Gene editing nuclease and its application in tilapia

Genome editing in East African cichlids and tilapias: state-of-the-art and future directions

African cichlid fishes of the Cichlidae family are a group of teleosts important for aquaculture and research. A thriving research community is particularly interested in the cichlid radiations of the East African Great Lakes. One key goal is to pinpoint genetic variation underlying phenotypic diversification, but the lack of genetic tools has precluded thorough dissection of the genetic basis of relevant traits in cichlids. Genome editing technologies are well established in teleost models like zebrafish and medaka. However, this is not the case for emerging model organisms, such as East African cichlids, where these technologies remain inaccessible to most laboratories, due in part to limited exchange of knowledge and expertise. The Cichlid Science 2022 meeting (Cambridge, UK) hosted for the first time a Genome Editing Workshop, where the community discussed recent advances in genome editing, with an emphasis on CRISPR/Cas9 technologies. Based on the workshop findings and discussions, in this review we define the state-of-the-art of cichlid genome editing, share resources and protocols, and propose new possible avenues to further expand the cichlid genome editing toolkit.

Review: Recent Applications of Gene Editing in Fish Species and Aquatic Medicine

Gene editing and gene silencing techniques have the potential to revolutionize our knowledge of biology and diseases of fish and other aquatic animals. By using such techniques, it is feasible to change the phenotype and modify cells, tissues and organs of animals in order to cure abnormalities and dysfunctions in the organisms. Gene editing is currently experimental in wide fields of aquaculture, including growth, controlled reproduction, sterility and disease resistance. Zink finger nucleases, TALENs and CRISPR/Cas9 targeted cleavage of the DNA induce favorable changes to site-specific locations. Moreover, gene silencing can be used to inhibit the translation of RNA, namely, to regulate gene expression. This methodology is widely used by researchers to investigate genes involved in different disorders. It is a promising tool in biotechnology and in medicine for investigating gene function and diseases. The production of food fish has increased markedly, making fish and seafood globally more popular. Consequently, the incidence of associated problems and disease outbreaks has also increased. A greater investment in new technologies is therefore needed to overcome such problems in this industry. To put it concisely, the modification of genomic DNA and gene silencing can comprehensively influence aquatic animal medicine in the future. On the ethical side, these precise genetic modifications make it more complicated to recognize genetically modified organisms in nature and can cause several side effects through created mutations. The aim of this review is to summarize the current state of applications of gene modifications and genome editing in fish medicine.

Exposure to estrone disrupts the endocrine system of western mosquitofish (Gambusia affinis)

Estrone (E1) is one of the predominant natural estrogens detected in aquatic environments, yet little is known about its effects on the endocrine system in fish. In this study, the sex ratio, secondary sexual characteristics, gonadal histology, and transcriptional levels of genes closely related to sex differentiation and hypothalamic-pituitary-gonadal-liver (HPGL) axis were assessed in western mosquitofish (Gambusia affinis) after a full life-cycle exposure to E1 (0, 25.4, 143, 740, and 4300 ng/L) for 119 days. The results showed that exposure to 4300 ng/L of E1 resulted in 100% female and inhibited the growth of females. Exposure to environmentally relevant concentrations of E1 (143 and 740 ng/L) led to obvious feminization of skeletons and anal fins in males. Exposure to 740 and 4300 ng/L of E1 increased the proportion of mature spermatocytes in females, and exposure to 143 and 740 ng/L decreased the proportion of mature spermatocytes in males. Moreover, the transcripts of genes related to sex differentiation and HPGL axis were changed in the E1-exposed adult fish and embryos inside females. This study has provided valuable data on the endocrine disruption effects of E1 at environmentally relevant concentrations in G. affinis.

