Aquaculture Stocks Research Articles

Full-length transcriptome assembly of black amur bream (Megalobrama terminalis) as a reference resource.

The genus Megalobrama holds significant economic value in China, with M. terminalis (Black Amur bream) ranking second in production within this group. However, lacking comprehensive genomic and transcriptomic data has impeded research progress. This study aims to fill this gap through an extensive transcriptomic analysis of M. terminalis. We utilized PacBio Isoform Sequencing to generate 558,998 subreads, totaling 45.52 Gb, which yielded 22,141 transcripts after rigorous filtering and clustering. Complementary Illumina short-read sequencing corrected 967,114 errors across these transcripts. Our analysis identified 12,426 non-redundant isoforms, with 11,872 annotated in various databases. Functional annotation indicated 11,841 isoforms matched entries in the NCBI non-redundant protein sequences database. Gene Ontology analysis categorized 10,593 isoforms, revealing strong associations with cellular processes and binding functions. Additionally, 8203 isoforms were mapped to pathways in the Kyoto Encyclopedia of Genes and Genomes, highlighting significant involvement in immune system processes and complement cascades. We notably identified key immune molecules such as alpha-2-macroglobulin and complement component 3, each with multiple isoforms, underscoring their potential roles in the immune response. Our analysis also uncovered 853 alternative splicing events, predominantly involving retained introns, along with 672 transcription factors and 426 long non-coding RNAs. The high-quality reference transcriptome generated in this study provides a valuable resource for comparative genomic studies within the Megalobrama genus, supporting future research to enhance aquaculture stocks.

Diploid and triploid Chinook salmon (Oncorhynchus tshawytscha) exhibit differential immunological responses toacute thermal stress.

Exposure to temperatures outside of a fish's optimal range results in suppression of the immune system, ultimately leaving aquaculture stocks susceptible to disease outbreaks. This effect is exacerbated in triploid fishes, which demonstrate greater susceptibility to stress than their diploid counterparts. This study investigates the impacts of acute heat stress on the abundance of immune transcripts and proteins in diploid and triploid Chinook salmon (Oncorhynchus tshawytscha), an important finfish crop. This study also demonstrates that acute heat stress induces significant increases in the abundance hsp70, hsp90 and il1b transcripts in the head kidneys, gills and heart ventricles of both diploid and triploid Chinook salmon. Widespread dysregulation of antigen-presentation transcripts was also observed in fish of both ploidies. These results suggest that acute heat stress activates acute-phase responses in Chinook salmon and dysregulates antigen presentation, potentially leaving fish more susceptible to infection. At the protein level, IL-1β was differentially expressed in the head kidney and ventricles of diploid and triploid salmon following heat shock. Differential expression of two tapasin-like proteins in diploid and triploid salmon subjected to heat shock was also observed. Altogether, these data indicate that diploid and triploid Chinook salmon respond differently to acute thermal stressors.

Genetic architecture and accuracy of predicted genomic breeding values for sea lice resistance in the St John River aquaculture strain of North American Atlantic salmon

Sea lice infections cause significant economic losses in Atlantic salmon (Salmo salar) farming. The objectives of this study were to (1) estimate the heritability of resistance to sea lice in the USDA's breeding program for North American (N.A.) Atlantic salmon; (2) elucidate the genetic architecture of sea lice resistance; and (3) assess the accuracy and bias of predicted breeding values for sea lice resistance using cross-validation analysis (CVA) and progeny testing of selection candidates (PTSC). Fish from year-class (YC) 2014 n=967 and YC 2018 n=941 were challenged with sea lice (Lepeophtheirus salmonis) and genotyped with the new USDA 50K SNP chip developed for the N.A. Atlantic salmon. Heritability estimates for sea lice count in the two year-classes were between 0.07 and 0.10. GWAS with weighted ssGBLUP (wssGBLUP) highlighted the polygenic architecture of the trait. With CVA, the genomic prediction methods x¯=0.54 had higher accuracy of predictions than the pedigree-based method x¯=0.43; and ssGBLUP had the highest accuracy of BV predictions (0.50–0.62) among the genomic prediction methods. With PTSC approach, the pedigree-based method PBLUP had higher estimated accuracy than the genomic prediction methods (0.48 vs. 0.30). Bias of BV predictions with CVA x¯=0.87range0.57−1.06 was lower than with PTSC x¯=1.22range0.44−2.35. Our retrospective assessment of the accuracy of indirect sib-based selection to improve sea lice resistance in the St John River aquaculture stock that is commonly used for farming of Atlantic salmon in North America demonstrated that substantial genetic gains can be obtained. Due to the polygenic architecture of the trait, the estimated accuracy of the ssGBLUP model was better than the wssGBLUP model. In our assessment, a larger training sample size will be needed to achieve optimal results with the whole genome-enabled selective breeding method due to the polygenic architecture of sea lice resistance coupled with low heritability of the trait.

