, MET, E2F2, COMT, ZBED1, TYRP2, FOXP2, THIKA, LORF2, MYH16 and SOX2). Significant differences (p < 0.05) were observed in the expression of all 11 genes in the dorsal skin tissue, in 10 genes except COMT in the ventral skin tissue, and in all 11 genes in the caudal fin tissue. These findings imply that the control of body color in the P. leopardus is the result of the joint action of multiple genes and signaling pathways. These findings will contribute to a more profound comprehension of the genetic attributes that underlie the development of black skin in the vibrant P. leopardus, thus furnishing a theoretical foundation for genetic enhancement.

In vitro modelling of the influence of alternative feeds (Hermetia illucens, Arthrospira platensis) on the resistance of different rainbow trout populations (Oncorhynchus mykiss) against the viral haemorrhagic septicaemia virus and Yersinia ruckeri.

Replacing fishmeal, a finite resource with high market demand, in the diet of carnivorous rainbow trout with proteins from alternative sources may be a challenge for these fish. Therefore, this study investigated whether replacing fishmeal with protein derived from Hermetia illucens or Arthrospira platensis could promote disease susceptibility in local trout populations with different growth performance. This was assessed in vitro by measuring susceptibility to infection with the viral haemorrhagic septicaemia virus (VHSV) or the bacterium Yersinia ruckeri. Analysis of fin tissue explants and primary cell cultures from scales from the three trout populations infected in vitro with VHSV and gill explants infected with Y. ruckeri showed no significant differences in virus replication or bacterial counts. Evaluation of the virucidal or bactericidal effect of skin mucus showed a significant reduction in viral load and bacterial count for all samples with mucus addition, but no significant difference was observed between the experimental groups. This study documents no apparent impairment of innate immune mechanisms in the skin and gills of trout after feeding a diet replacing fishmeal with Arthrospira or Hermetia proteins. This underlines the potential of these alternative protein sources for the further development of sustainable trout aquaculture.

Identification of candidate variants and genes associated with temperature tolerance in olive flounders by Genome-Wide Association Study (GWAS)

The Republic of Korea is one of the largest producers of farm-raised olive flounder (Paralichthys olivaceus), accounting for nearly half of the global production. However, global warming has affected the aquaculture industry worldwide as it impacts survival, growth, and immunity and accelerates increases in pathogen load. In this study, we identified thermal stress-related genes in olive flounder using a genome-wide association study (GWAS) to provide a basis for marker-assisted selection and the development of temperature-resistant olive flounder in response to global warming. In total, 768 healthy olive flounder (weight of 159 ± 29.9 g and length of 25.42 ± 1.63 cm) were subjected to thermal stress (19.4–32.5 °C), and dead fish (537) were collected every 30 min. The fin tissues were isolated from all dead and surviving fish (231) and used for gDNA extraction. A high-quality 70 K SNP chip was used for genotyping, and 58,920 SNPs were obtained from 726 individuals after quality filtering. The GWAS identified 216 statistically significant SNPs at the Bonferroni cutoff (8.5 × 10−7). All significant SNPs were located on chromosome (chr) 18 (39 SNPs), chr 19 (176 SNPs), and contig 28 (AGQT02031776.1). After the SNP annotation, 13, 67, and 135 SNPs were identified in exons, introns, and intergenic regions, respectively. Gene and functional annotations revealed that almost all significant SNPs were directly or indirectly associated with the thermal stress response. Annotated genes were further categorized into the following functional groups: metabolic, neural and neuroendocrine, molecular and cellular, and physiological and behavioral responses. The significant SNP-harboring genes identified in this study could be used for marker-assisted genomic selection in future breeding programs.

Transcriptomic and targeted immune transcript analyses confirm localized skin immune responses in Atlantic salmon towards the salmon louse.

Atlantic salmon (Salmo salar) are highly susceptible to infestations with the ectoparasite Lepeophtheirus salmonis, the salmon louse. Infestations elicit an immune response in the fish, but the response does not lead to parasite clearance, nor does it protect against subsequent infestations. It is, however, not known why the immune response is not adequate, possibly because the local response directly underneath the louse has been poorly evaluated. The present study describes the transcriptomic response by RNA sequencing of skin at the site of copepodid attachment. Analysing differentially expressed genes, 2864 were higher and 1357 were lower expressed at the louse attachment site compared to uninfested sites in the louse infested fish, while gene expression at uninfested sites were similar to uninfested control fish. The transcriptional patterns of selected immune genes were further detailed in three skin compartments/types: Whole skin, scales only and fin tissue. The elevation of pro-inflammatory cytokines and immune cell marker transcripts observed in whole skin and scale samples were not induced in fin, and a higher cytokine transcript level in scale samples suggest it can be used as a nonlethal sampling method to enhance selective breeding trials. Furthermore, the immune response was followed in both skin and anterior kidney as the infestation developed. Here, newly moulted preadult 1 stage lice induced a higher immune response than chalimi and adult lice. Overall, infestation with salmon louse induce a modest but early immune response with an elevation of mainly innate immune transcripts, with the response primarily localized to the site of attachment.