Methionine (Met) and lysine (Lys), as primary limiting amino acids, play important roles in regulating muscle quality in aquatic animals. This study investigated the effects of dietary Met and Lys supplementation on the growth performance, antioxidant function, and muscle quality of Hefang crucian carp (HCC) using physiological and transcriptomic analyses. Fish were fed three diets for 8 weeks: a basal diet (LA) and two diets supplemented with DL-methionine at 1.7% (MA) and 3.4% (HA), respectively, while L-lysine supplementation was fixed at 3.4%. The results indicated that dietary Met and Lys supplementation had no significant effect on the growth performance of HCC (p > 0.05), but significantly reduced serum triglyceride (TG) and cholesterol levels (T-CHO) (p < 0.05). Additionally, serum total protein (TP) content was significantly increased in the MA group (p < 0.05). Analysis of serum antioxidant enzyme activities indicated that appropriate Met and Lys supplementation improved antioxidant capacity and upregulated the expression of antioxidant-related genes (Nrf2, GPX1a, GSTO1, GSTP1) in the muscle. Moreover, the MA group exhibited superior muscle hardness and gumminess, while the HA group had higher springiness and chewiness (p < 0.05). Muscle fiber density was significantly increased, whereas diameter and area showed opposite trends in fish fed 1.7% Met and 3.4% Lys (p < 0.05). Furthermore, appropriate Met and Lys supplementation significantly affected muscle fiber development genes (MyoD, MyoG, and MRF4), with MyoG highest in the HA group and MyoD and MRF4 highest in the MA group (p < 0.05). Comparative transcriptomic analysis of muscle tissue showed DEGs were mainly enriched in pathways correlated with muscle quality, involving cardiac muscle contraction, actin cytoskeleton regulation, PPAR signaling pathway and ECM-receptor interaction. Taken together, our findings enhance the understanding of the molecular mechanisms underlying the effects of dietary Met and Lys on muscle quality in HCC, providing valuable insights for the development of nutritional strategies in the aquaculture industry.

Aquaculture development increasingly faces the dual requirement of increasing economic output and reducing environmental pressure under limited aquatic resources. Existing studies have examined aquaculture efficiency, environmental performance, and production optimization separately, but region-specific strategies that jointly address economic improvement and environmental-emission mitigation remain insufficiently developed. This study proposes a data-driven modeling and computational framework to identify regional green modes of fishery production, with dual properties of higher economic output and lower environmental-emission intensity. In this framework, data-analysis techniques, including missing-value imputation, regional aquaculture classification, nonlinear variable reconstruction, and Lasso regression, are integrated with scenario-based optimization models under alternative management priorities. By applying the proposed framework to provincial fishery data from China during 2017-2024, the results reveal clear heterogeneity in green fishery production modes across different aquatic-resource systems. In particular, under the economic-priority scenario with emission-reduction constraints, the optimized outputs increase by 11.19% and 6.54% in Zone 1 (an inland freshwater system) and Zone 2 (a coastal-intensive system), respectively. Under the environmental-priority scenario with required economic-growth condition, moderate emission-reduction potential is identified in Zone 1, whereas substantial emission reduction is observed in Zone 2. Furthermore, in view of the determined green fishery strategy by our framework, the nearest-optimum province is identified for each zone. By elasticity analysis, it is further found that technology-extension funding and fishery medicine expenditure are two synergistic production investments in Zones 1 and 2, whereas seedling and feed-related investments display properties of region-specific coordination. Summarily, the proposed computational framework in this paper provides an efficient tool of analyzing the regional green fishery production strategies and the regional heterogeneity in virtue of data-driven modeling and advanced optimization techniques.