Determinants and framework for implementing sustainable climate-smart aquaculture insurance system for fish farmers: Evidence from Ghana

The just-ended Sharm El-Sheikh Climate Change Conference in November 2022 brought to light the need to mitigate climate change adaptation related to risk and challenges through Climate financing, has made it very paramount the need to protect fish farmers' investments from climate change-related risk through the development of climate-smart insurance products and covers to help mitigate climate change effects on aquaculturists. As a result, this paper examines aquaculture farmers' preference for climate-smart aquaculture insurance products, challenges of climate-smart aquaculture insurance, and their preferred insurance cover. Survey data was collected from 140 fish farmers and analysed via Multinomial logistic regression, Bivariate Probit regression and Kendall's coefficient of concordance. Climate-Induced Aquaculture Stock Mortality Insurance (CIASMI) was the most-preferred climate-smart insurance product. Insurance Cover for Diseases (ICD) was the least preferred. The results further indicated that membership in a farmer organisation, farm income, credit access, climate-related peril and anthropogenic-related peril had a positive influence, whereas years of education had a negative influence on climate-smart aquaculture insurance participation.Moreover, production system had a negative relationship with mode of participation while number of employees, farm income and climate-related peril influenced mode of participation positively. The results also revealed that age, sex, stock size, awareness, income, climate and environmental-related peril, and anthropogenic-related peril significantly influenced the choice for climate-smart aquaculture insurance products, specifically climate risk related to stock mortality insurance and climate-related to consequential loss insurance. Finally, delay in claim settlement was the most pressing constraint. In contrast, lack of experts in disease diagnosis was the least ranked constraint of climate-smart aquaculture insurance. Therefore, this study provides insights for the Fisheries Commission, Ghana Agricultural Insurance Pool (GAIP), World Cover and other agricultural insurance companies globally to draft climate-smart insurance products for aquaculturists.

ISOTHERMAL RECOMBINANT POLYMERASE AMPLIFICATION AND CRIPSR(CAS12A) ASSAY DETECTION OF RENIBACTERIUM SALMONINARUM AS AN EXAMPLE FOR WILDLIFE PATHOGEN DETECTION IN ENVIRONMENTAL DNA SAMPLES.

Improving rapid detection methods for pathogens is important for research as we collectively aim to improve the health of ecosystems globally. In the northern hemisphere, the success of salmon (Oncorhynchus spp.) populations is vitally important to the larger marine, aquatic, and terrestrial ecosystems they inhabit. This has led to managers cultivating salmon in hatcheries and aquaculture to bolster their populations, but young salmon face many challenges, including diseases such as bacterial kidney disease (BKD). Early detection of the BKD causative agent, Renibacterium salmoninarum, is useful for managers to avoid outbreaks in hatcheries and aquaculture stocks to enable rapid treatment with targeted antibiotics. Isothermal amplification and CRIPSR-Cas12a systems may enable sensitive, relatively rapid, detection of target DNA molecules from environmental samples compared to quantitative PCR (qPCR) and culture methods. We used these technologies to develop a sensitive and specific rapid assay to detect R. salmoninarum from water samples using isothermal recombinase polymerase amplification (RPA) and an AsCas12a RNA-guided nuclease detection. The assay was specific to R. salmoninarum (0/10 co-occurring or closely related bacteria detected) and sensitive to 0.0128 pg/µL of DNA (approximately 20-40 copies/µL) within 10 min of Cas activity. This assay successfully detected R. salmoninarum environmental DNA in 14/20 water samples from hatcheries with known quantification for the pathogen via previous qPCR (70% of qPCR-positive samples). The RPA-CRISPR/AsCas12a assay had a limit of detection (LOD) of >10 copies/µL in the hatchery water samples and stochastic detection below 10 copies/µL, similar to but slightly higher than the qPCR assay. This LOD enables 37 C isothermal detection, potentially in the field, of biologically relevant levels of R. salmoninarum in water. Further research is needed to develop easy-to-use, cost-effective, sensitive RPA/CRISPR-AsCas12a assays for rapidly detecting low concentrations of wildlife pathogens in environmental samples.

