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The current study evaluated the effects of nano delivery of Spirulina platensis on growth performance, digestive enzymes, and biochemical, immunological, and antioxidative status, as well as resistance to Aeromonas veronii and some physical stressor challenges in Nile tilapia, Oreochromis niloticus. Three experimental fish groups (n = 270) with mean weights of 26 ± 0.30 g and mean lengths of 10 ± 0.5 cm were used; the first additive-free basal diet served as the control group, whereas the following two groups were supplemented with spirulina nanoparticles (SPNP) at 0 (control), 0.25, and 0.5%/kg diet for 4 weeks. Following the feeding trial, fish were challenged with hypoxia, cold stresses, and pathogenic bacteria (A. veronii) infection (9 × 108 CFU/ml). SPNP supplementation, especially 0.5%, (p 0.25% SPNP > 0% SPNP compared with the control. Protection in the incorporated fish groups exposed to A. veronii was 100% compared with the control group, which showed 50% cumulative mortalities. In conclusion, dietary SPNP supplementation improved growth performance, antioxidant activity, immune response, digestive enzymes, related gene expression, and resistance of Nile Tilapia to hypoxia, cold, and A. veronii infection. Thus, SPNP could be used as a natural therapy for controlling those stressors.

Stress enhances the disease susceptibility in fish by altering the innate immune responses, which are essential defense mechanisms. The use of probiotics is increasingly popular in the aquaculture industry. Yellow perch is a promising candidate for aquaculture. We investigated the efficiency of a mixed Bacillus species in minimizing the potential problems resulting from husbandry practices such as hypoxia and exposure to air in yellow perch. We showed that hypoxia and air exposure conditions induced a significant reduction in the early innate immune response (lysozyme activity, interferon-induced-GTP-binding protein-Mx1 [mx], interleukin-1β [il1β], serum amyloid-A [saa]), and a substantial increase in cortisol, heat shock protein (Hsp70), glutathione peroxidase (Gpx), superoxide dismutase (Sod1) that associated with a decline in insulin-like growth factor-1 (Igf1). Mixed Bacillus species administration improved the early innate responses, reduced cortisol, Hsp70, Gpx and Sod1, and elevated Igf1 levels. Bacillus species treated group showed faster recovery to reach the baseline levels during 24 h compared to untreated group. Therefore, mixed Bacillus species may enhance yellow perch welfare by improving the stress tolerance and early innate immune response to counterbalance the various husbandry stressors. Further studies are warranted to investigate the correlations between the aquaculture practices and disease resistance in yellow perch.

In current study, Yellow perch (P. flavescens) was exposed to common forms of physical stressors and antioxidative effects of dietary incorporated Astragalus membranaceus (AM) and Glycyrrhiza glabra (liquorice) were assessed. To address this, for a four-week five groups of fish (31 ± 1.0 g, average weight) received 1, 2, and 3% (w/w) Glycyrrhiza glabra; and 1% G. glabra- A. membranaceus mixture daily. Control group fed an additive-free basal diet. Immunological, biochemical and histopathological profiles were evaluated; and fish were redistributed to be exposed to heat, cold, hypoxia and capture stressors. The current findings demonstrated that A. membranaceus and G. glabra dietary incorporation remarkably enhanced antioxidative and biochemical parameters. Also, the study showed markedly up-regulation of related genes expression; and revealed better liver histology in supplemented groups over the control. In conclusion, A. membranaceus and G. glabra dietary supplementation markedly enhanced antioxidantive responses throughout the experimental period, indicating the ability of both herbal plants to confer protection against different physical stressors.

Terminologies of ovary development, by somewhat subjective describing and naming main changes of oocytes, have been criticized for confusing and inconsistency of terms and classifications, and the incurred consequences impede communication among researchers. In the present work, we developed regression between ovary development and three ribosome RNA (rRNA) indexes, namely 5S rRNA percent, 18S rRNA percent, and 5S–18S rRNA ratio, using close relationship between volume percent of primary growth stage oocytes or gonadosomatic index and rRNA content, demonstrating species-specific quantification of ovary development can be established in species with either synchronous and asynchronous oogenesis. This approach may be extended to any species with primary growth oocytes, e.g. anurans and reptiles, to predict maturity stages in females. We further confirmed that 5S rRNA percent and 5S/18S rRNA ratio can serve as markers to distinguish sexes unambiguously. A micro-invasive sampling method may be invented for non-lethal prediction of ovary development and sex because only a small amount of ovary sample (