This study aimed to compare intestinal architecture, gene expression, and microbiota between Baling Tieshan organic bighead carp (BTOBC) and pond-cultured bighead carp (PCBC) using histological, transcriptomic, and metagenomic approaches. HE staining revealed that BTOBC exhibited more regular villous arrangement, increased villous height, shallower crypt depth, higher villus-to-crypt ratio, and a greater number of goblet cells compared to PCBC. Transmission electron microscopy showed that intestinal microvilli were more tightly arranged, goblet cells displayed more regular and intact morphology, and mast cell degranulation was observed in BTOBC, whereas PCBC showed loosened tight junctions with increased intercellular gaps. Transcriptomic analysis identified 4548 differentially expressed genes (q < 0.05, |log(2)Foldchange| > 2), with "intestinal immune network for IgA production" and "MAPK signaling pathway" as key pathways. BTOBC showed significant upregulation of BCR, BCMA, MHC, IgA, PIgR, and TCR expression (p < 0.05) in "intestinal immune network for IgA production" pathway, alongside downregulation of BSK2, MKP, Evi1, P38, NFAT-2 and CREB in the MAPK signaling pathway (p < 0.05). Immunofluorescence results indicated that sIgA expression levels in the foregut, midgut, and hindgut of BTOBC were significantly higher than those in PCBC (p < 0.05). Metagenomic analysis demonstrated that BTOBC, feeding naturally on phytoplankton, harbored higher relative abundance of Microcystis and lower abundance of potential pathogens Cetobacterium and Aeromonas compared to PCBC (p < 0.05). Further Wilcoxon test-based differential analysis of genes annotated to these 9 signaling pathways identified 10 genes with significant differences (p < 0.05). CARD database analysis detected 52 and 84 antimicrobial-resistance genes in BTOBC and PCBC, respectively, with significantly higher loads in PCBC (p < 0.05). These multi-layer analyses demonstrate that organically raised BTOBC possess a more robust intestinal barrier and functionally superior microbiome, conferring stronger systemic immunity. Our findings provide a theoretical framework for sustainable bighead-carp aquaculture.

Eutrophication significantly impacts on aquatic ecosystems. The accumulation of nutrients such as nitrogen and phosphorus in water bodies leads to a series of ecological problems, including water quality deterioration, reduced dissolved oxygen levels, and decreased transparency. These issues significantly impact the physical and chemical properties of water bodies, the diversity of aquatic organisms, community structure, and ecological functions. Carassius cuvieri (CC) and Triploid Crucian carp No. 2 (TCC) are common freshwater aquaculture fish species with extensive farming foundations and economic value. Their survival and growth are closely tied to environment conditions. This study uses CC and Triploid TCC as research subjects, conducting a 30-day eutrophication aquaculture experiment in a mildly eutrophic water body (TN: 0.868 mg/L; TP: 0 mg/L) as the initial environment. Combining morphological, histological, transcriptomic, inhibitor-treatment, and qRT-PCR techniques, we explored the molecular mechanisms underlying the adaptation of crucian carp to eutrophication environments. The results showed that, as the degree of eutrophication increased, growth indices of both CC and TCC were affected to varying degrees. Peripheral blood cell and histological section observations revealed abnormal blood cell morphology, increased white blood cell counts, nuclear displacement and aggregation in hepatocytes, curved and thinned gill filaments, and broken and damaged gill filaments in both fish species; High-throughput sequencing results showed that differentially expressed genes in liver tissue were primarily enriched in immune-mediated infectious-diseases, lipid-metabolism, and signal-transduction pathways. mRNA expression analysis of crucian carp embryos treated with the TLR5 inhibitor TH1020 suggested that changes in certain genes within the TLRs signaling pathway may be associated with the activation of downstream cascades and the secretion of pro-inflammatory cytokines, collectively facilitating fish adaptation eutrophication. This study provides scientific experimental evidence for optimising large-scale fish farming models, monitoring of aqua-culture environmental quality, and maintaining the balance of aquatic ecosystems. TCC copes better with eutrophication through stronger antioxidant and immune responses, whereas CC shows more pronounced gill and liver damage.

In aquaculture, ecological adaptability and stress resistance are two critical determinants of breeding and production values for the farmed fish. As an economically important species, cultivation of Megalobrama amblycephala is limited often by its lower hypoxia tolerance in practice. In this paper, a technique of acute cold stress is proposed to induce its hypoxia tolerance during early embryonic development, and a subpopulation of Megalobrama amblycephala with normal survival rates is successfully established. It is found that there exists highly expressed foxo3b in this subpopulation, and using the primary cells isolated from the larvae of Megalobrama amblycephala, a cell model is constructed to simulate the acute cold stress in vitro. On the basis of the proposed cell model, it is shown that the samples with high foxo3b expression can mitigate the effects of acute cold exposure, owing to the activated antioxidant genes, the reduced oxidative damage, and the alleviated cold stress-induced apoptosis. It is also demonstrated that the highly expressed foxo3b can positively regulate hif-3α transcription, which subsequently modulates the metabolic profiles under hypoxic conditions through the HIF-3α/PPAR-γ pathway. Consequently, hypoxia tolerance of Megalobrama amblycephala is enhanced. Clearly, these results are beneficial for cultivating new aquaculture strains with lower oxygen tolerance traits.

