Search Results (958)

Oujiang color common carp display four striking varieties of pigmentation, but their epigenetic basis is unclear. We integrated genome-wide DNA methylation (MBD-seq) and transcriptomes (RNA-seq) from dorsal skin of four Oujiang color common carp varieties with three biological replicates. Black-spotted groups (RB, WB) showed approximately 6% higher global methylation than non-black-spotted groups (WR, WW), with differential methylation enriched in introns (>23%) and intergenic regions (>47%). Integrative analyses revealed a strong inverse association between promoter methylation and gene expression; 96 pigmentation-related genes were identified, spotlighting genes such as ASIP and frmA as key epigenetically silenced regulators in black-spotted carp. RT-qPCR confirmed directional concordance with RNA-seq for ASIP, frmA, DGAT2, SCARB1, and FOSB. Pathway enrichment implicated melanogenesis metabolism, tyrosine metabolism, lipid metabolism, and fatty acid metabolism, suggesting an interplay between pigment deposition and metabolic regulation. Collectively, the findings present an exploratory view of epigenetic control of coloration and underscore promoter methylation as a core layer influencing color diversity in Oujiang color common carp. Full article

Amphioxus belongs to the subphylum Cephalochordata and occupies a transitional position in evolution between invertebrates and vertebrates. Due to the lack of viruses suitable for immunostimulation in amphioxus, this study for the first time explored the pathogenicity and waterborne transmission of Grass Carp Reovirus (GCRV), a double-stranded RNA virus, during its infection of amphioxus. Soaking amphioxus in GCRV suspension can cause obvious damage to gill tissues and severely disrupt the structure of gill filaments. The virus survived in seawater for no more than 48 h. Infection kinetics studies showed that the expression of VP5 (a viral capsid protein) mRNA in gill tissues peaked at 14 h. After co-culturing GCRV-infected amphioxus with healthy amphioxus for 72 h, the gills of healthy amphioxus showed obvious pathological damage. Additionally, the presence of the virus was verified by RT-PCR amplification of VP5 expression, indicating that GCRV can be transmitted via water. Transcriptome sequencing analysis showed that the Mitogen-Activated Protein Kinase (MAPK), calcium signaling pathway, and chitin metabolic pathway were significantly activated in amphioxus after GCRV stimulation. This study confirmed that GCRV can infect cephalochordates, revealing its gill-tropism and water-borne transmission ability, providing a new perspective for studying the cross-species infection mechanism of aquatic viruses and the prevention and control of aquatic diseases. Full article

Cold stress poses a critical threat to fish survival by triggering metabolic dysfunction, oxidative damage, immune suppression, and apoptosis. However, hybrid polyploid fish triploid crucian carp (3nRCR, 3n = 150) demonstrate superior stress tolerance. In this study, we investigated the cold adaptation mechanisms in different ploidy cyprinid fishes: triploid crucian carp compared to its diploid improved red crucian carp (Carassius auratus red var., RCC, 2n = 100, ♀) and improved allotetraploid (4nAT, 4n = 200, ♂) progenitors. Under controlled cooling, 3nRCR lost equilibrium at a significantly lower temperature (3.2 °C) than RCC (4.0 °C) and 4nAT (4.5 °C), confirming its superior enhanced cold resistance. Histological examination revealed minimal tissue damage in 3nRCR, characterized by reduced gill inflammation and cellular apoptosis. Transcriptomics revealed triploid-specific molecular strategies: 3nRCR uniquely activated retinol metabolism and metabolic rewiring (arginine/proline metabolism, oxidative phosphorylation). Notably, in the immune-related NLR signaling pathway, both nlrp1 and nlrp3 (key inflammasome components) were significantly downregulated in 3nRCR (p < 0.01). In contrast, genes involved in endoplasmic reticulum (ER) stress response, including chop and nrf2, were markedly upregulated, indicating a reinforced cellular stress resolution mechanism absent in both RCC and 4nAT. Our results demonstrate that triploid cold adaptation is orchestrated through a balanced interaction among mitochondrial apoptosis, ER stress, and inflammasome pathways. These findings provide novel insights into hybrid polyploid adaptation mechanisms and targets for cold-resilient aquaculture breeding. Full article