The use of genotyping has enabled the characterization and mapping of genes and the study of stock identification, population genetics, evolution, ecological speciation, and invasion, as well as genomic evaluation, sex control and sex determination, nutrition, biomarkers for disease, and quantitative trait loci mapping for marker-assisted selection in fisheries and aquaculture. High-throughput variant discovery has been made possible in multiple species by the recent advent of next-generation DNA sequencing technologies. New genotyping methods that are high-throughput, accurate, and inexpensive are urgently needed for gaining full access to the abundant genetic variation of organisms. This approach is known as genotyping-by-sequencing (GBS), which holds great promise as a research tool because of its ability to allow simultaneous marker discovery and genotyping at low cost and with a simple molecular biology workflow for fisheries and aquaculture studies. Since it was first developed for rice in 2009, GBS has been applied in over 50 species/studies by the end of 2014. It is also increasingly in use in fisheries and aquaculture and has been applied in nearly 40 species/studies from 2015 to present. This review summarizes the genotyping methodologies, recent advances in next-generation DNA sequencing technologies to achieve GBS, and the promises this approach holds as a genome-wide genotyping application in fisheries and aquaculture. Additionally, we discuss the potential of whole-genome sequencing (WGS) in GBS and present the advances of WGS in fisheries and aquaculture.

The effects of dietary administration of Astragalus membranaceus nanoparticles (ANP) on immune and anti-oxidative responses, growth performance and disease resistance of Oreochromis niloticus were evaluated in the present study. Fish were divided into three groups and received the ANP at rates of 0 (control), 1, and 2%/kg diet for four weeks. After the four-week feeding trial, three fish from each replicate were sampled for immune and anti-oxidative responses evaluation, ten fish from each group were challenged with A. veronii, and nine fish from each group were subjected to cold and hypoxia challenges. It was obvious from the results that ANP significantly enhanced lysozyme activity and nitrous oxide (NO) activities, as well as improved superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx) activities. Also, aspartate aminotransferase, alanine transaminase, glucose, and cortisol measurements showed significantly lower levels in incorporated groups compared to the control. Growth performance; and amylase and lipase digestive enzymes activities also showed markedly improved results. Expression of heat shock protein 70 (HSP70) and interleukin 1, beta (IL-1β) genes were significantly upregulated throughout the entire experimental period. When challenged with A. veronii, the mortality of treated groups was significantly (P

Yellow perch (Perca favescens) is an important native North American fish in ecology and aquaculture. However, molecular markers are minimal for this species, especially those with genome-wide distribution. Single sequence repeat markers are always developed based on sequences from a single individual, which is time consuming with a low success rate. In this study, combining data from HiSeq and MiSeq platforms, we applied restriction site-associated DNA sequencing (RAD-Seq) to yellow perch geographic demes to develop large numbers of polymorphic genetic markers, including single nucleotide polymorphisms and simple sequence repeats, and to evaluate nucleotide diversity. A total of 258,056 contigs were assembled with the length of 605 ± 71 (mean ± SD) bp, which were longer than those just using HiSeq data. Nucleotide diversity (π) was 0.00304 with 95% confidence intervals from 0.00303 to 0.00304. Based on the assembled sequences, a total of 59,766 perfect single sequence repeats were detected, with AC/GT being the most common repeat motif and GC being the rarest. Based on this breeding population, 41,736 high-quality single nucleotide polymorphisms and 10,412 polymorphic single sequence repeats were obtained. Validation of amplification by randomly selecting 40 polymorphic single sequence repeats showed a high success rate (85%). Our approach for polymorphic single sequence repeats development enables new usage of data from RAD-seq techniques. These developed markers could be used in finfish broodstock management, genetic improvement and resource conservation, and would contribute to sustainable development of fisheries and the aquaculture industries.