Combination of RNAseq and RADseq to Identify Physiological and Adaptive Responses to Acidification in the Eastern Oyster (Crassostrea virginica).

Ocean acidification (OA) is a major stressor threatening marine calcifiers, including the eastern oyster (Crassostrea virginica). In this paper, we provide insight into the molecular mechanisms associated with resilience to OA, with the dual intentions of probing both acclimation and adaptation potential in this species. C. virginica were spawned, and larvae were reared in control or acidified conditions immediately after fertilization. RNA samples were collected from larvae and juveniles, and DNA samples were collected from juveniles after undergoing OA-induced mortality and used to contrast gene expression (RNAseq) and SNP (ddRADseq) profiles from animals reared under both conditions. Results showed convergence of evidence from both approaches, particularly in genes involved in biomineralization that displayed significant changes in variant frequencies and gene expression levels among juveniles that survived acidification as compared to controls. Downregulated genes were related to immune processes, supporting previous studies demonstrating a reduction in immunity from exposure to OA. Acclimation to OA via regulation of gene expression might confer short-term resilience to immediate threats; however, the costs may not be sustainable, underscoring the importance of selection of resilient genotypes. Here, we identified SNPs associated with survival under OA conditions, suggesting that this commercially and ecologically important species might have the genetic variation needed for adaptation to future acidification. The identification of genetic features associated with OA resilience is a highly-needed step for the development of marker-assisted selection of oyster stocks for aquaculture and restoration activities.

Applications of Environmental DNA (eDNA) in Monitoring the Endangered Status and Evaluating the Stock Enhancement Effect of Tropical Sea Cucumber Holothuria Scabra.

The tropical sea cucumber Holothuria scabra is naturally found in the Indo-West Pacific. However, due to their commercial value, natural H. scabra populations have declined significantly in recent years, resulting in its status as an endangered species. Surveys of H. scabra resource pose a challenge due to its specific characteristics, such as sand-burrowing behavior. To overcome this problem, our study established a convenient and feasible method for assessing H. scabra resources using environmental DNA (eDNA) monitoring technology. First, H. scabra-specific TaqMan primers and probe were designed based on its cox1 gene, followed by the development of an eDNA monitoring method for H. scabra in two separate sea areas (Xuwen and Daya Bay). The method was subsequently employed to investigate the distribution of H. scabra and assess the effects of aquaculture stock enhancement through juvenile releasing in the Weizhou Island sea area. The H. scabra eDNA monitoring approach was found to be more appropriate and credible than traditional methods, and a positive impact of stocking on H. scabra populations was observed. In summary, this is the first report to quantify eDNA concentration in a Holothuroidea species, and it provides a convenient and accurate method for surveying H. scabra resources. This study introduces novel concepts for eDNA-based detection of endangered marine benthic animals and monitoring their population distribution and abundance.

First report on the life history of the marine amphipod Ceradocus mizani and its implication for aquaculture

AbstractThe search for alternative live feed for aquaculture stocks has inspired research into marine amphipods. In this study, the life history of Ceradocus mizani was evaluated to better understand how this amphipod might be used in aquaculture as an alternative feed. The amphipods did not display copulatory behavior during the study period. The females were multivoltine and attained sexual maturity on average in 23.6 days at a mean length of 4.64 mm. The incubation period lasted 8.8 days, and the mean number of juveniles produced per brood during that incubation period was relatively low (7.58). Females produced a mean of 5.2 consecutive broods and 39.4 total juveniles over the life span. (i.e., 0.33 juveniles/day). Sex ratio was female skewed (1.55:1). Female size and the number of juveniles produced per brood were positively correlated (R2 = 0.63). The mean life span for females and males was 119.4 and 91.2 days, respectively. Mean maximum length was 9.26 mm for males and 8.18 mm for females. This is the first account of the life history of C. mizani and forms the basis for future studies of this marine amphipod.