The aim of our study was to make one step further to verify a method that can turn back mycotoxin-contaminated crops into the circular economy. Thus, the possibility of utilizing aflatoxin B1 (AfB1)-contaminated corn by yellow mealworms (Tenebrio molitor) was investigated to be used as fish feed components. Four different self-contaminated corn samples were used in our study, of which one was below and three were above the threshold limit (20 µg/kg) regulated by the European Union. The highest applied AfB1 concentration in our study for insect feeding was 415 µg/kg (more than twenty times higher than the threshold). After a five-week feeding period insect mortality was not increased, even in the highly contaminated group, compared to the negative control. The mycotoxin in the dried and ground insects was only detected in the case of feeding with the highest-concentration corn, however it remained as low as 2.2 µg/kg. For studying the possible physiology effects, insect grounds were used in feeding experiments of common carp (Cyprinus carpio) fries. Results showed that insect meal, even if originated from a highly mycotoxin-contaminated crop, did not have a significant effect on the examined fish fries, compared with the control groups. The AfB1 concentrations of the leftover frass after insect rearing were also measured, and in the case of the highest concentration mealworm group, it was 157.6 µg/kg (other groups were under 20 µg/kg). Toxicity of frass extracts from different contaminated groups was also studied using microinjected zebrafish (Danio rerio) embryos. Extracts of the highly contaminated frass samples caused 91.67 ± 3.33% mortality and led to numerous phenotypic changes, which highlights the need for responsible usage of the by-product. However, the effects of injected frass samples, originating from corn with lower and more environmentally relevant AfB1 concentrations, were significantly lower. Full article

Fish barrier technology by pulsed direct current has broad application potential to guide fish to suitable waters. The primary objective of this investigation was to study the effects of electric pulse frequency and water velocity on fish deterrence by pulsed direct current. The test fish were adults of two common carp species, Hypophthalmichthys nobilis (bighead carp, standard length 0.460–0.545 m) and Cyprinus carpio (Eurasian carp, standard length 0.292–0.335 m). Experiments were conducted in the 20 m swimming chamber of a 50 m flume, with a pulsed electric barrier produced by vertical electrodes located in the middle of the swimming chamber. The effectiveness of the electric barrier in deterring fish from swimming upstream past the electrodes was tested. The electric pulse generator produces a square wave pulse, with a voltage of 150 V and width of 2 ms. There were four electric pulse frequency treatments (4 Hz, 6 Hz, 8 Hz, 10 Hz), and two water velocity treatments (0.2 m/s, 0.6 m/s), with 10 replicates of each treatment. There were four primary findings. (1) Of the 160 fish tested, no fish was stunned and only 4 trembled (lost the ability to swim) for more than 2 s after encountering the electric barrier. (2) At a given water velocity, the crossing probability decreased as pulse frequency increased, and the decrease was largest when the frequency increased from 8 to 10 Hz. (3) At a given electric pulse frequency, the crossing probability was higher at the high water velocity, and barrier efficiency was more sensitive to velocity at higher pulse frequencies. (4) H. nobilis, a stronger swimmer, crossed more often than C. carpio. This study can provide ideas for the management of invasive species. However, the study was conducted under controlled laboratory conditions, and field experiments should be carried out before field applications. Full article

The ability of common carp to withstand both short-term and long-term oxygen deprivation has been well documented; however, the potential genetic mechanisms behind common carp’s hypoxia response remain unclear. Therefore, to understand the possible genetic foundation of their response to hypoxia, comparative genomic analyses were conducted among six common carp varieties: Color, Songpu, European, Yellow, Mirror, and Hebao common carps. We identified 118 single-copy orthologous positively selected genes (PSGs) (dN/dS > 1) in all common carps under study, with GO functions directly related to the cellular responses to hypoxia in Color and European common carp PSGs, such as oxygen transport activity, oxygen binding activity, respiratory burst activity, and superoxide anion production. The Bayes Empirical Bayes (BEB) technique identified possible amino acid substitutions in mitochondrial and hypoxic genes under positive selection. Exonic and intronic structural variations (SVs) were discovered in the CYGB2 hypoxia-related gene of Color and European common carps, as well as in several mitochondrial genes, including MRPL20, MRPL32, NSUN3, GUF1, TMEM17B, PDE12, ACAD6, and COX10 of Color, European, Songpu, Yellow, and Hebao common carps. Moreover, Color common carp and Songpu common carp were found to share the greatest percentage of collinear genes (49.8%), with seven Songpu common carp chromosomes (chr A2, chr A9, chr A13, chr B13, chr B15, chr B2, and chr B12) showing distinct translocation events with the corresponding chromosomes of Color common carp. Additionally, we found 570 translocation sites that contained 3572 translocation-related genes in Color common carp, some of which are directly relevant to mitochondrial and hypoxic GO functions and KEGG pathways. Our results offer strong genome-wide evidence of the possible evolutionary response of Cyprinus carpio to hypoxia, providing important insights into the potential molecular mechanisms that explain their survival in hypoxic environments and guiding future research into carp hypoxia tolerance. Full article

