Direct production of XY(DMY-) sex reversal female medaka (Oryzias latipes) by embryo microinjection of TALENs

Integrating gonadal RNA-seq and small RNA-seq to analyze mRNA and miRNA changes in medaka sex differentiation

MicroRNAs are important post-transcriptional regulators, yet the molecular crosstalk between miRNAs and their target genes during sex differentiation remains poorly understood. Medaka (Oryzias latipes), the first fish in which the sex determination gene was identified, serves as an ideal model for studying this process. Here, we generated gonadal RNA-seq and small RNA-seq data from XYDMY- females, wild-type females and males to explore this crosstalk. A total of twenty-seven RNA-seq datasets, comprising 188 Gb of raw reads, and twenty-seven small RNA-seq datasets, totaling 18 Gb of raw reads, were collected, covering 10, 30 and 120 days. After optimizing the mapping and normalizing, we conducted transcriptional and post-transcriptional dynamic analyses of differentially expressed genes and miRNAs between WT females and males, as well as between WT females and XYDMY- females. Additionally, we integrated the RNA-seq and small RNA-seq data to construct comprehensive interaction networks and performed a detailed analysis of the temporal dynamics in gene and miRNA expression. These resources offer valuable insights into the transcriptional regulation of gonadal differentiation and development in vertebrates.

Horizon scanning of potential environmental applications of terrestrial animals, fish, algae and microorganisms produced by genetic modification, including the use of new genomic techniques

With scientific progress and the development of new genomic techniques (NGTs), the spectrum of organisms modified for various purposes is rapidly expanding and includes a wide range of taxonomic groups. An improved understanding of which newly developed products may be introduced into the market and released into the environment in the near and more distant future is of particular interest for policymakers, regulatory authorities, and risk assessors. To address this information need, we conducted a horizon scanning (HS) of potential environmental applications in four groups of organisms: terrestrial animals (excluding insects and applications with gene drives), fish, algae and microorganisms. We applied a formal scoping review methodology comprising a structured search of the scientific literature followed by eligibility screening, complemented by a survey of grey literature, and regulatory websites and databases. In all four groups of organisms we identified a broad range of potential applications in stages of basic as well as advanced research, and a limited number of applications which are on, or ready to be placed on, the market. Research on GM animals including fish is focused on farmed animals and primarily targets traits which increase performance, influence reproduction, or convey resistance against diseases. GM algae identified in the HS were all unicellular, with more than half of the articles concerning biofuel production. GM algae applications for use in the environment include biocontrol and bioremediation, which are also the main applications identified for GM microorganisms. From a risk assessor's perspective these potential applications entail a multitude of possible pathways to harm. The current limited level of experience and limited amount of available scientific information could constitute a significant challenge in the near future, for which risk assessors and competent authorities urgently need to prepare.

Identification and functional analysis of Dmrt1 gene and the SoxE gene in the sexual development of sea cucumber, Apostichopus japonicus

Members of the Doublesex and Mab-3-related transcription factor (Dmrt) gene family handle various vital functions in several biological processes, including sex determination/differentiation and gonad development. Dmrt1 and Sox9 (SoxE in invertebrates) exhibit a very conserved interaction function during testis formation in vertebrates. However, the dynamic expression pattern and functional roles of the Dmrt gene family and SoxE have not yet been identified in any echinoderm species. Herein, five members of the Dmrt gene family (Dmrt1, 2, 3a, 3b and 5) and the ancestor SoxE gene were identified from the genome of Apostichopus japonicus. Expression studies of Dmrt family genes and SoxE in different tissues of adult males and females revealed different expression patterns of each gene. Transcription of Dmrt2, Dmrt3a and Dmrt3b was higher expressed in the tube feet and coelomocytes instead of in gonadal tissues. The expression of Dmrt1 was found to be sustained throughout spermatogenesis. Knocking-down of Dmrt1 by means of RNA interference (RNAi) led to the downregulation of SoxE and upregulation of the ovarian regulator foxl2 in the testes. This indicates that Dmrt1 may be a positive regulator of SoxE and may play a role in the development of the testes in the sea cucumber. The expression level of SoxE was higher in the ovaries than in the testes, and knocking down of SoxE by RNAi reduced SoxE and Dmrt1 expression but conversely increased the expression of foxl2 in the testes. In summary, this study indicates that Dmrt1 and SoxE are indispensable for testicular differentiation, and SoxE might play a functional role during ovary differentiation in the sea cucumber.