Bitterling (Rhodeus ocellatus), particularly in male, is renowned for its vibrant color and the potential stronger aesthetic appeal. However, their biological coloration mechanism is still unclear. In this study, we first compared the cytological differences of body color between the female and male bitterling, and the results indicate that the specific distributional features of erythrophores play a fundamental role in forming the sexual dimorphism of body color in bitterling. By analyzing the transcriptomic data from different body color areas of male bitterling, it is further revealed that the genes associated with carotenoid metabolism (scarb1, bco1, plin2, cyp2j4), melanin synthesis (wnt2), and pteridine synthesis (spr, gch1) are closely related to the body color formation of male bitterling. Particularly, myh1s gene is identified to be associated with formation of the red and yellow body color in the fish. Clearly, these findings can provide insights into the cellular basis of body color formation and highlight the potential roles of myh1s gene in deepening understanding pigment cell development and farming ornamental fish.

Targeted delivery technology has significant technological advantages owing to its high efficiency, strong specificity, and reliable biosafety. However, its application in aquatic species remains limited. In this study, we identificate a conserved receptor-binding site in N-terminal domain of vitellogenin (VtgN) from cyprinid species. An ovarian-targeted delivery system is established in cyprinid fish. Using VtgN-mediated delivery cyp19a1a, we successfully induced functional females in an all-male cyp19a1a- /- population. These findings facilitate the development of a novel, safe, and controllable strategy for fish genetic manipulation. Furthermore, this approach offers significant potential for single-sex breeding and functional genomics research in aquaculture.

Artificial gynogenesis provides one of efficient strategies for fish germplasm improvement. But in aquaculture practice, it is still difficult to expand the offspring population and breeding scale owing to the unisexuality of gynogenetic strains. This study indicates that the gynogenesis blunt snout bream (GBSB), an all-female population, can be sex reversal to the pseudo-male at high temperatures of 34 +/- 1 degrees C. By hormone test experiments on GBSB, it is validated that higher temperature causes a decreasing estrogen level and an increasing androgen level. Observation results also show that the two-year old pseudo male GBSB reaches sexual maturity and produces functional haploid sperms. Genotypic sex identification further confirms that the absence of male genetic marker for blunt snout bream in the pseudo-male GBSB. It is concluded that high-temperature cultivation is an effective strategy of inducing the sex reversal of GBSB, and the results can lay a foundation for large scale breeding of gynogenesis strains in fish.

The delivery of antigens into host cells via the type III secretion system (T3SS) represents a highly effective strategy employed by bacteria to elicit host immune responses and protect against bacterial infections. In this study, we engineered recombinant strains by heterologously biosynthesizing the T3SS from Photorhabdus luminescens TT01 in the avirulent Aeromonas salmonicida DBFF01 strain using tilapia and carp as model. The GAPDH from Edwardsiella tarda was N-terminally fused with the translocation signal of the type III effector LopT and co-expressed with its chaperone, SlcT, in T3SS-expressing A. salmonicida DBFF01, thereby constructing a bivalent vaccine targeting both E. tarda and A. salmonicida. The detection of GAPDH delivery in eukaryotic cells indicates that the heterologous biosynthetic T3SS in A. salmonicida DBFF01 possesses functional activity and can effectively transport GAPDH to carp epithelial cells (EPCs). In vivo trials revealed that tilapia immunized with the bivalent vaccine achieved 100 % relative percentage survival rate when challenged with lethal E. tarda EIB202. Furthermore, the recombinant strains effectively colonized fish tissues without inducing pathology. The vaccination significantly enhanced innate immune enzyme activities and elevated serum IgM levels as well as proinflammatory cytokines (IL-6, TNF-alpha, IFN-alpha), and antigen-presenting cell (APC) activation. These findings establish T3SS as a versatile and potent tool for vaccine delivery in aquaculture, combining high efficacy, safety, and robust immune activation to combat bacterial pathogens.