The invasive Silver Carp (Hypophthalmichthys molitrix) in North America represents a promising resource for surimi production; however, its gel formability deteriorates significantly during frozen storage. This study investigated the deterioration of gel properties in Silver Carp surimi over six months of frozen storage, and showed that short-term frozen storage (<2 months) was beneficial for surimi gel-forming ability, while extended frozen storage (>2 months) tended to have detrimental effects. The adverse effect of long-term frozen storage could be mitigated via using food additives (e.g., manufactured microfiber, transglutaminase, and chicken skin collagen), among which transglutaminase was the most effective. Transglutaminase at a relatively low level (0.1 wt%) could effectively negate frozen storage’s effects, and produced surimi gel with quality attributes (e.g., gel strength, hardness, and chewiness) at levels comparable to those from fresh fish samples. To assess the effects of the addition of various food additives for quality improvement, a synthetic data-driven machine learning (SDDML) approach was developed. After testing multiple algorithms, the random forest model was shown to yield synthetic data points that represented experimental data characteristics the best (R² values of 0.871–0.889). It also produced improved predictions for gel quality attributes from control variables (i.e., additive levels) compared to using experimental data alone, showing the potential to overcome data scarcity issues when only limited experimental data are available for ML models. A synthetic dataset of 240 data points was shown to supplement the experimental dataset (60 points) well for assessment of the Frozen Silver Carp (FSC) surimi gel quality attributes. The SDDML method could be used to find optimal recipes for generating additive profiles to counteract the adverse effects of frozen storage and to improve surimi gel quality to upgrade underutilized invasive species to value-added food products. Full article

Columnaris disease is a highly contagious infection that affects nearly all freshwater fish species worldwide. Grass carp, one of the most economically significant freshwater fish species in China, is particularly susceptible to the disease, leading to large-scale mortality. Flavobacterium columnare and F. covae are the primary pathogens causing columnaris disease in Chinese grass carp aquaculture. Herein, we compare mortality rates, replication rates of typical columnaris symptoms, histopathological changes, and bacterial content in the tissues of grass carp following infection using four challenge models. The mortality rate in grass carp challenged via intraperitoneal injection was 86.7%. All fish infected via intramuscular and intradermal injections died, while immersion resulted in lower mortality. Gill corrosion rates were 67%, 53%, and 87%, respectively, in the intramuscular injection, intradermal injection, and immersion groups. Correspondingly, skin ulceration rates were 75%, 91%, and 63%. However, surface symptoms in the intraperitoneal injection group were milder. Histopathological analysis revealed similar lesions in grass carp subjected to immersion, intramuscular, and intradermal infection, which differed from carp infected via intraperitoneal injection. The trends in bacterial loads in the gills and skin were similar, although the absolute bacterial content varied between tissues. Bacterial loads in the immersion and intraperitoneal injection groups were lower than those in the other groups. Based on these findings, we determined that the optimal model for simulating columnaris disease in grass carp is the intradermal injection of F. covae in 10–12 cm fish. The infection model generated via intradermal injection resembles natural F. covae infection and can serve as a good tool for evaluating the protective effect of anti-F. covae infection vaccines in grass carp. Full article

This study examines the genetic diversity and population structure of silver carp (Hypophthalmichthys molitrix), an ecologically and economically important freshwater species. Samples were collected from 17 sites along the Yangtze River, including LCH, LCS, LJHK, and LXZX, as well as one population from the United States (SV). Restriction-site associated DNA sequencing (RAD-seq) generated 759,453 high-quality single-nucleotide polymorphisms (SNPs) for population genomic analyses, including genetic differentiation (F_ST), population structure, and linkage disequilibrium (LD) decay. Genetic variation was primarily found within populations (78.05%), with 21.94% among populations. Most sites exhibited low genetic differentiation (F_ST < 0.05), suggesting high admixture along the river, although a few sites displayed elevated values (F_ST > 0.15). Rapid LD decay in LCH, LCS, and LJZ indicated frequent recombination and moderate to large effective population sizes. These patterns reflect the influence of geographic and ecological factors on population structure. Conservation strategies should maintain genetic connectivity while protecting distinct genetic resources. Populations with high differentiation, such as LXZX and LWZ, warrant targeted management to preserve unique genetic diversity. Full article