Arsenic (As) is found in waters such as seawater, warm springs, groundwater, rivers, and lakes. In aquatic environments, As occurs as a mixture of arsenate and arsenite, with arsenate usually predominating. The unrestricted application of As pesticides, industrial activities, and mining operations has led to the global occurrence of soluble As above permissible levels of 0.010 mg/L. Continuous exposure of freshwater organisms including fish to low concentrations of As results in bioaccumulation, notably in liver and kidney. As a consequence As induces hyperglycemia, depletion of enzymatic activities, various acute and chronic toxicity, and immune system dysfunction. Here we review arsenic chemistry, the occurrence of arsenic in aquatic system, the transformation and metabolism of arsenic; arsenic bioaccumulation and bioconcentration; behavioral changes; and acute and other effects such as biochemical, immunotoxic, and cytogenotoxic effects on fish.

The current work assessed the potential immunomodulatory and growth-promoting effects of Astragalus membranaceus (AM) and Glycyrrhiza glabra (liquorice) in Yellow perch (Perca flavescens). In this regard, fish with an average weight of 31 ± 1.0 g were divided into five groups, and fed daily with an additive-free basal diet (control); 1, 2, and 3% (w/w) Glycyrrhiza glabra, and the fifth diet was incorporated with a combination of 1% G. glabra-AM for a four-week period. Immunological, biochemical and growth parameters were measured; and sub-groups of fish were exposed to 1-week starvation. The results showed that incorporating AM and liquorice in the diet significantly improved Immunological [superoxide dismutase (SOD), glutathione peroxidase (GPx), catalase (CAT), Lipid peroxidase (LPx) and lysozyme activities], biochemical [Aspartate Aminotransferase (AST) and Alanine Transaminase (ALT) activities; and glucose and cortisol concentrations] and growth performance parameters [body mass gain (BMG), specific growth rate (SGR), length, condition factor (K) and feed conversion ratio (FCR)]. In addition, markedly up-regulated the expression of related genes [Insulin-Like Growth Factor-1 (IGF-1), Serum amyloid A (SAA), Complement Component C3 (CCC3), Alpha 2 Macroglobulin (A2M), SOD and GPx] in treated fish groups compared to the control. Conclusively, feeding AM and liquorice diets significantly increased (P

The current study assessed the effect of dietary canthaxanthin and lycopene supplementation at different concentrations on growth performance and antioxidant status in yellow perch (Perca flavescens). In this regard, fish with initial weight (32 ± 1.0 g) were divided into five groups in triplicate, and fed on carotenoid-free diet (control), canthaxanthin (CTX) (50 and 100 mg/kg diet), and lycopene (200 and 400 mg/kg diet) for 60 days. Growth parameters and antioxidant enzymes were evaluated after 30 and 60 days post feeding. Tissue liver and intestine from six fish per treatment was collected for antioxidant and digestive enzymes analysis. The results revealed a significant increase (P < 0.05) of lipid content in the group fed lycopene at a dietary level 400 mg/kg for 60 days, compared to the control. Moreover, dietary carotenoids exhibited no significant effect on growth performance; this was evidenced by no significant up-regulation of growth hormone (gh) and insulin-like growth factor 1b (igf-1b) genes after 30 and 60 days post feeding. Intestinal lipase and trypsin activities were significantly improved with dietary lycopene especially at a dose of (400 mg/kg diet) for 60 days. Malondialdehyde (MDA) level in liver was also significantly decreased with dietary lycopene (400 mg/kg diet) for 60 days. Hepatic superoxide dismutase (SOD), catalase (CAT), and Glutathione peroxidase (GSH-Px) activities were significantly decreased with dietary CTX, especially at dose (100 mg/kg diet) and lycopene at a concentration of 200 and 400 mg/kg diet after 60 days feeding. Additionally, the immune-related gene interleukin-1 beta (il-1b) mRNA expression level revealed up-regulation in groups fed on CTX at different concentrations for 30 days, and fish fed lycopene at a concentration level 400 mg/kg diet for 60 days. The obtained results concluded that dietary supplementation of canthaxanthin and lycopene could enhance immune response and maintain antioxidants defense of fish. Therefore, it considered as a functional aquafeed ingredient for yellow perch.