PHARMACOKINETICS OF MELOXICAM AFTER SINGLE ORAL AND INTRAMUSCULAR ADMINISTRATION IN CHINA ROCKFISH (SEBASTES NEBULOSUS).

Fish species are important for various purposes including aquaculture stock and display animals, but there are significant gaps in the medical knowledge regarding pharmacological parameters and effective pain management. Meloxicam is a nonsteroidal anti-inflammatory drug (NSAID) that has been studied in few teleost species and with several administration routes. However, these species were typically freshwater or euryhaline fish, and evaluation in marine species is lacking. The pharmacokinetic properties of meloxicam were determined in nine adult China rockfish (Sebastes nebulosus), presumed healthy based on physical examination and benign medical histories. Based on a pilot study, China rockfish were given 1 mg/kg meloxicam via IM injection in the epaxial musculature, and, after a 48-h washout period, 1 mg/kg meloxicam was given by PO gavage. Blood samples were collected from the caudal vein at baseline and at nine time intervals over a 48-h time period following administration of meloxicam. Plasma meloxicam concentrations were determined by reverse phase high-performance liquid chromatography, and noncompartmental analysis was performed. The mean peak plasma concentration after IM injection was 4.9 µg/ml, and the mean terminal half-life was 5.0 h. The mean peak plasma concentration after PO administration was 0.07 µg/ml. Based on these findings, IM injected meloxicam reaches plasma levels consistent with therapeutic concentrations in select mammals, and peak levels were maintained for ≤12 h. Single-dose PO administration failed to achieve similar concentrations, and clinical practicality is unknown. Further studies evaluating NSAID multidose regimes and their pharmacodynamic effects may provide additional dosing information.

Chromosome genome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution.

The meagre, Argyrosomus regius, has recently become a species of increasing economic interest for the Mediterranean aquaculture and there is ongoing work to boost production efficiency through selective breeding. Access to the complete genomic sequence will provide an essential resource for studying quantitative trait-associated loci and exploring the genetic diversity of different wild populations and aquaculture stocks in more detail. Here, we present the first complete genome for A. regius, produced through a combination of long and short read technologies and an efficient in-house developed pipeline for assembly and polishing. Scaffolding using previous linkage map data allowed us to reconstruct a chromosome level assembly with high completeness, complemented with gene annotation and repeat masking. The 696Mb long assembly has an N50 = 27.87Mb and an L50 = 12, with 92.85% of its length placed in 24 chromosomes. We use this new resource to study the evolution of the meagre genome and other Sciaenids, via a comparative analysis of 25 high-quality teleost genomes. Combining a rigorous investigation of gene duplications with base-wise conservation analysis, we identify candidate loci related to immune, fat metabolism and growth adaptations in the meagre. Following phylogenomic reconstruction, we show highly conserved synteny within Sciaenidae. In contrast, we report rapidly evolving syntenic rearrangements and gene copy changes in the sex-related dmrt1 neighbourhood in meagre and other members of the family. These novel genomic datasets and findings will add important new tools for aquaculture studies and greatly facilitate husbandry and breeding work in the species.

Transcriptomic response to ISAV infection in the gills, head kidney and spleen of resistant and susceptible Atlantic salmon

