Freshwater Fisheries Research Center

BACKGROUND: An emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively. RESULTS: The assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes. CONCLUSION: As the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology.

Abstract Global aquaculture development increased rapidly in recent years, and the sector has become one of the fastest‐growing industries in the animal‐derived food production system. However, disease outbreak remains a major challenge that hinders sustainable production through an advanced level of intensification. Recently, antibiotics applied have been restricted globally against aquatic disease outbreaks due to their apparent accumulation in the tissues, which imposes on the development of resistant bacteria. Naturally available medicinal plants were tested to combat some pathogens affecting humans and animals, as they contain a wide range of active substances that can induce biological functions. Currently, medicinal plants are being tested in aquaculture as a safe and eco‐friendly substance to modulate immune status, enhance growth performance and prevent fish disease. Moreover, different parts (e.g. leaf, flower and rhizome) and forms (e.g. crude, extract and active ingredient) of plants are used to modulate specific biological functions (e.g. growth promoter, anti‐stress, immunostimulants, appetite stimulation, antibacteria, anti‐parasite and anti‐virus). Medicinal plants are also used to defend the aquaculture animal from external stressors, such as poor water quality, high environmental temperature and overcrowding. This paper aims to provide information on the role of currently used medicinal plants on aquaculture animals and their action mechanisms. In conclusion, the current review suggested that the utilisation of medicinal plants remained untapped in uncovering the biological activities of active substances against a variety of diseases across diverse species of aquaculture animals.

Abstract China has dominated global aquaculture production for more than two decades. Aquaculture production in China increased from 24.6 million metric tons (mmt) in 2000 to 47.5 mmt in 2014, an increment of 93.1%. Along with the fast‐growing aquaculture industry, aquafeed production in China increased from 5.1 mmt in 2000 to 19.0 mmt in 2014, an increment of 272.5%. However, despite the rapid increase in aquafeed production, the fishmeal usage in aquafeeds in China has remained stable over the years. Fishmeal imports into China remained relatively steady at 1.0–1.5 mmt per annum from 2000 to 2014. An often unacknowledged fact is that China contributes more than 60% to the world aquaculture production at a cost of only 25–30% of the world fishmeal output. This review attempts to explain why the fishmeal usage has not increased proportionately with the increasing aquafeed production in China from several angles: (i) the current status of fishmeal usage in Chinese aquaculture; (ii) the relationship between the decreasing dietary inclusions of fishmeal and improved feed techniques, especially the use of alternative protein sources for fishmeal; (iii) the dominance of Chinese aquaculture by low trophic level species of plants, filter feeders, herbivores and omnivores and consequent low demands for fishmeal; and (iv) the increasing price of fishmeal and the management of exploitation of wild fisheries in the main fishmeal exporting countries to China. The trends and prospects of fishmeal usage in the future in Chinese aquaculture and the associated consequences are also addressed. Like other countries, China is now actively developing both resource conservation‐based capture fisheries and environment‐friendly freshwater and marine aquaculture systems. Aquaculture will be the main source of aquatic food in the future and will also indirectly contribute to save the world wild fisheries, and China will be main player that will continue to contribute towards this end.

The current status of the farming of Macrobrachium species in China is presented, including the scale of production and with an emphasis on its farming technology. The problems faced and research needed for the further development of freshwater prawn farming of China is also reviewed. Finally, this paper discusses the prospects and future expansion in this sector of national aquaculture.

The aquafeed industry continues to expand in response to the rapidly growing aquaculture sector. However, the identification of alternative protein sources in aquatic animal diets to replace conventional sources due to cost and sustainability issues remains a major challenge. Recently, insects have shown tremendous results as potential replacers of fishmeal in aquafeed. The present study aimed to review the utilization of insects in aquafeeds and their effects on aquatic animals' growth and feed utilization, immune response and disease resistance, and fish flesh quality and safety. While many insect species have been investigated in aquaculture, the black soldier fly (Hermetia illucens), and the mealworm (Tenebrio molitor) are the most studied and most promising insects to replace fishmeal in aquafeed. Generally, insect rearing conditions and biomass processing methods may affect the product's nutritional composition, digestibility, shelf life and required insect inclusion level by aquatic animals. Also, insect-recommended inclusion levels for aquatic animals vary depending on the insect species used, biomass processing method, and test organism. Overall, while an appropriate inclusion level of insects in aquafeed provides several nutritional and health benefits to aquatic animals, more studies are needed to establish optimum requirements levels for different aquaculture species at different stages of development and under different culture systems.