Dynamic developmental states of follicles are regarded to be determinants of sexual maturation in fish ovaries. However, it is still a challenge to identify the critical points at which the developmental processes of different types of follicles interact and affect the ovarian development. In this study, four subtypes of the primary follicle (PF) in the ovarian folliculogenesis of zebrafish, i.e., the so-called PF-i, PF-ii, PF-iii, and PF-iv, are first identified by discontinuous NaCl-Percoll gradient centrifugation, as well as their respective morphological features. Then, for the four subtypes of PFs, stage-specific comparative analysis is employed to identify the differentially expressed genes and the differentially methylated regions, which have been validated to be significantly enriched in biological processes encompassing ribosomal biogenesis, meiotic progression, transcriptional regulation, and mitochondrial respiration. Results from transcriptional analysis further demonstrate significant changes in the expression profiles at different developmental stages from the PF-ii to the PF-iii. By molecular biology identification, it is shown that the enhancement of Notch and mTOR pathways can significantly regulate the ovarian development through the pacing effect of primary follicles. Clearly, all these uncovered results could provide a deeper understanding of the initial regulation of ovarian maturation, as well as a new multidisciplinary analytic tool to study follicle candidate regulators in the developmental process of other fish.

Hypoxic stress causes cell damage and serious diseases in organisms, especially in aquatic animals. It is important to elucidate the changes in metabolic function caused by hypoxia and the mechanisms underlying these changes. This study focuses on the low oxygen tolerance feature of a new blunt snout bream strain (GBSBF1). Our data show that GBSBF1 has a different lipid and carbohydrate metabolism pattern than wild-type bream, with altering glycolysis and lipid synthesis. In GBSBF1, the expression levels of phd2 and vhl genes are significantly decreased, while the activation of HIF-3α protein is observed to have risen significantly. The results indicate that enhanced HIF-3α can positively regulate gpd1ab and gpam through PPAR-γ, which increases glucose metabolism and reduces lipolysis of GBSBF1. This research is beneficial for creating new aquaculture strains with low oxygen tolerance traits.

Azoospermia and asthenospermia are common manifestations of male infertility, but it needs further studies to understand the intrinsic regulation mechanism. As a popular model organism, zebrafish is often used to assess reproductive complications. In this study, by analyzing miRNA transcriptome of the mature triploid zebrafish testis afflicted with spermatogenic dysfunctions, leading to the identification of 36 miRNAs that are differentially expressed in comparison with diploid, which are predicted to target 2737 genes. Subsequent functional annotation of these genes pinpointed two miRNAs might association with spermatogenesis. Inhibitory experiments showed that NC_007115.7.7_998413 inhibited conducts a substantial decline in sperm density, and conducted lower embryo fertilization rate than control. And putative target genes qRT-PCR evaluation showed that spata2 was significant down-regulate upon inhibited NC_007115.7.7_998413. In summary, this research positions newly identified miRNA NC_007115.7.998413 as a regulatory factor in male zebrafish reproductive development, enhancing our comprehension of the molecular regulated pathways involved in spermatogenesis.

Muscle is one of the important quality of fish. However, there is still a lack of sufficient understanding of the mechanism of muscle growth regulation in fish. In this study, the expression patterns of 10 reported muscle development related genes are analyzed in zebrafish during growth or under water flow stress. Myogenic regulatory factors (MyoD, MyoG, MRF4), myostatin regulatory genes (Mstna, Mstnb) and myoblast development-related genes (Pax7, Prmt5, Desmin, MYHC) are significantly increased expression at somite stage and muscle effect stage embryos in zebrafish. The mRNA levels of the muscle development related genes are up-regulated in 7-day fries and 30-day juvenile of zebrafish. And there are differences in the expression levels of seven muscle development related genes (MyoD, Myf5, MyoG, Mstna, Mstnb, Desmin, MYHC) between the large and small individuals of 20-day-old zebrafish. Results indicated that short-term water flow stressing can promote zebrafish muscle growth, while prolonged water flow stress may lead to motor fatigue and affect growth in zebrafish. This research provides a foundation for further exploration of the growth regulation mechanism in fish, and is helpful on fish farming.

The softshell turtle genus Pelodiscus has a long and complex taxonomic history. It was long believed that no specimens of the original description of Pelodiscus axenaria exist and as such, a detailed description and molecular phylogenetic analysis of P. axenaria from its type specimen locality Taoyuan, Hunan, China, were not possible. Recent studies revealed that P. axenaria belongs to a species complex comprising at least four morphologically challenging but genetically divergent lineages. In this study, we redescribe the original type specimen series (4 males and 6 females) of P. axenaria from Yuanjiang area of Taoyuan based on morphological and molecular evidence. Our molecular phylogenetic analysis provided evidence that Pelodiscus shipian and Pelodiscus jiangxiensis clearly cluster within our P. axenaria clade and as such should be regarded as junior synonyms of Pelodiscus axenaria. The specimens that Gong et al. (2022) regarded as P. axenaria in their studies, clearly represent a new and herein newly described species. The proposed neotype of P. axenaria by Gong et al. (2022), which represents this new species, is designated as the holotype of this new species, Pelodiscus huike sp. nov.