BackgroundInfectious Salmon Anaemia virus (ISAV) is an orthomyxovirus responsible for large losses in Atlantic salmon (Salmo salar) aquaculture. Current available treatments and vaccines are not fully effective, and therefore selective breeding to produce ISAV-resistant strains of Atlantic salmon is a high priority for the industry. Genomic selection and potentially genome editing can be applied to enhance the disease resistance of aquaculture stocks, and both approaches can benefit from increased knowledge on the genomic mechanisms of resistance to ISAV. To improve our understanding of the mechanisms underlying resistance to ISAV in Atlantic salmon we performed a transcriptomic study in ISAV-infected salmon with contrasting levels of resistance to this virus.ResultsThree different tissues (gills, head kidney and spleen) were collected on 12 resistant and 12 susceptible fish at three timepoints (pre-challenge, 7 and 14 days post challenge) and RNA sequenced. The transcriptomes of infected and non-infected fish and of resistant and susceptible fish were compared at each timepoint. The results show that the responses to ISAV are organ-specific; an important response to the infection was observed in the head kidney, with up-regulation of immune processes such as interferon and NLR pathways, while in gills and spleen the response was more moderate. In addition to immune related genes, our results suggest that other processes such as ubiquitination and ribosomal processing are important during early infection with ISAV. Moreover, the comparison between resistant and susceptible fish has also highlighted some interesting genes related to ubiquitination, intracellular transport and the inflammasome.ConclusionsAtlantic salmon infection by ISAV revealed an organ-specific response, implying differential function during the infection. An immune response was observed in the head kidney in these early timepoints, while gills and spleen showed modest responses in comparison. Comparison between resistance and susceptible samples have highlighted genes of interest for further studies, for instance those related to ubiquitination or the inflammasome.

Applying genetic technologies to combat infectious diseases in aquaculture.

Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies-sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter- and intra-species variation in pathogen/parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture.

Catches, size and age composition of the spawning stock muksun Coregonus muksun in the Middle Ob (Tomsk region)

Muksun Coregonus muksun is one of the most valuable whitefish species. It lives in large rivers of Siberia. This is a typical semi-anadromous species. There are presents data on the catches of muksun in the Middle Ob (on spawning grounds and migration routes to them), which generally reflects the number of spawning stock of this species rising to spawn. It is shown that in the middle of the 20th century the catches of muksun averaged 47 tons per year. In the early 1970s, there was a sharp short-term increase in its catches to an average of 215 tons per year, which may be caused by the start of intensive work on collecting whitefish caviar in the area of their spawning run for obtain fish stock for pasture aquaculture in the lakes of Western Siberia. Since the early 1980s, muksun catches have fallen catastrophically, and its fishing is currently prohibited. On the spawning grounds of the Middle Ob, specimens under the age of 16+ were noted. Until the end of the 1990s, the age and size composition of the Muksun spawning stock remained relatively stable. In recent years, there has been an increase of younger fish and, accordingly, a decrease in the average size of fish in the catches. At present (2017–2019), specimens with a fishing length from 392 to 523 mm (on average 457 mm) and a weight of 747 to 1915 g (on average 1233 g) have been noted in the catches of muksun.

Performance and Fecundity of Triploid Eastern Oysters Crassostrea virginica (Gmelin, 1791) and Challenges for Tetraploid Production

The goal of this study was to initiate a program for producing Florida tetraploid founders to meet the needs of the fast-growing oyster farming industry in the Gulf of Mexico. The objectives were to: (1) produce chemically induced triploids originated from Florida wild stocks and (2) screen and identify triploid females for induction of tetraploid founders. By use of Florida wild stocks from different locations, chemically induced triploids were produced in three spawn groups. Compared with diploid siblings, triploids at juvenile stages did not show significant fast growth (shell metrics and body weight) in every group, but at 1-y-old in spawning season did show significantly faster growth (P < 0.0001) than their diploid siblings. Among triploids, the occurrence of female averaged 1.66% (43 out of 2,597 triploids), ranging from 0.68%, 1.2%, and 4.26% in the three spawn groups. Oocytes from these 43 triploid females averaged 214,715 per female ranging from <100 to 1,800,000. Flow cytometry analysis of gonad from the nonfemale triploids (n = 186) showed five types of ploidy composition. A majority of these nonfemale triploids (66.1%) showed 3n only, indicating no gametogenesis occurred, and other different ploidy compositions showed initiation of gametogenesis with different chromosome segregations. Tetraploid induction was conducted by fertilizing the oocytes from triploid females with sperm from diploid males followed by polar body inhibition. The fertilization varied greatly ranging from 12% to 91%, and survival to D-stage swimming larvae ranged from 0% to 24%. Ploidy of pooled D-stage larvae indicated a tetraploid composition ranging from 38% to 80%. Heavy mortality of putative tetraploid larvae occurred at about 7–9 days and juveniles (1, 3, and approximately 200) were harvested in three groups. Unfortunately, these juveniles were lost during a hurricane in October 2018 at the growout site of one collaborating farm before individual ploidy examination. Although no confirmed tetraploid founders were harvested, the occurrence and fecundity of triploid females were documented in detail, which should be useful for future development of tetraploid stock for oyster aquaculture.