Testis-specific expression pattern of dmrt1 and its putative regulatory region in the sea urchin (Mesocentrotus nudus)

Sea urchin (Mseocentrotus nudus) is an economically important mariculture species in several Asian countries. The growth rate and immunocompetence differ by sex in this species. However, the mechanisms of sex determination in M. nudus have remain unclear. In the present study, we focus on the dmrt1 gene of M. nudus (Mndmrt1) to investigate its dynamic expression pattern during different developmental stages. Real-time quantitative PCR (RT-qPCR) revealed that Mndmrt1 exhibits testis-specific expression and undetectable during the whole embryogenesis. With the development of ontogenetic, Mndmrt1 transcripts are first detected at 9 months post-fertilization (mpf). In addition, both the transcripts and protein of Mndmrt1 gene were specifically expressed in spermatogonia and spermatocytes, indicating that it might be a male germ cells marker in sea urchin. Significantly, the 1441 bp promoter sequence of Mndmrt1 gene was obtained by DNA walking, and one positive regulatory region at -1197/ -968 in the promoter, as well as one negative regulatory region at -1441/ -1198 have been identified by promoter activity analysis. Moreover, two regulatory regions contain multiple putative binding sites for transcription factors, including Sp1, Egr1, Sox5, CEBP, GATA and SRY. These findings suggest that Mndmrt1 may be related to testis differentiation and spermatogenesis in sea urchin and will provide an insight into understanding the regulatory mechanism of the dmrt1 gene.

The application of genome editing technology in fish

The advent and development of genome editing technology has opened up the possibility of directly targeting and modifying genomic sequences in the field of life sciences with rapid developments occurring in the last decade. As a powerful tool to decipher genome data at the molecular biology level, genome editing technology has made important contributions to elucidating many biological problems. Currently, the three most widely used genome editing technologies include: zinc finger nucleases (ZFN), transcription activator like effector nucleases (TALEN), and clustered regularly interspaced short palindromic repeats (CRISPR). Researchers are still striving to create simpler, more efficient, and accurate techniques, such as engineered base editors and new CRISPR/Cas systems, to improve editing efficiency and reduce off-target rate, as well as a near-PAMless SpCas9 variants to expand the scope of genome editing. As one of the important animal protein sources, fish has significant economic value in aquaculture. In addition, fish is indispensable for research as it serves as the evolutionary link between invertebrates and higher vertebrates. Consequently, genome editing technologies were applied extensively in various fish species for basic functional studies as well as applied research in aquaculture. In this review, we focus on the application of genome editing technologies in fish species detailing growth, gender, and pigmentation traits. In addition, we have focused on the construction of a zebrafish (Danio rerio) disease model and high-throughput screening of functional genes. Finally, we provide some of the future perspectives of this technology.

Sex determination, gonadal sex differentiation, and plasticity in vertebrate species

A diverse array of sex determination (SD) mechanisms, encompassing environmental to genetic, have been found to exist among vertebrates, covering a spectrum from fixed SD mechanisms (mammals) to functional sex change in fishes (sequential hermaphroditic fishes). A major landmark in vertebrate SD was the discovery of the SRY gene in 1990. Since that time, many attempts to clone an SRY ortholog from nonmammalian vertebrates remained unsuccessful, until 2002, when DMY/dmrt1by was discovered as the SD gene of a small fish, medaka. Surprisingly, however, DMY/dmrt1by was found in only 2 species among more than 20 species of medaka, suggesting a large diversity of SD genes among vertebrates. Considerable progress has been made over the last 3 decades, such that it is now possible to formulate reasonable paradigms of how SD and gonadal sex differentiation may work in some model vertebrate species. This review outlines our current understanding of vertebrate SD and gonadal sex differentiation, with a focus on the molecular and cellular mechanisms involved. An impressive number of genes and factors have been discovered that play important roles in testicular and ovarian differentiation. An antagonism between the male and female pathway genes exists in gonads during both sex differentiation and, surprisingly, even as adults, suggesting that, in addition to sex-changing fishes, gonochoristic vertebrates including mice maintain some degree of gonadal sexual plasticity into adulthood. Importantly, a review of various SD mechanisms among vertebrates suggests that this is the ideal biological event that can make us understand the evolutionary conundrums underlying speciation and species diversity.

Construction of a High-Density Linkage Map and QTL Fine Mapping for Growth- and Sex-Related Traits in Channel Catfish (Ictalurus punctatus)

A high-density genetic linkage map is of particular importance in the fine mapping for important economic traits and whole genome assembly in aquaculture species. The channel catfish (Ictalurus punctatus), a species native to North America, is one of the most important commercial freshwater fish in the world. Outside of the United States, China has become the major producer and consumer of channel catfish after experiencing rapid development in the past three decades. In this study, based on restriction site associated DNA sequencing (RAD-seq), a high-density genetic linkage map of channel catfish was constructed by using single nucleotide polymorphisms (SNPs) in a F₁ family composed of 156 offspring and their two parental individuals. A total of 4,768 SNPs were assigned to 29 linkage groups (LGs), and the length of the linkage map reached 2,480.25 centiMorgans (cM) with an average distance of 0.55 cM between loci. Based on this genetic linkage map, 223 genomic scaffolds were anchored to the 29 LGs of channel catfish, and a total length of 704.66 Mb was assembled. Quantitative trait locus (QTL) mapping and genome-wide association analysis identified 10 QTLs of sex-related and six QTLs of growth-related traits at LG17 and LG28, respectively. Candidate genes associated with sex dimorphism, including spata2, spata5, sf3, zbtb38, and fox, were identified within QTL intervals on the LG17. A sex-linked marker with simple sequence repeats (SSR) in zbtb38 gene of the LG17 was validated for practical verification of sex in the channel catfish. Thus, the LG17 was considered as a sex-related LG. Potential growth-related genes were also identified, including important regulators such as megf9, npffr1, and gas1. In a word, we constructed the high-density genetic linkage map and developed the sex-linked marker in channel catfish, which are important genetic resources for future marker-assisted selection (MAS) of this economically important teleost.