Role of sex steroids in fish sex determination and differentiation as revealed by gene editing

The involvement of sex steroids in sex determination and differentiation is relatively conserved among non-mammalian vertebrates, especially in fish. Thanks to the advances in genome sequencing and genome editing, significant progresses have been made in the understanding of steroidogenic pathway and hormonal regulation of sex determination and differentiation in fish. It seems that loss of function study of single gene challenges the traditional views that estrogen is required for ovarian differentiation and androgen is needed for testicular development, but it is not so in essence. Steroidogenic enzymes can be classified into two categories based on expression and enzyme activities in fish. One type, encoded by star2, cyp17a1 and cyp19a1a, is involved in estrogen production and exclusively expressed in the gonads. Mutation of these genes results in the up-regulation of male pathway genes and sex reversal from genetic female to male. The other type, encoded by the duplicated paralogs of the above genes, including star1, cyp11a1, cyp17a2 and cyp19a1b, as well as cyp11c1 gene, is dominantly expressed both in gonads and extra-gonadal tissues. Mutation of these genes alters the steroids (androgen, DHP and cortisol) production and spermatogenesis, fertility, secondary sexual characteristics and sexual behavior, but usually does not affect the sex differentiation. For the estrogen receptors (esr1, esr2a and esr2b), single mutation failed to, but double and triple mutation leads to sex reversal from female to male, indicating that at least Esr2a and Esr2b are required to mediate the role of estrogen in sex determination proved by gene editing experiments. Taken together, results from gene editing enrich our understanding of steroid synthesis pathways and further confirm the critical role of estrogen in female sex determination by antagonizing the male pathway in fish.

Advances in Reproductive Endocrinology and Neuroendocrine Research Using Catfish Models

Catfishes, belonging to the order siluriformes, represent one of the largest groups of freshwater fishes with more than 4000 species and almost 12% of teleostean population. Due to their worldwide distribution and diversity, catfishes are interesting models for ecologists and evolutionary biologists. Incidentally, catfish emerged as an excellent animal model for aquaculture research because of economic importance, availability, disease resistance, adaptability to artificial spawning, handling, culture, high fecundity, hatchability, hypoxia tolerance and their ability to acclimate to laboratory conditions. Reproductive system in catfish is orchestrated by complex network of nervous, endocrine system and environmental factors during gonadal growth as well as recrudescence. Lot of new information on the molecular mechanism of gonadal development have been obtained over several decades which are evident from significant number of scientific publications pertaining to reproductive biology and neuroendocrine research in catfish. This review aims to synthesize key findings and compile highly relevant aspects on how catfish can offer insight into fundamental mechanisms of all the areas of reproduction and its neuroendocrine regulation, from gametogenesis to spawning including seasonal reproductive cycle. In addition, the state-of-knowledge surrounding gonadal development and neuroendocrine control of gonadal sex differentiation in catfish are comprehensively summarized in comparison with other fish models.

Crucial role of dead end gene for primordial germ cell survival in rice field eel (Monopterus albus)

The dead end gene has been identified as a essential factor for Primordial germ cells (PGCs) migration and survival in many species, but its role in Monopterus albus is unclear. In order to clarify the function of dead end gene in M.albus PGCs migration and survival, we first characterized the expression profile of M.albus dead end (Madnd) in developing embryos and various tissues. qRT-PCR revealed that Madnd transcripts were exclusively detected in gonad, including ovary, testis and ovotestis.Embryos injected with a Madnd morpholino (Madnd-MO) exhibited down-regulation of the vasa gene. Furthermore, the GFP signal show the PGCs migration in control group were injected with GFP-nanos3 3'-UTR mRNA for visualization, as described in a previous study, yet it was disappeared after embryos injected with Madnd-MO.Finally, we characterized the genomics sequence of the Madnd gene and designed five gRNAs for genome editing. Three gRNAs were selected for microinjection according to the results of in vitro tests. gRNAd1 was used for microinjection with the Cas9 protein and was confirmed to be effective. Our analysis in this study suggested that Madnd play a key role in PGCs migration and survival in M. albus. These data provide the basis for the production of fast-growing and reproductively M.albus sterile.