Exposure to stress induces a series of responses and influences a wide range of biological processes including sex differentiation in fish. The present work investigated the molecular and physiological response to thermal stress throughout the early development stage covering the whole period of sex differentiation of bluegill, Lepomis macrochirus. Larvae were treated using three temperatures, 17, 24, and 32°C from 6 to 90 days posthatching (dph) in 30-L round tanks. There is no significant difference of the sex ratio and survival among the three temperature groups in the geographic population used in this study. Two ovarian differentiation-related genes foxl2 and cyp19a1a were detected at 7 dph suggesting that these genes have already played a role prior to sex differentiation. The expression of foxl2 reached the peak and was thermosensitive just prior to the onset of ovarian differentiation at 27 dph. Histological examination displayed that the proliferation of germ cells and ovarian differentiation were delayed at the low-temperature treatment (17°C) at 97 dph compared with higher temperatures. In conclusion, the water temperature regulates the sex differentiation of bluegill through modulation of the expression of foxl2 and cyp19a1a. A comparative study of the expression profile of sex differentiation-related genes in species will shed light on the evolution of sex-determination mechanisms and the impact of stress on sex differentiation.

Egg disinfection is considered the most important routine work in hatcheries to avoid fungal and/or bacterial infection of fish eggs. The aim of this study was to determine the effectiveness of three disinfectants: formalin, iodine and sodium chloride on the hatching success of yellow perch eggs. The disinfectants were tested in triplicate at different concentrations for 15 and 30 min bath treatments. Two experiments were conducted; formalin at five concentrations (25, 50, 100, 150 and 200 mg L−1) and 25 mg L−1 iodine were tested in the first experiment. The second experiment involved formalin at three concentrations (250, 500 and 1000 mg L−1), iodine at three concentrations (50, 100 and 250 mg L−1) and sodium chloride at three concentrations (500, 1000 and 3000 mg L−1) were used. Iodine and sodium chloride-treated eggs hatched earlier than formalin-treated eggs. The highest mean percentage of eyed stage, hatching rate and survival to first feeding fry was observed at 200 mg L−1 formalin for 30 min, 50 mg L−1 iodine for 15 min and 500 mg L−1 sodium chloride for 30 min. High concentrations of formalin (1000 mg L−1), iodine (250 mg L−1) and sodium chloride (1000 and 3000 mg L−1) showed toxicity to yellow perch eggs, resulting in low hatching rate and survival to first feeding fry. We recommended formalin at a concentration of 150–200 mg L−1 for 30 min as an effective, easily available and low-cost disinfectant for routine use to improve yellow perch hatchability.

Stress is a major factor that causes diseases and mortality in the aquaculture industry. The goal was to analyze the expression of stress-related biomarkers in response to different stressors in yellow perch, which is an important aquaculture candidate in North America and highly sensitive to handling in captivity. Three fish groups were established, each having four replicates, and subjected to water temperatures of 14, 20, and 26°C and acute handling stress was performed followed by a salt treatment for 144h at a salinity of 5 ppt. Serum and hepatic mRNA levels of heat shock protein (hsp70), insulin-like growth factor 1 (Igf1), glutathione peroxidase (Gpx), superoxide dismutase 1 (Sod1), and glutathione reductase (Gsr) were quantified at seven times interval over 144 h using ELISA and RT-qPCR. Handling stress caused a significant down-regulation in Hsp70, Gpx, Sod1, and Gsr at a water temperature of 20°C compared to 14 and 26°C. Igf1 was significantly upregulated at 20°C and down-regulated at 14 and 26°C. Salt treatment had a transient reverse effect on the targeted biomarkers in all groups at 72 h, then caused an upregulation after 144 h, compared to the control groups. The data showed a negative strong regulatory linear relationship between igf1 with hsp70 and anti-oxidative gene expressions. These findings could provide valuable new insights into the stress responses that affect fish health and could be used to monitor the stress.

Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries.Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop for Aquaculture Genomics, Genetics, and Breeding held in late March 2016 in Auburn, Alabama, with participants from all parts of the United States.