Generating Gene Knockout Oryzias latipes and Rice Field Eel Using TALENs Method

Transcription activator-like effector nucleases (TALENs) methods based on engineered nucleases enable precise manipulations with genomic DNA. Within the field, genetic manipulation has surpassed the proof of principle stage and is now utilized in both applied strategies and performing in economic organism. The generation and study of gene modified (GM) fish using TALENs provides a novel and essential tool for fishes molecular breeding. The medaka, Oryzias latipes, is a small, freshwater fish and an idea model organism to study reproductive mechanism. Rice Field eel is a valuable model organism of high economic importance in PR China. In this chapter, we describe microinjection of Oryzias latipes and Rice Field eel embryos, in the context of preparing, evaluating, performing gene knockout and generate gene knockout fish with TALENs in detail, which are easy to prepare and proved to be efficient in targeting of a wide range of cleavage sites. Our procedure will facilitate broader applications of TALENs in freshwater aquaculture organism.

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.

Mettl3 Mutation Disrupts Gamete Maturation and Reduces Fertility in Zebrafish

N⁶-methyladenosine (m⁶A), catalyzed by Mettl3 methyltransferase, is a highly conserved epigenetic modification in eukaryotic messenger RNA (mRNA). Previous studies have implicated m⁶A modification in multiple biological processes, but the in vivo function of m⁶A has been difficult to study, because mettl3 mutants are embryonic lethal in both mammals and plants. In this study, we have used transcription activator-like effector nucleases and generated viable zygotic mettl3 mutant, Zmettl3^m/m , in zebrafish. We find that the oocytes in Zmettl3^m/m adult females are stalled in early development and the ratio of full-grown stage (FG) follicles is significantly lower than that of wild type. Human chorionic gonadotropin-induced ovarian germinal vesicle breakdown in vitro and the numbers of eggs ovulated in vivo are both decreased as well, while the defects of oocyte maturation can be rescued by sex hormone in vitro and in vivo In Zmettl3^m/m adult males, we find defects in sperm maturation and sperm motility is significantly reduced. Further study shows that 11-ketotestosterone (11-KT) and 17β-estradiol (E2) levels are significantly decreased in Zmettl3^m/m , and defective gamete maturation is accompanied by decreased overall m⁶A modification levels and disrupted expression of genes critical for sex hormone synthesis and gonadotropin signaling in Zmettl3^m/m Thus, our study provides the first in vivo evidence that loss of Mettl3 leads to failed gamete maturation and significantly reduced fertility in zebrafish. Mettl3 and m⁶A modifications are essential for optimal reproduction in vertebrates.

Genetic analysis of the reproductive axis in fish using genome-editing nucleases

Reproduction in fish is controlled by the brain-pituitary-gonad reproductive axis. Although genes of the reproductive axis are conserved from fish to humans, their in vivo functions are less clear in fish. Mutant lines of the reproductive axis have been systematically investigated in zebrafish and medaka using recently developed genome-editing nucleases. Here, we review recent progress in the genetic analysis of the reproductive axis in fish as well as the opportunities and challenges of applying genome-editing nucleases in fisheries.

Autosomal gsdf acts as a male sex initiator in the fish medaka

Sex is pivotal for reproduction, healthcare and evolution. In the fish medaka, the Y-chromosomal dmy (also dmrt1bY) serves the sex determiner, which activates dmrt1 for male sex maintenance. However, how dmy makes the male decision via initiating testicular differentiation has remained unknown. Here we report that autosomal gsdf serves a male sex initiator. Gene addition and deletion revealed that gsdf was necessary and sufficient for maleness via initiating testicular differentiation. We show that gsdf transcription is activated directly by dmy. These results establish the autosomal gsdf as the first male sex initiator. We propose that dmy determines maleness through activating gsdf and dmrt1 without its own participation in developmental processes of sex initiation and maintenance. gsdf may easily become a sex determiner or other autosomal genes can be recruited as new sex determiners to initiate gsdf expression. Our findings offer new insights into molecular mechanisms underlying sex development and evolution of sex-controlling genes in vertebrates.