Regulation of spermatogenesis and reproductive capacity by Igf3 in tilapia

A novel insulin-like growth factor (igf3), which is exclusively expressed in the gonads, has been widely identified in fish species. Recent studies have indicated that Igf3 regulates spermatogonia proliferation and differentiation in zebrafish; however, detailed information on the role of this Igf needs further in vivo investigation. Here, using Nile tilapia (Oreochromis niloticus) as an animal model, we report that igf3 is required for spermatogenesis and reproduction. Knockout of igf3 by CRISPR/Cas9 severely inhibited spermatogonial proliferation and differentiation at 90 days after hatching, the time critical for meiosis initiation, and resulted in less spermatocytes in the mutants. Although spermatogenesis continued to occur later, more spermatocytes and less spermatids were observed in the igf3-/- testes when compared with wild type of testes at adults, indicating that Igf3 regulates spermatocyte to spermatid transition. Importantly, a significantly increased occurrence of apoptosis in spermatids was observed after loss of Igf3. Therefore, igf3-/- males were subfertile with drastically reduced semen volume and sperm count. Conversely, the overexpression of Igf3 in XY tilapia enhanced spermatogenesis leading to more spermatids and sperm count. Transcriptomic analysis revealed that the absence of Igf3 resulted in dysregulation of many genes involved in cell cycle, meiosis and pluripotency regulators that are critical for spermatogenesis. In addition, in vitro gonadal culture with 17α-methyltetosterone (MT) and 11-ketotestosterone (11-KT) administration and in vivo knockout of cyp11c1 demonstrated that igf3 expression is regulated by androgens, suggesting that Igf3 acts downstream of androgens in fish spermatogenesis. Notably, the igf3 knockout did not affect body growth, indicating that this Igf specifically functions in reproduction. Taken together, our data provide genetic evidence for fish igf3 in the regulation of reproductive capacity by controlling spermatogenesis.

Expression of Vasa, Nanos2 and Sox9 during initial testicular development in Nile tilapia (Oreochromis niloticus) submitted to sex reversal

Sexual differentiation and early gonadal development are critical events in vertebrate reproduction. In this study, the initial testis development and expression of the Vasa, Nanos2 and Sox9 proteins were examined in Nile tilapia Oreochromis niloticus submitted to induced sex reversal. To that end, 150O. niloticus larvae at 5 days post-hatching (dph) were kept in nurseries with no hormonal addition (control group) and 150 larvae were kept with feed containing 17α-methyltestosterone to induce male sex reversal (treated group). Morphological sexual differentiation of Nile tilapia occurred between 21 and 25 dph and sex reversal resulted in 94% males, whereas the control group presented 53% males. During sexual differentiation, gonocytes (Gon) were the predominant germ cells, which decreased and disappeared after that stage in both groups. Undifferentiated spermatogonia (Aund) were identified at 21 dph in the control group and at 23 dph in the treated group. Differentiated spermatogonia (Adiff) were found at 23 dph in both groups. Vasa and Nanos2 occurred in Gon, Aund and Adiff and there were no significant differences between groups. Vasa-labelled Adiff increased at 50 dph in both groups and Nanos2 presented a high proportion of labelled germ cells during sampling. Sertoli cells expressed Sox9 throughout the experiment and its expression was significantly greater during sexual differentiation in the control group. The results indicate that hormonal treatment did not alter initial testis development and expression of Vasa and Nanos2 in Nile tilapia, although lower expression of Sox9 and a delay in sexual differentiation was detected in the treated group.