Viral Diseases of Some Species from Penaeid Shrimp in Iraqi marine waters

A total of 140 specimens of penaeid shrimps from Metapenaeus affinis and Penaeus semisulcatus were collected from different parts of Iraqi coastal waters to detect three species of viruses Infectious Hypodermal and Hematopoietic Necrosis virus (IHHNV), White Spot Syndrome Virus (WSSV) and Monodon Baculovirus (MBV). PCR and nest PCR used to identify the viruses. The main important results in this study were detection two of more important viruses, (IHHNV) and (WSSV). So, we thought the studied shrimp was not suitable for aquaculture stock without screening because which may play a vertical and horizontal vector role. This study represents the first attempt to detect viral shrimp diseases in Iraq.

The impact of outbreeding on the immune function and disease status of eight hybrid Chinook salmon crosses after Vibrio anguillarum challenge

Aquaculture in North America is currently dominated by Atlantic salmon, but there has been an increasing interest in the production of species native to the Pacific coast. Chinook salmon is relatively new to production; therefore, the selection of appropriate stocks is critical. Often genes from wild populations are incorporated into farmed stocks to avoid performance decreases associated with inbreeding. The present study focuses on assessing the immunological performance of one inbred stock and seven outbred/hybrid crosses after challenge with the marine pathogen, Vibrio anguillarum. Throughout exposure challenge to both pathogen and sterile PBS, significant differences in mortality were observed between crosses. Fish were also assessed for major histocompatibility complex (MHC) class II β1 genotype, and although particular alleles did not confer resistance, crosses with better survival had more individuals presenting a heterozygous genotype. The stress induced during infection resulted in several individuals presenting signs of Bacterial Kidney Disease (Renibacterium salmoninarum) indicating that chronic co-infection may have contributed to susceptibility. When spleen samples from the highest and lowest performing hybrid crosses were assessed for cytokine and respiratory burst gene expression throughout bacterial challenge, high surviving crosses presented lower expression of inflammatory cytokine transcripts (IL-1β, IL-6 and TNFα) when compared to low performing crosses. Interestingly, microsatellite analysis revealed no significant differences in inbreeding coefficient or allelic richness between crosses despite observed variation in immune performance. Understanding the impact of outbreeding on the immune function of farmed, and often inbred, Chinook salmon could aid in future development of high-quality aquaculture stocks for this species.

Genetic diversity of Nile tilapia (Oreochromis niloticus) populations in Ethiopia: insights from nuclear DNA microsatellites and implications for conservation

BackgroundNile tilapia, Oreochromis niloticus (Linnaeus, 1758) is among the economically most important freshwater fish species in East Africa, and a major source of protein for local consumption. Human induced translocations of non-native stocks for aquaculture and fisheries have been found as a potential threat to the genetic diversity and integrity of local populations. In the present study, we investigate the genetic structure of O. niloticus from 16 waterbodies across Ethiopia using 37 microsatellite loci with SSR-GBAS techniques.ResultsThe samples are structured into three main clusters shaped either by biogeographic factors or stocking activities. High FST values (Global FST = 0.438) between populations indicate a high level of genetic differentiation and may suggest long term isolation even within the same drainage systems. Natural populations of the Omo-Turkana system and the lakes in the Southern Main Ethiopian Rift showed the highest genetic variability while low variability was found in stocked populations of lakes Hora, Hashenge and Hayq.ConclusionsThe results presented herein, may provide an essential basis for the management and conservation of the unique genetic resources in northern East Africa, and advance our understanding of biodiversity, phylogeny, evolution and development towards phylogenetically more accurate taxonomic classifications.