BACKGROUND: A large number of single nucleotide polymorphisms (SNPs) have been identified in common carp (Cyprinus carpio) but, as yet, no high-throughput genotyping platform is available for this species. C. carpio is an important aquaculture species that accounts for nearly 14% of freshwater aquaculture production worldwide. We have developed an array for C. carpio with 250,000 SNPs and evaluated its performance using samples from various strains of C. carpio. RESULTS: The SNPs used on the array were selected from two resources: the transcribed sequences from RNA-seq data of four strains of C. carpio, and the genome re-sequencing data of five strains of C. carpio. The 250,000 SNPs on the resulting array are distributed evenly across the reference C.carpio genome with an average spacing of 6.6 kb. To evaluate the SNP array, 1,072 C. carpio samples were collected and tested. Of the 250,000 SNPs on the array, 185,150 (74.06%) were found to be polymorphic sites. Genotyping accuracy was checked using genotyping data from a group of full-siblings and their parents, and over 99.8% of the qualified SNPs were found to be reliable. Analysis of the linkage disequilibrium on all samples and on three domestic C.carpio strains revealed that the latter had the longer haplotype blocks. We also evaluated our SNP array on 80 samples from eight species related to C. carpio, with from 53,526 to 71,984 polymorphic SNPs. An identity by state analysis divided all the samples into three clusters; most of the C. carpio strains formed the largest cluster. CONCLUSIONS: The Carp SNP array described here is the first high-throughput genotyping platform for C. carpio. Our evaluation of this array indicates that it will be valuable for farmed carp and for genetic and population biology studies in C. carpio and related species.

The Asian arowana (Scleropages formosus), one of the world's most expensive cultivated ornamental fishes, is an endangered species. It represents an ancient lineage of teleosts: the Osteoglossomorpha. Here, we provide a high-quality chromosome-level reference genome of a female golden-variety arowana using a combination of deep shotgun sequencing and high-resolution linkage mapping. In addition, we have also generated two draft genome assemblies for the red and green varieties. Phylogenomic analysis supports a sister group relationship between Osteoglossomorpha (bonytongues) and Elopomorpha (eels and relatives), with the two clades together forming a sister group of Clupeocephala which includes all the remaining teleosts. The arowana genome retains the full complement of eight Hox clusters unlike the African butterfly fish (Pantodon buchholzi), another bonytongue fish, which possess only five Hox clusters. Differential gene expression among three varieties provides insights into the genetic basis of colour variation. A potential heterogametic sex chromosome is identified in the female arowana karyotype, suggesting that the sex is determined by a ZW/ZZ sex chromosomal system. The high-quality reference genome of the golden arowana and the draft assemblies of the red and green varieties are valuable resources for understanding the biology, adaptation and behaviour of Asian arowanas.

BACKGROUND: Oriental river prawn, Macrobrachium nipponense, is a commercially important species found in brackish and fresh waters throughout China. Chronic hypoxia is a major physiological challenge for prawns in culture, and the hepatopancreas, muscle and gill tissues play important roles in adaptive processes. However, the effects of dissolved oxygen availability on gene expression and physiological functions of those tissues of prawns are unknown. Adaptation to hypoxia is a complex process, to help us understand stress-sensing mechanism and ultimately permit selection for hypoxia- tolerant prawns, we performed transcriptomic analysis of juvenile M. nipponense hepatopancreas, gill and muscle tissues by RNA-Seq. RESULTS: Approximately 46,472,741; 52,773,612 and 58,195,908 raw sequence reads were generated from hepatopancreas, muscle and gill tissues, respectively. A total of 62,722 unigenes were generated, of the assembled unigenes, we identified 8,892 genes that were significantly up-regulated, while 5,760 genes were significantly down-regulated in response to chronic hypoxia. Genes from well known functional categories and signaling pathways associated with stress responses and adaptation to extreme environments were significantly enriched, including genes in the functional categories "response to stimulus", "transferase activity" and "oxidoreductase activity", and the signaling pathways "oxidative phosphorylation", "glycolysis/gluconeogenesis" and "MAPK signaling". The expression patterns of 18 DEGs involved in hypoxic regulation of M. nipponense were validated by quantitative real-time reverse-transcriptase polymerase chain reactions (qRT-PCR; average correlation coefficient = 0.94). In addition, the hepatopancreas and gills exhibited histological differences between hypoxia and normoxia groups. These structural alterations could affect the vital physiological functions of prawns in response to chronic hypoxia, which could adversely affect growth and survival of M. nipponense. CONCLUSIONS: Gene expression changes in tissues from the oriental river prawn provide a preliminary basis to better understand the molecular responses of M. nipponense to chronic hypoxia. The differentially expressed genes (DEGs) identified in M. nipponense under hypoxia stress may be important for future genetic improvement of cultivated prawns or other crustaceans through transgenic approaches aimed at increasing hypoxia tolerance.