Genomics to accelerate genetic improvement in tilapia

Selective breeding of tilapia populations started in the early 1990s and over the past three decades tilapia has become one of the most important farmed freshwater species, being produced in more than 125 countries around the globe. Although genome assemblies have been available since 2011, most of the tilapia industry still depends on classical selection techniques using mass spawning or pedigree information to select for growth traits with reported genetic gains of up to 20% per generation. The involvement of international breeding companies and research institutions has resulted in the rapid development and application of genomic resources in the last few years. GWAS and genomic selection are expected to contribute to uncovering the genetic variants involved in economically relevant traits and increasing the genetic gain in selective breeding programs, respectively. Developments over the next few years will probably focus on achieving a deep understanding of genetic architecture of complex traits, as well as accelerating genetic progress in the selection for growth-, quality- and robustness-related traits. Novel phenotyping technologies (i.e. phenomics), lower-cost whole-genome sequencing approaches, functional genomics and gene editing tools will be crucial in future developments for the improvement of tilapia aquaculture.

Evolution of gonadotropin signaling on gonad development: insights from gene knockout studies in zebrafish

Gonadal development is precisely regulated by the two gonadotropins luteinizing hormone (LH) and follicle-stimulating hormone (FSH). Much progress on understanding the functions of LH and FSH signaling on gonad development has been achieved in the past decades, mostly from studies in mammals, especially genetic studies in both mouse and human. The functions of both LH and FSH signaling in nonmammalian species are still largely unknown. In recent years, using zebrafish, a teleost phylogenetically distant from mammals, we and others have genetically analyzed the functions of gonadotropins and their receptors through gene knockout studies. In this review, we will summarize the pertinent findings and discuss how the actions of gonadotropin signaling on gonad development have evolved during evolution from fish to mammals.

Roles of estrogens in fish sexual plasticity and sex differentiation

Fish sex could be reversed at the undifferentiated stage of gonad by administration of exogenous estrogen (E2) or blockade of endogenous estrogen synthesis with aromatase inhibitors, which is designated as primary sex reversal (PSR). Recent studies have well demonstrated that gonochoristic fish maintain their sexual plasticity after sex determination/differentiation. The differentiated ovary could be transdifferentiated into functional testis, and vice versa, the differentiated testis could be transdifferentiated into ovary. By analyzing these two secondary sex reversal (SSR) models, it was found that induction of male-to-female sex reversal initiates from dorsal (near the blood vessel) to the ventral, while induction of female-to-male sex reversal initiates from the ventral to dorsal. Down regulation of endogenous estrogen is the prerequisite for the ovarian transdifferentiation. However, exogenous estrogen alone is not sufficient for inducing differentiated testis to ovary. Administration of E2 and simultaneous blockage of androgen synthesis could induce testicular transdifferentiation. Therefore, endogenous estrogen is critical for the ovarian differentiation/maintenance and androgen is critical for testicular maintenance. Recently, genetic studies with genome editing technologies also showed that disruption of Cyp19a1a induced testicular development, indicating that cyp19a1a is the key gene essential for estrogen synthesis and ovary differentiation/maintenance. Knockout of male pathway genes or overexpression of female pathway genes could up-regulate cyp19a1a expression and increase estrogen level so as to promote ovary. Conversely, knockout of female pathway genes or overexpression of male pathway genes could down-regulate cyp19a1a expression and decrease estrogen level so as to promote testis (transgenic or knockout sex reversal, TSR). Epigenetic regulation of cyp19a1a play a critical role in natural sex reversal (NSR), but its relation with PSR, SSR and TSR needs further detailed investigations. In all, these studies further highlighted the important roles of endogenous estrogens in fish sex differentiation/maintenance.

Divergence, evolution and adaptation in ray-finned fish genomes

With the rapid development of next-generation sequencing technologies and bioinformatics, over 50 ray-finned fish genomes by far have been sequenced with high quality. The genomic work provides abundant genetic resources for deep understanding of divergence, evolution and adaptation in the fish genomes. They are also instructive for identification of candidate genes for functional verification, molecular breeding, and development of novel marine drugs. As an example of other omics data, the Fish-T1K project generated a big database of fish transcriptomes to integrate with these published fish genomes for potential applications. In this review, we highlight the above-mentioned recent investigations and core topics on the ray-finned fish genome research, with a main goal to obtain a deeper understanding of fish biology for theoretical and practical applications.