Genome editing on finfish: Current status and implications for sustainability

AbstractNovel genome editing techniques allow for efficient and targeted improvement of aquaculture stock and might be a solution to solve challenges related to disease and environmental impacts. This review has retrieved the latest research on genome editing on aquacultured finfish species, exploring the technological progress and the scope. Genome editing has most often been used on Nile tilapia (Oreochromis niloticus Linnaeus), followed by Atlantic salmon (Salmo salar Linnaeus). More than half of the studies have focused on developing solutions for aquaculture challenges, while the rest can be characterized as basic research on fish genetics/physiology or technology development. Main traits researched are reproduction and development, growth, pigmentation, disease resistance, use of trans‐GFP and study of the omega‐3 metabolism, respectively. There is a certain correlation between the species identified and their commercial relevance, indicating the relevance of most studies for present challenges of aquaculture. Reviewing geographical origin of the research, China has been in the forefront (29 publications), followed by the United States (9) and Norway (7). The research seems not to be dependent on regulative conditions in the respective countries, but merely on the purpose and objectives for the use of genome editing technologies. Some technical barriers identified in the studies are presented together with solutions to overcome these‐off‐target effects, ancestral genome duplication and mosaicism in F0. One of the objectives for use is the contribution to a more sustainable aquaculture, where the most prominent issues are solutions that contribute to minimizing impact on biodiversity.

Genetic diversity and structure of the commercially important native fish pacu (Piaractus mesopotamicus) from cultured and wild fish populations: relevance for broodstock management

Pacu (Piaractus mesopotamicus) is one of the most important Neotropical freshwater fish species produced by aquaculture in South America. This study is the first attempt to inquire about aquaculture stocks in Argentina regarding genetic diversity and structure. Neither genetic characterization nor pedigree records are available for pacu stocks in farms in Argentina. The presence of hybrids in both natural environment (Lower Paraná River) and farms has not been evaluated yet at the southern region of pacu distribution. Genetic characterization of pacu broodstocks, corresponding to 8 farms, and wild individuals from four areas at Lower Paraná River was performed. Pacu hybrids were not detected neither in wild nor in farm stocks analyzed. In general, similar levels of genetic diversity were observed between cultured and wild fish populations. Global genetic differentiation (Fst = 0.055) indicated a low level of structure and AMOVA showed that genetic variation was mostly within populations. Reduced contemporary effective population size (Ne) was observed, and probably reflects the bottleneck by founder effect in farmed fish populations. Moreover, kinship analysis showed that in fish farms, on average, 43.00% of the individuals were genetically related, whereas in wild population it was 36.40%. We recommend that broodstock management practices, such as using large Ne, single pair mating, precise records, and tagging of brood fish, should be implemented to avoid unintentional mismanagement.

Microsatellite marker-based variation in the growth hormone genes of Nile tilapia (Oreochromis niloticus)

Polymorphisms in growth hormone genes have been found to cause variation in growth performance of fish. The objective of the study was to reveal variations in microsatellite loci located in the growth hormone genes of Nile tilapia (Oreochromis niloticus). Five microsatellite loci namely GH-MS01, IGFII, IGFII-MS01, IGFII-MS03, and STR were analyzed to assess the genetic variation in the growth hormone genes of four stocks of O. niloticus viz. FBG-Mini Hatchery, FM-Mini hatchery, Eon Aquaculture Ltd. and BFRI. The microsatellite markers were amplified by polymerase chain reaction, separated by polyacrylamide gel electrophoresis and visualized through ethidium bromide staining. All the five loci were found to be polymorphic. The average number of alleles of FM-Mini hatchery stock (3.8) was found to be highest and that of the FBG-Mini hatchery (2.8) and Eon Aquaculture stocks was found to be lowest. The average observed heterozygosity (Ho) value of the FM-Mini hatchery stock was the highest (0.140) and that of FBG-Mini hatchery stock was the lowest (0.040). On the other hand, the average expected heterozygosity (He) was highest in the BFRI stock (0.660) and lowest in the FM-Mini hatchery and FBG-Mini hatchery stock (0.432). The fixation index (1 - (Ho / He) values were positive in all the loci (except locus GH-MS01 in Eon Aquaculture stock), which means these stocks (O. niloticus) were deficient in heterozygosity. Deviation from Hardy-Weinberg expectation at STR locus in FBG-Mini hatchery and Eon Aquaculture stocks were not significant but in all other cases the deviations were found to be significant. The results provide evidence that genetic variation exists within the growth hormone genes in all four stocks of O. niloticus. The polymorphisms that have been detected in the present study can be used to study association with growth and thus selection of fast growing Nile tilapia in Bangladesh.