BACKGROUND: The oriental river prawn, Macrobrachium nipponense, is an important aquaculture species in China, even in whole of Asia. The androgenic gland produces hormones that play crucial roles in sexual differentiation to maleness. This study is the first de novo M. nipponense transcriptome analysis using cDNA prepared from mRNA isolated from the androgenic gland. Illumina/Solexa was used for sequencing. METHODOLOGY AND PRINCIPAL FINDING: The total volume of RNA sample was more than 5 ug. We generated 70,853,361 high quality reads after eliminating adapter sequences and filtering out low-quality reads. A total of 78,408 isosequences were obtained by clustering and assembly of the clean reads, producing 57,619 non-redundant transcripts with an average length of 1244.19 bp. In total 70,702 isosequences were matched to the Nr database, additional analyses were performed by GO (33,203), KEGG (17,868), and COG analyses (13,817), identifying the potential genes and their functions. A total of 47 sex-determination related gene families were identified from the M. nipponense androgenic gland transcriptome based on the functional annotation of non-redundant transcripts and comparisons with the published literature. Furthermore, a total of 40 candidate novel genes were found, that may contribute to sex-determination based on their extremely high expression levels in the androgenic compared to other sex glands,. Further, 437 SSRs and 65,535 high-confidence SNPs were identified in this EST dataset from which 14 EST-SSR markers have been isolated. CONCLUSION: Our study provides new sequence information for M. nipponense, which will be the basis for further genetic studies on decapods crustaceans. More importantly, this study dramatically improves understanding of sex-determination mechanisms, and advances sex-determination research in all crustacean species. The huge number of potential SSR and SNP markers isolated from the transcriptome may shed the lights on research in many fields, including the evolution and molecular ecology of Macrobrachium species.

To investigate the effects of different carbohydrate (CHO) levels in the diet of Wuchang bream Megalobrama amblycephala, the fish were randomly divided into six treatment groups. Five groups were fed 19, 25, 31, 38 and 47% CHO, respectively, for 8 weeks, and a control group was fed a diet with no CHO. Growth performance and feed utilization were significantly (P < 0.05) affected by the dietary carbohydrate level. Maximum weight gain and specific growth rate occurred at the 31% dietary carbohydrate level. Compared to the control, the 31% CHO group had a significantly increased serum total protein content, respiratory burst activity of leucocytes, serum complement 3 (C3) levels, serum lysozyme activity, serum alkaline phosphatase (AKP) activity and hepatic total antioxidative capacity (T-AOC), as well as a decrease in serum glutamic-oxaloacetic transaminase (GOT) activity. Compared to the control, the 47% CHO group had significantly increased serum GOT activity, and a tendency toward an increase in serum cortisol content and a decrease in serum lysozyme activity, hepatic superoxide dismutase (SOD) activity and T-AOC. The relative level of hepatic heat shock protein 70 (HSP70) mRNA in fish fed the 38% CHO diet was significantly higher than those of fish fed the 19, 25 and 31% CHO diets, respectively (P < 0.05). After challenge with Aeromonas hydrophila, fish fed the 47% CHO had the significantly lowest post-challenge survival, and fish fed the 31% CHO had the significantly highest post-challenge survival (P < 0.05). The results of this study suggest that ingestion of excessive dietary CHO can impact the non-specific immune responses, decrease the hepatic antioxidant abilities, and thus affect the health status of M. amblycephala.