This study examines the impacts of climate change on fisheries and aquaculture in Bangladesh, one of the most climate-vulnerable countries in the world. The fisheries and aquaculture sectors contribute significantly to the national GDP and support the livelihoods of 12% of the total population. Using a Critical Literature Review (CLR) approach, peer-reviewed articles, government reports, and official datasets published between 2006 and 2025 were reviewed across databases such as Scopus, Web of Science, FAO, and the Bangladesh Department of Fisheries (DoF). The analysis identifies major climate drivers, including rising temperature, erratic rainfall, salinity intrusion, sea-level rise, floods, droughts, cyclones, and extreme events, and reviews their differentiated impacts on key components of the sector: inland capture fisheries, marine fisheries, and aquaculture systems. For inland capture fisheries, the review highlights habitat degradation, biodiversity loss, and disrupted fish migration and breeding cycles. In aquaculture, particularly in coastal systems, this study reviews the challenges posed by disease outbreaks, water quality deterioration, and disruptions in seed supply, affecting species such as carp, tilapia, pangasius, and shrimp. Coastal aquaculture is also particularly vulnerable to cyclones, tidal surges, and saline water intrusion, with documented economic losses from events such as Cyclones Yaas, Bulbul, Amphan, and Remal. The study synthesizes key findings related to climate-resilient aquaculture practices, monitoring frameworks, ecosystem-based approaches, and community-based adaptation strategies. It underscores the need for targeted interventions, especially in coastal areas facing increasing salinity levels and frequent storms. This study calls for collective action through policy interventions, research and development, and the promotion of climate-smart technologies to enhance resilience and sustain fisheries and aquaculture in the context of a rapidly changing climate. Full article

Abnormalities were observed in the testes of common carp Cyprinus carpio collected from Willow Beach, Arizona, USA, a site on the lower Colorado River, downstream of Lake Mead and Hoover Dam. Testicular tissue collected from this site in 2003 exhibited numerous large, pigmented macrophage aggregates (MAs) and a novel, previously undescribed hypertrophy and proliferation of putative Sertoli cells. In testes samples collected in 2007, numerous testicular MA, testicular oocytes, and proliferations of Sertoli cells were observed. Three carp collected in 2007 also had raised nodules within the testes, and, microscopically, seminoma, spermatogenic seminoma, and mixed stromal cell–germ cell neoplasms were diagnosed. Several risk factors for these adverse effects were identified. Carp collected at this site in 2003 ranged in age from 35 to 54 years and had the oldest mean age of the thirteen sites sampled within the Colorado River basin. This site also has an unusual thermal regime when compared to other sites studied in Lake Mead and upstream sites, in that temperatures varied little over the seasons (amplitude around 1.5 °C) and barely reached 15 °C. Additionally, carp from this site had the highest total polychlorinated biphenyl (PCB) body burden. Hence, advanced age, low water temperature, and exposure to PCBs and other environmental contaminants may contribute to the observed abnormalities, highlighting the complex environmental factors initiating pre-neoplastic and neoplastic changes in wild carp. Full article

The size and mass of fish are crucial parameters in aquaculture management. However, existing research primarily focuses on conducting fish size and mass estimation under ideal conditions, which limits its application in actual aquaculture scenarios with complex water quality and fluctuating lighting. A non-contact size and mass measurement framework is proposed for complex underwater environments, which integrates the improved FishKP-YOLOv11 module based on YOLOv11, stereo vision technology, and a Random Forest model. This framework fuses the detected 2D key points with binocular stereo technology to reconstruct the 3D key point coordinates. Fish size is computed based on these 3D key points, and a Random Forest model establishes a mapping relationship between size and mass. For validating the performance of the framework, a self-constructed grass carp dataset for key point detection is established. The experimental results indicate that the mean average precision (mAP) of FishKP-YOLOv11 surpasses that of diverse versions of YOLOv5–YOLOv12. The mean absolute errors (MAEs) for length and width estimations are 0.35 cm and 0.10 cm, respectively. The MAE for mass estimations is 2.7 g. Therefore, the proposed framework is well suited for application in actual breeding environments. Full article