High Efficiency Targeting of Non-coding Sequences Using CRISPR/Cas9 System in Tilapia

The CRISPR/Cas9 has been successfully applied for disruption of protein coding sequences in a variety of organisms. The majority of the animal genome is actually non-coding sequences, which are key regulators associated with various biological processes. In this study, to understand the biological significance of these sequences, we used one or dual gRNA guided Cas9 nuclease to achieve specific deletion of non-coding sequences including microRNA and 3' untranslated region (UTR) in tilapia, which is an important fish for studying sex determination and evolution. Co-injection of fertilized eggs with single gRNA targeting seed region of miRNA and Cas9 mRNA resulted in indel mutations. Further, co-injection of fertilized eggs with dual gRNAs and Cas9 mRNA led to the removal of the fragment between the two target loci, yielding maximum efficiency of 11%. This highest genomic deletion efficiency was further improved up to 19% using short ssDNA as a donor. The deletions can be transmitted through the germline to the next generation at average efficiency of 8.7%. Cas9-vasa 3'-UTR was used to increase the efficiency of germline transmission of non-coding sequence deletion up to 14.9%. In addition, the 3'-UTR of the vasa gene was successfully deleted by dual gRNAs. Deletion of vasa 3'-UTR resulted in low expression level of vasa mRNA in the gonad when compared with the control. To summarize, the improved CRISPR/Cas9 system provided a powerful platform that can assist to easily generate desirable non-coding sequences mutants in non-model fish tilapia to discovery their functions.

Genome editing in fishes and their applications

There have been revolutionary progresses in genome engineering in the past few years. The newly-emerged genome editing technologies including zinc-finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeats associated with Cas9 (CRISPR/Cas9) have enabled biological scientists to perform efficient and precise targeted genome editing in different species. Fish represent the largest group of vertebrates with many species having values for both scientific research and aquaculture industry. Genome editing technologies have found extensive applications in different fish species for basic functional studies as well asapplied research in such fields as disease modeling and aquaculture. This mini-review focuses on recent advancements and applications of the new generation of genome editing technologies in fish species, with particular emphasis on their applications in understanding reproductive functions because the reproductive axis has been most systematically and best studied among others and its function has been difficult to address with reverse genetics approach.

Distinct and Cooperative Roles of amh and dmrt1 in Self-Renewal and Differentiation of Male Germ Cells in Zebrafish

Spermatogenesis is a fundamental process in male reproductive biology and depends on precise balance between self-renewal and differentiation of male germ cells. However, the regulative factors for controlling the balance are poorly understood. In this study, we examined the roles of amh and dmrt1 in male germ cell development by generating their mutants with Crispr/Cas9 technology in zebrafish. Amh mutant zebrafish displayed a female-biased sex ratio, and both male and female amh mutants developed hypertrophic gonads due to uncontrolled proliferation and impaired differentiation of germ cells. A large number of proliferating spermatogonium-like cells were observed within testicular lobules of the amh-mutated testes, and they were demonstrated to be both Vasa- and PH3-positive. Moreover, the average number of Sycp3- and Vasa-positive cells in the amh mutants was significantly lower than in wild-type testes, suggesting a severely impaired differentiation of male germ cells. Conversely, all the dmrt1-mutated testes displayed severe testicular developmental defects and gradual loss of all Vasa-positive germ cells by inhibiting their self-renewal and inducing apoptosis. In addition, several germ cell and Sertoli cell marker genes were significantly downregulated, whereas a prominent increase of Insl3-positive Leydig cells was revealed by immunohistochemical analysis in the disorganized dmrt1-mutated testes. Our data suggest that amh might act as a guardian to control the balance between proliferation and differentiation of male germ cells, whereas dmrt1 might be required for the maintenance, self-renewal, and differentiation of male germ cells. Significantly, this study unravels novel functions of amh gene in fish.