Quantitative real-time PCR (qPCR) is widely used in molecular biology, although the accuracy of the quantitative results is determined by the stability of the reference genes used. Recent studies have investigated suitable reference genes for some crustaceans under various conditions, but studies in Macrobrachium nipponense are currently lacking. In this study, we selected the following seven genes from among 35 commonly used housekeeping genes as candidate qPCR reference genes for temporal and spatial expression: EIF (eukaryotic translation initiation factor 5A), 18S (18S ribosomal RNA), EF-1α (elongation factor-1α), GAPDH (glyceraldehyde-3-phosphate dehydrogenase), TUB (α-tubulin), β-act (β-actin), and RPL18 (Ribosomal protein L18). The stability of each reference gene was evaluated by GeNorm, NormFinder, BestKeeper, and comparative ∆C t methods, and was comprehensively ranked using RefFinder. RPL18 was shown to be the most suitable reference gene for adult M. nipponense tissues, while EIF was the most stable in different ovarian and embryo stages and in white spot syndrome virus infection, and β-act was the most stable reference gene under hypoxia stress. The reliability of the rankings was confirmed by RNA interference experiments. To the best of our knowledge, this represents the first systematic analysis of reference genes for qPCR experiments in M. nipponense, and the results will provide invaluable information for future research in closely related crustaceans.

BACKGROUND: The Chinese mitten crab, Eriocheir sinensis, is one of the most studied and economically important crustaceans in China. Its transition from a swimming to a crawling method of movement during early development, anadromous migration during growth, and catadromous migration during breeding have been attractive features for research. However, knowledge of the underlying molecular mechanisms that regulate these processes is still very limited. FINDINGS: A total of 258.8 gigabases (Gb) of raw reads from whole-genome sequencing of the crab were generated by the Illumina HiSeq2000 platform. The final genome assembly (1.12 Gb), about 67.5 % of the estimated genome size (1.66 Gb), is composed of 17,553 scaffolds (>2 kb) with an N50 of 224 kb. We identified 14,436 genes using AUGUSTUS, of which 7,549 were shown to have significant supporting evidence using the GLEAN pipeline. This gene number is much greater than that of the horseshoe crab, and the annotation completeness, as evaluated by CEGMA, reached 66.9 %. CONCLUSIONS: We report the first genome sequencing, assembly, and annotation of the Chinese mitten crab. The assembled draft genome will provide a valuable resource for the study of essential developmental processes and genetic determination of important traits of the Chinese mitten crab, and also for investigating crustacean evolution.

How two subgenomes in allo-tetraploids adapt to coexistence and coordinate through structure and expression evolution requires extensive studies. In the present study, we report an improved genome assembly of allo-tetraploid common carp, an updated genome annotation of allo-tetraploid goldfish and the chromosome-scale assemblies of a progenitor-like diploid Puntius tetrazona and an outgroup diploid Paracanthobrama guichenoti. Parallel subgenome structure evolution in the allo-tetraploids was featured with equivalent chromosome components, higher protein identities, similar transposon divergence and contents, homoeologous exchanges, better synteny level, strong sequence compensation and symmetric purifying selection. Furthermore, we observed subgenome expression divergence processes in the allo-tetraploids, including inter-/intrasubgenome trans-splicing events, expression dominance, decreased expression levels, dosage compensation, stronger expression correlation, dynamic functionalization and balancing of differential expression. The potential disorders introduced by different progenitors in the allo-tetraploids were hypothesized to be alleviated by increasing structural homogeneity and performing versatile expression processes. Resequencing three common carp strains revealed two major ecotypes and uncovered candidate genes relevant to growth and survival rate.