Sucralose, a persistent and widely used artificial sweetener, has emerged as a significant contaminant in aquatic environments, raising concerns about its ecological and physiological effects on aquatic species. This study investigates the impact of environmentally relevant concentrations of sucralose on the muscle quality of common carp (Cyprinus carpio), a bioindicator species. Using High-Performance Liquid Chromatography (HPLC), sucralose was quantified in water and fish muscle tissues, revealing its persistence and bioaccumulation. Sucralose exposure disrupted critical physicochemical, textural, and structural properties of fish muscle. Protein carbonyl content increased up to 10-fold, while lipid peroxidation levels rose significantly, indicating oxidative stress. Sulfhydryl groups were reduced by more than 40%, and water-holding capacity decreased by 12%, compromising muscle functionality. Textural profile analysis revealed alterations in hardness, cohesiveness, and elasticity, linked to covalent bond formation induced by protein oxidation. Furthermore, electrophoretic analysis confirmed myosin degradation, underscoring sucralose’s role as a pro-oxidant, even at low concentrations. These findings demonstrate that sucralose can adversely affect aquatic organisms by impairing muscle integrity, with potential consequences for their survival, ecological roles, and food web dynamics. This study underscores the urgent need to regulate and monitor artificial sweeteners in aquatic systems to mitigate long-term ecological impacts. Full article

To assess the influence of dietary bile acid (BA) on the phenotype associated with hepatic lipid metabolism and its regulation of lipid homeostasis in gibel carp (Carassius auratus gibelio) under high-fat diet (HFD) conditions, five HFDs were designed using soybean oil (SO) as the single lipid source and supplemented with 0, 200, 400, 600, and 800 mg/kg BA (designated as BA0, BA200, BA400, BA600, and BA800, respectively). Juvenile fish (32.37 ± 0.13 g) were fed five BA-added HFDs (12% SO) for 8 weeks. Considerably lower levels of aspartate transaminase, alanine aminotransferase, low-density lipoprotein, triglyceride, and total cholesterol in the serum were observed in gibel carp fed with HFDs with 400–600 mg/kg BA (p < 0.05). The hepatocytes of the BA400 and BA600 groups were intact without abnormal architecture or histopathological changes, compared to other groups. The presence of most genes related to fatty acid biosynthesis decreased significantly with the addition of 400–600 mg/kg BA (p < 0.05), while the gene expressions of hormone-sensitive lipase, adiponectin receptor 2, and peroxisome proliferator-activated receptor α were variably up-regulated, along with the elevation of dietary BA (p < 0.05). Critical genes involved in bile acid and cholesterol synthesis were obviously down-regulated in gibel carp receiving 600–800 mg/kg dietary BA (p < 0.05), despite the sterol 27-hydroxylase (cyp27a1) gene in the BA800 group (p < 0.05). Moreover, hepatopancreas from the BA0 and BA600 groups were isolated for transcriptome sequencing, identifying 7040 differentially expressed genes (DEGs). The enriched KEGG pathways of DEGs mainly included steroid biosynthesis, protein digestion and absorption, etc. Seven randomly selected DEGs were validated using qRT-PCR and were in agreement with the RNA-seq results. Consequently, the appropriate supplementation of dietary BA for juvenile gibel carp is recommended at doses of 400–600 mg/kg in SO-based HFDs, which could contribute to the amelioration of HFD-induced excessive fat deposition in the hepatopancreas of gibel carp by both inhibiting fatty acid intake, biosynthesis, and steroid production and enhancing lipid decomposition. The findings may elucidate the physiological role of exogenous BA in fish and its underlying mechanism, providing references for the reasonable application of BA in aquafeeds and the prevention of HFD-induced metabolic dysfunction in fish. Full article

Grass carp (Ctenopharyngodon idella), a key species in freshwater aquaculture, is particularly vulnerable to opportunistic pathogens, including Aeromonas hydrophila and Aeromonas veronii. While the pathogenic mechanisms of individual infections have been extensively characterized, the host immune responses during co-infection remain poorly understood. This research explored the renal pathological alterations and transcriptomic shifts in grass carp subjected to simultaneous infection by A. hydrophila and A. veronii. Mortality occurred as early as 24 h post-challenge, ultimately reaching a cumulative death rate of 65%. Quantitative analysis of renal bacterial burden revealed a marked increase in colonization at 3 days post-infection (dpi). The histopathological assessment showed progressive kidney damage, including tubular collapse, epithelial necrosis, interstitial edema, and widespread epithelial desquamation, with the most severe lesions observed at 5 dpi and partial signs of recovery by 7 dpi. A total of 1106 and 472 genes were found to be differentially expressed at 1 and 5 dpi, respectively, based on transcriptome profiling. The functional enrichment analysis indicated that the differentially expressed genes (DEGs) were mainly involved in the complement and coagulation cascade pathways. Notably, the immune-related genes exhibited a biphasic trend, with predominant downregulation at 1 dpi followed by marked upregulation by 5 dpi, indicating dynamic changes in immune modulation during co-infection. These results provide new insights into host responses during dual bacterial infections in fish and may inform disease prevention strategies in aquaculture. Full article