GCN2-eIF2α signaling pathway plays crucial roles in cell growth,development, and protein synthesis. However, in polyploid fish, the function of this pathway is rarely understood. In this study, genes associated with the GCN2-eIF2α pathway (pkr, pek, gcn2, eif2α) are founded lower expression levels in the triploid crucian carp (3nCC) muscle compared to that of the red crucian carp (RCC). In muscle effect stage embryos of the 3nCC, the mRNA levels of this pathway genes are generally lower than those of RCC, excluding hri and fgf21. Inhibiting gcn2 in 3nCC embryos downregulates downstream gene expression (eif2α, atf4, fgf21), accelerating embryonic development. In contrast, overexpressing of eif2α can alter the expression levels of downstream genes (atf4 and fgf21), and decelerates the embryonic development. These results demonstrate the GCN2-eIF2α pathway's regulatory impact on 3nCC growth, advancing understanding of fish rapid growth genetics and offering useful molecular markers for breeding of excellent strains.

Sinilabeo decorus tungting（Nichols） is a wild endemic fish in Hunan Province, however, due to overfishing and environmental damage, the germplasm resources of wild S. decorus tungting are scarce. In order to effectively protect germplasm resources of S. decorus tungting, artificial breeding research has been carried out. In the process of domestication and parental cultivation, it was found that there were two somatotypes in the wild population: the high-back type and the flatback type. The countable traits analysis showed that there was no significant difference between the two different somatotypes S. decorus tungting on fin formula and scales. To explore the genetic differences between the two somatotypes of S. decorus tungting, Cytb and ITS1 gene sequences were used as molecular markers to analyze the genetic differences. The results showed that based on the Cytb and ITS1 gene sequences, both the high-back type and the flatback type were showed a bias in base composition. And two somatotypes of S. decorus tungting were showed high haplotype diversity and low nucleotide diversity. In addition, the results of genetic distance analysis and NJ tree construction showed that the degree of genetic differentiation of the two somatotypes was low, which did not reach the level of population differentiation. In conclusion, the high-back type and flatback type belongs to the same population.The results of this study enriched the molecular biological data of S. decorus tungting, and provided theoretical basis for the protection and industrial development of S. decorus tungting germplasm resources. The reasons for the formation of the high back type of S. decorus Tungting was unknown and needs further study.

Gene editing technique has been widely applied for gene function characterization. However, such an approach is often time-consuming to obtain homozygous mutant. In this article, through timing the earlier injection of embryos, the gene editing efficiency is significantly improved, and together with the technique of the UV inactivated sperm and heat shock treatment for blocking the first cleavage, the gene-edited homozygous zebrafish are successfully obtained in F0 generation, rather than in the third or more generations as reported in the existing results. It is concluded that genetic purification of artificial gynogenesis can play critical role in more efficiently preparing the gene-edited homozygous individuals in fish.

Triploid crucian carp is a new breed of aquaculture with rapid growth characteristics. However, its growth regulation mechanism has not yet been elucidated. In this study, our results show that the expression levels of mTOR signaling pathway-related genes (AKT1, AKT2, AKT3, mTOR, 4E-BP1 and S6K1) are higher in the muscle and intestine tissues of triploid crucian carp than those of diploid red crucian carp. Embryos of triploid crucian carp exhibit a faster growth rate comparing to red crucian carp. And in muscle effect stage, the mRNA levels of mTOR signaling pathway related genes in triploid crucian carp are higher than red crucian carp, except for AKT2. Inhibition of mTOR activity with rapamycin leads to slower embryonic development and the eliminated expression of mTOR in the embryos of neurula, muscle effect, and eye pigmentation stages. Conversely, overexpression of the upstream gene AKT2 can promote the development of zebrafish embryos and affect the expression of mTOR signaling pathway. These data highlight the significant role of mTOR signaling pathway in regulating fish embryonic development and rapid growth, and might offer new insights and avenues for exploring fish embryonic development, improving fish growth.