The authors examined the current status of sturgeon aquaculture in China, including its geographic distribution, an account on farmed species, overall production trends, state of controlled reproduction, seedling output and export. The study is based on a nationwide survey of 125 farms undertaken July and August 2009 together with data from previous studies. The census shows that: (i) the main provinces in increasing order of production are Sichuan (including Chongqing), Beijing, Hubei, Shandong and Hunan, (ii) Acipenser baerii, (and its hybrids) and A. schrenckii are the dominant cultured species, accounting for 95% of the total production, (iii) the production of farmed sturgeon has experienced a steady increase, from 17 424 t in 2006 to 21 000 t in 2009, (iv) the total reserves of captive stocks have continuously increased, reaching at present an estimated 1.22 million individuals, (v) the total supply of fertilized eggs or larvae from farmed broodstocks in China has gone up during the past 3 years, and can now basically meet the domestic demand for farming, while the number of seedlings obtained from the wild and imported from other countries gradually declined, and (vi) since 2006, China has started to export farmed caviar and the exports have been increasing year by year, meanwhile, the number of caviar processing factories has also increased. Moreover, other value-added products derived from farmed sturgeon (e.g. medical and health products, cosmetics, leather etc.) appeared in recent years on China markets. Corresponding to the sturgeon aquaculture development in China, some additional future aquaculture strategies are discussed: (i) make full use of the resources, (ii) strengthen management strategies and upgrade the culture techniques, (iii) develop and implement labeling systems for good quality control, (iv) foster deep-processing (value added products) in sturgeon farming to widen market options, (v) enhance extensive genetic studies and research on gynogenesis and cryopreservation of gametes for better resource management, (vi) improve the knowledge on early sex-differentiation in sturgeon, and (vii) prepare standards for management of sustainable sturgeon aquaculture. Considering the current progress of sturgeon aquaculture, the prospects of future sturgeon farming are assessed: (i) there will be a potential for considerable aquaculture to serve the caviar market, and farmed caviar may replace wild products, (ii) product diversification will increase and target for export markets, (iii) hatchery operations to produce juveniles from controlled reproduction will completely replace supply from wild and imported resources, and (iv) an industry chain will be gradually established to ensure sustainable sturgeon aquaculture production in China.

The authors reviewed the aquacultural history of Acipenseriformes in China, related the legal status and examined the current status of the cultured species or hybrids, origins of seedlings, quantities of production, geographic distribution in farming, and the sustainability for both restocking programmes and human consumption. The census shows that since 2000, the production of cultured sturgeons in China appears to have become the largest in the world. As of 2000, the rapid growth of sturgeon farming in China mainly for commercial purposes has shifted harvests in the Amur River from caviar production to the artificial culture of sturgeon seedlings. This dramatic development has also caused a series of extant and potential problems, including insufficient market availability and the impact of exotic sturgeons on indigenous sturgeon species. Annual preservation of sufficient higher-age sturgeons should be a national priority in order to establish a sustainable sturgeon-culture industry and to preserve a gene pool of critically endangered sturgeon species to prevent their extinction.

BACKGROUND: Genetic diversity within a species reflects population evolution, ecology, and ability to adapt. Genome-wide population surveys of both natural and introduced populations provide insights into genetic diversity, the evolutionary processes and the genetic basis underlying local adaptation. Grass carp is the most important freshwater foodfish species for food and water weed control. However, there is as yet no overall picture on genetic variations and population structure of this species, which is important for its aquaculture. RESULTS: We used 43,310 SNPs to infer the population structure, evidence of local adaptation and sources of introduction. The overall genetic differentiation of this species was low. The native populations were differentiated into three genetic clusters, corresponding to the Yangtze, Pearl and Heilongjiang River Systems, respectively. The populations in Malaysia, India and Nepal were introduced from both the Yangtze and Pearl River Systems. Loci and genes involved in putative local selection for native locations were identified. Evidence of both positive and balancing selection was found in the introduced locations. Genes associated with loci under putative selection were involved in many biological functions. Outlier loci were grouped into clusters as genomic islands within some specific genomic regions, which likely agrees with the divergence hitchhiking scenario of divergence-with-gene-flow. CONCLUSIONS: This study, for the first time, sheds novel insights on the population differentiation of the grass carp, genetics of its strong ability in adaption to diverse environments and sources of some introduced grass carp populations. Our data also suggests that the natural populations of the grass carp have been affected by the aquaculture besides neutral and adaptive forces.