Stress of aquatic animals occurs due to physical and physiological disturbances in the aquatic environment or system when transportation, crowding, handling or changes of physical and chemical factors take place. There are three regulatory systems having a vital role in stress response: the neural, endocrine and immune systems. Fish exhibit multiple genomic and physiological responses to adjust the compensatory or adaptive mechanism that allows them to mitigate the stressors, maintain their haemostasis and survive. In this review, we describe multiple important genes that are associated with responses to environmental and husbandry stressors and that could be used as biomarkers of environmental and husbandry stressors in fish. The described environmental and husbandry stressors include salinity, temperature, hypoxia and hyperoxia, confinement, density and handling. The main role of stress response in aquatic animals is to compensate or adapt their biological systems and arrange the metabolism to afford the energy required by the stressor and a wide array of metabolic processes and pathways are involved. We summarized and discussed highly significant genes in several organs and tissues that are involved and active during this adaption process. The traditional stress biomarkers in some circumstances have some difficulties in interpretation of results and lead to tricky diagnosis and searching and understanding alternative tools is critical for aquaculture, fisheries and fish welfare. Using genomic tools to study the candidate genes associated with stress responses are often unique signatures or imprints of specific stressors and could determine early signs of stressors.

Considering the divergent temperature habitats and morphological traits of four Percidae species: yellow perch (Perca flavescens), Eurasian perch (Perca fluviatilis), pike perch (Sander lucioperca), and ruffe (Gymnocephalus cernua), we stepped into the transcriptome level to discover genes and mechanisms that drive adaptation to different temperature environments and evolution in body shape. Based on 93,566 to 181,246 annotated unigenes of the four species, we identified 1,117 one-to-one orthologous genes and subsequently constructed the phylogenetic trees that are consistent with previous studies. Together with the tree, the ratios of nonsynonymous to synonymous substitutions presented decreased evolutionary rates from the D. rerio branch to the sub-branch clustered by P. flavescens and P. fluviatilis. The specific 93 fast-evolving genes and 57 positively selected genes in P. flavescens, compared with 22 shared fast-evolving genes among P. fluviatilis, G. cernua, and S. lucioperca, showed an intrinsic foundation that ensure its adaptation to the warmer Great Lakes and farther south, especially in functional terms like “Cul4-RING E3 ubiquitin ligase complex.” Meanwhile, the specific 78 fast-evolving genes and 41 positively selected genes in S. lucioperca drew a clear picture of how it evolved to a large and elongated body with camera-type eyes and muscle strength so that it could occupy the highest position in the food web. Overall, our results uncover genetic basis that support evolutionary adaptation of temperature and body shape in four Percid species, and could furthermore assist studies on environmental adaptation in fishes.

There is increasing evidence that temperature effects on sex ratio in fish species are ubiquitous. Temperature effects on sex ratio could be influenced by parent, strain, and population, whether in fish species with temperature-dependent sex determination or genetic sex determination plus temperature effects. In the present study, effects of genotype-temperature interactions on sex determination in bluegill sunfish were further investigated, based on our previous results, using four geographic strains: Hebron, Jones, Hocking, and Missouri. In the Hebron strain, the two higher-temperature treatment groups (24 °C and 32 °C) produced more males than the low-temperature treatment group (17 °C) from 6 days post-hatching (dph) to 90 dph. In contrast, the low-temperature treatment produced more males than the other two higher-temperature treatments in the Jones strain. No significant effects of temperature on sex ratio were detected in the other two strains. Our results from sex ratio variance in different treatment times suggest that the thermosensitive period of sex differentiation occurs prior to 40 dph. Our results further confirmed that genotype-temperature interactions influence sex determination in bluegill. Therefore, to significantly increase the proportion of males, which grow faster and larger than females, a consumer- and environment-friendly approach may be achieved through selection of temperature sensitivity in bluegill.