Hepatic steatosis is the most common phenomenon of lipid metabolism disorder in farmed fish, but its molecular mechanism is poorly understood. Therefore, the present study was aimed to investigate steatosis induced by high-fat diet (HFD) and explore underlying mechanism in tilapia. The fish were fed on control diet or HFD for 90 days. The blood and liver tissues were collected to determine biochemical parameters, genes expression and proteins level after 30, 60 and 90 days and analyzed lipid accumulation, endoplasmic reticulum (ER) stress and autophagy. After 30 days of feeding, the plasma and hepatic lipid content (TG, TCH, LDL-C and HDL-C) and fatty acids (FAs) transportation (fabp1 and CD36) were enhanced significantly in HFD-fed tilapia. After 60 days, the lipid metabolism disorder, such as increase of TG synthesis and free CH formation, and decrease of FAs β-oxidation and biosynthesis, was observed in liver of HFD-fed tilapia. Further, with increasing lipid accumulation, ER stress was induced and worsen hepatic steatosis via activating IRE1 signaling pathway in liver of HFD group after 90 days. Meanwhile, the autophagy was suppressed via impairing AMPK and BFET pathways in HFD-fed tilapia liver after 90 days. Our results demonstrated that HFD feeding induced extensive lipid deposition, promoted ER stress, suppressed autophagy in tilapia liver. Interestingly, these pathological features were positively correlated with the duration of HFD feeding.

The research documented in this article estimates the levels and determinants of farm-level technical efficiencies (TE) in freshwater pond polyculture systems in China, India, Thailand, and Vietnam. The levels of country-specific TE were estimated for different production intensity levels by estimating stochastic production frontier functions involving the model for technical inefficiency effects. The results were compared with estimates from past studies of aquaculture TE. It was found that yield, input levels, and TE increases in line with intensity levels. TE estimates ranged from 42% among extensive farms in Vietnam to 93% among intensive farms in China. For low intensity farms, increased technical efficiency, and the resulting increased productivity, could be achieved by increasing human capital (through effective and efficient training and extension), provision of basic infrastructure (such as roads), easier access to seed supplies, and security of tenure or a well-defined system of land use rights. Increasing technical efficiency and productivity among intensive farms will result more from the continuous development of new technology and cross-country technology transfer. However, the realization of these potential increases in TE depends on governments in these countries continuing to provide adequate support for freshwater aquaculture development.

Natural selection and selective breeding for genetic improvement have left detectable signatures within the genome of a species. Identification of selection signatures is important in evolutionary biology and for detecting genes that facilitate to accelerate genetic improvement. However, selection signatures, including artificial selection and natural selection, have only been identified at the whole genome level in several genetically improved fish species. Tilapia is one of the most important genetically improved fish species in the world. Using next-generation sequencing, we sequenced the genomes of 47 tilapia individuals. We identified a total of 1.43 million high-quality SNPs and found that the LD block sizes ranged from 10-100 kb in tilapia. We detected over a hundred putative selective sweep regions in each line of tilapia. Most selection signatures were located in non-coding regions of the tilapia genome. The Wnt signaling, gonadotropin-releasing hormone receptor and integrin signaling pathways were under positive selection in all improved tilapia lines. Our study provides a genome-wide map of genetic variation and selection footprints in tilapia, which could be important for genetic studies and accelerating genetic improvement of tilapia.

Abstract Aquaculture, especially of non‐native species and translocated domestic species, is a greatly encouraged way of relieving the conflicts between food and economic demand and resource depletion. We herein summarized the introduction history of non‐native fish for aquacultural use in China, including 105 species introduced from abroad and 61 species translocated domestically across river basins, which has brought great economic benefits but high ecological risks. Of these, one‐fourth have successfully established wild populations in natural waters and 15% have successfully invaded. We presented specific examples of seven aquaculture species/taxa and three aquarium species/taxa to explain their outcomes. The notable economic benefits, complex species composition and strain selection of tilapias, carps and sturgeons may together facilitate their invasion, and result in fish diversity decline, genetic pollution, and loss of ecosystem service. We specifically reviewed invasion cases in lakes and reservoirs and found that lakes in western China and reservoirs made by major hydroprojects are hotspots for non‐native species, and this has led to the disappearance of endemic species and changes to the original faunal composition. The escaped non‐native fish introduced via aquaculture has changed the original fish biogeography, resulting in the loss of assemblage uniqueness and causing faunal homogeneity. China has achieved significant progress in completing the Aichi Targets by improving the legal system and strengthening conservational actions on controlling non‐native species. Further actions, especially on risk assessment and management of non‐native species are expected for a healthy outlook for the aquaculture industry of China.