The current study aimed to develop a method to rapidly, sensitively and practically screen for the epidermal growth factor receptor (EGFR) T790M mutation. This method combines an allele-specific competitive blocker (ACB) with a TaqMan quantitative polymerase chain reaction (PCR) amplification refractory mutation system (ARMS) in a one-step reaction. Using a mimic of a human genomic DNA panel containing serially diluted mutant alleles, the performance efficacy of this method was assessed. Using this method, the EGFR T790M mutation was detected in tyrosine kinase inhibitor (TKI)-naive samples obtained from 27 non-small cell lung cancer (NSCLC) patients with EGFR-activating mutations. The association between de novo T790M mutations and the clinical benefit of EGFR-TKI treatment was also analysed. The sensitivity of this method was as low as 0.01%. In the samples from the 27 NSCLC patients, this method identified 6 mutant patients (22.2%), which was higher than the detection rate with scorpion ARMS (0.0%). No clinical variables were associated with the occurrence of a de novo T790M mutation. The median progression-free survival time in the TKI-naive patients with a T790M mutation was shorter that that of patients without the mutation, but the difference was not significant (3.2 vs. 19.5 months, respectively; P=0.256). The median overall survival time in the groups with or without T790M mutation also did not significantly differ (10 vs. 20 months, respectively; P=0.689). Overall, the ACB-ARMS PCR method could be useful for detecting the EGFR T790M mutation in clinical samples that contain only a small number of mutant alleles. The clinical significance of a de novo T790M mutation should be further investigated.

Transcriptome sequencing could facilitate discovery of sex-biased genes, biological pathways and molecular markers, which could help clarify the molecular mechanism of sex determination and sexual dimorphism, and assist with selective breeding in aquaculture. Yellow perch has unique gonad system and sexual dimorphism and is an alternative model to study mechanism of sex determination, sexual dimorphism and sexual selection. In this study, we performed the de novo assembly of yellow perch gonads and muscle transcriptomes by high throughput Illumina sequencing. A total of 212,180 contigs were obtained, ranging from 127 to 64,876 bp, and N50 of 1,066 bp. The assembly RNA-Seq contigs (≥200bp) were then used for subsequent analyses, including annotation, pathway analysis, and microsatellites discovery. No female- and pseudo-male-biased genes were involved in any pathways while male-biased genes were involved in 29 pathways, and neuroactive ligand receptor interaction and enzyme of trypsin (enzyme code, EC: 3.4.21.4) was highly involved. Pyruvate kinase (enzyme code, EC: 2.7.1.40), which plays important roles in cell proliferation, was highly expressed in muscles. In addition, a total of 183,939 SNPs, 11,286 InDels and 41,479 microsatellites were identified. This study is the first report on transcriptome information in Percids, and provides rich resources for conducting further studies on understanding the molecular basis of sex determinations, sexual dimorphism, and sexual selection in fish, and for population studies and marker-assisted selection in Percids.

This study was designed to assess the potential effects of Astragalus membranaceus (AM) on the growth performance and antioxidative stress response in bluegill sunfish (Lepomis macrochirus) exposed to challenging cold water temperature conditions. In this regard, fish with an average weight of 43 ± 1 g were divided into four groups and fed daily with an AM-free diet (control), and 1.5, 3, and 4.5 % (w/w) AM-incorporated diets for an 8-week period. Oxidative stress response, biochemical, and growth parameters were measured, and subgroups of fish were exposed to the outside challenging cold pond water temperature (1.6–9.9 °C) with an average of 7.0 ± 0.1 °C beyond the optimal temperature. The results showed that incorporating AM in the diet significantly improved growth performance parameters (body mass gain, specific growth rate, length, condition factor, and feed conversion ratio) and biochemicals (aspartate aminotransferase and alanine transaminase activities, and glucose and cortisol concentrations). In addition, markedly up-regulated superoxide dismutase, glutathione peroxidase, and catalase activities were observed in AM-treated fish groups over the control. Conclusively, feeding AM diets significantly increased (P

International audience; The molecular mechanisms that underlie sex determination and differentiation are conserved and diversified. In fish species, temperature-dependent sex determination and differentiation seem to be ubiquitous and molecular players involved in these mechanisms may be conserved. Although how the ambient temperature transduces signals to the undifferentiated gonads remains to be elucidated, the genes downstream in the sex differentiation pathway are shared between sex-determining mechanisms. In this paper, we review recent advances on the molecular players that participate in the sex determination and differentiation in fish species, by putting emphasis on temperature-dependent sex determination and differentiation, which include temperature-dependent sex determination and genetic sex determination plus temperature effects. Application of temperature-dependent sex differentiation in farmed fish and the consequences of temperature-induced sex reversal are discussed.

Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries. Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop for Aquaculture Genomics, Genetics, and Breeding held in late March 2016 in Auburn, Alabama, with participants from all parts of the United States.