Generation of clonal zebrafish line by androgenesis without egg irradiation

Genome-wide DNA methylation and gene expression patterns of androgenetic haploid tiger pufferfish (Takifugu rubripes) provide insights into haploid syndrome

Androgenesis is an important chromosome set manipulation technique used in sex control in aquaculture. Haploid embryos exhibit haploid syndrome with body abnormalities and even die during early embryonic development. In this study, we used whole genome bisulfite sequencing (WGBS) to investigate the genome-wide DNA methylation profiles in haploid females (1n-X) and males (1n-Y), and diploid females (2n-XX) and males (2n-XY) of tiger pufferfish (Takifugu rubripes), an economically important fish in China. A total of 96.32 Gb clean data was produced. Differentially methylated regions (DMRs) were found between haploids and diploids, which may be related to abnormal development and early embryonic death in haploids. There were 3,641 hyper-methylated differentially methylated genes (DMGs) and 2,179 hypo-methylated DMGs in haploid vs. diploid comparisons in both females and males. These DMGs were mainly related to genomic stability maintenance and cell cycle regulation. slf1, actr8, gas2, and pbrm1 genes were selected to validate the methylation sequencing. After combining the methylation data with the corresponding transcriptome data, we identified several genes, including guca2a, myoc, fezf2, rprml, telo2, s100a1, and marveld1, which exhibited differential expression levels modulated by DNA methylation. In conclusion, our study revealed different methylation and expression profiles between haploid and diploid T. rubripes for the first time. Several DMGs were identified between different ploidy levels, which may be related to haploid syndrome formation. The results expand the understanding of the effects of ploidy on the early development of teleosts and provide knowledge about target genes and networks to improve the survival rate of haploids.

An updated review of cold shock and cold stress in fish

Temperature is critical in regulating virtually all biological functions in fish. Low temperature stress (cold shock/stress) is an often-overlooked challenge that many fish face as a result of both natural events and anthropogenic activities. In this study, we present an updated review of the cold shock literature based on a comprehensive literature search, following an initial review on the subject by M.R. Donaldson and colleagues, published in a 2008 volume of this journal. We focus on how knowledge on cold shock and fish has evolved over the past decade, describing advances in the understanding of the generalized stress response in fish under cold stress, what metrics may be used to quantify cold stress and what knowledge gaps remain to be addressed in future research. We also describe the relevance of cold shock as it pertains to environmental managers, policymakers and industry professionals, including practical applications of cold shock. Although substantial progress has been made in addressing some of the knowledge gaps identified a decade ago, other topics (e.g., population-level effects and interactions between primary, secondary and tertiary stress responses) have received little or no attention despite their significance to fish biology and thermal stress. Approaches using combinations of primary, secondary and tertiary stress responses are crucial as a research priority to better understand the mechanisms underlying cold shock responses, from short-term physiological changes to individual- and population-level effects, thereby providing researchers with better means of quantifying cold shock in laboratory and field settings.

Control of Developmental Speed in Zebrafish Embryos Using Different Incubation Temperatures

The zebrafish is a valuable model organism that is widely used in studies of vertebrate development. In the laboratory, zebrafish embryonic development is normally carried out at 28.5°C. In this study, we sought to determine whether it was possible to modify the speed of embryonic development through the use of short- and long-term variations in incubation temperature. After incubation at 20°C-32°C, most early-stage embryos survived to the epiboly stage, whereas more than half of the embryos died at <20°C or >32°C. The rate of development differed between embryos incubated at the lowest (18°C) and highest (34°C) temperatures: a difference of 60 min was observed at the 2-cell stage and 290 min at the 1k-cell stage. When blastulae that had developed at 28°C were transferred to a temperature lower than 18°C for one or more hours, they developed normally after being returned to the original 28°C. Analyses using green fluorescent protein-buckyball mRNA and in situ hybridization against vasa mRNA showed that primordial germ cells increase under low-temperature culture; this response may be of use for studies involving heterochronic germ cell transplantation. Our study shows that embryonic developmental speed can be slowed, which will be of value for performing time-consuming, complicated, and delicate microsurgical operations.

Production of triploid, doubled haploid (DH) and meiogynogenetic brook trout (Salvelinus fontinalis) – efficiency and development of body deformities

In the present research we produced triploid, mitogynogenetic (doubled haploid; DH) and meiogynogenetic brook trout (Salvelinus fontinalis) to examine efficiency of these technologies and potential susceptibility of chromosome set manipulated individuals for the spinal disorders. Triploidy was induced by shocking (High Hydrostatic Pressure – HHP) of fertilized eggs 30 min. after insemination. In turn, gynogenetic development was induced by activation of eggs with UV-irradiated sperm. Activated eggs were then exposed to HHP shock applied 30 and 420 minutes after insemination to provide meiogynogenotes and gynogenetic DHs, respectively. When compared to non-manipulated diploids, the highest survival rates were observed among triploid brook trout while DHs showed the highest mortality. Malformation rates in the diploid larvae from the control groups did not exceed 7.0% while percentage of malformed triploid individuals equaled 19.1%. Drastically increased number of deformed larvae (> 30%) was observed in both DH and meiogynogenetic individuals. Intensification of kyphosis and scoliosis was clearly demonstrated in the gynogenetic and triploid brook trout. Genetic factors such as increased number of sets of chromosomes in triploids and expression of lethal alleles in the gynogenetic fish plus side effects of HHP shock utilized for retention of the second polar body or inhibition of the first cell cleavage when induced triploid and gynogenetic development have been discussed to affect survival rates and prevalence for the skeletal deformities in the chromosome set manipulated brook trout.

A 13-plex of tetra- and penta-STRs to identify zebrafish

The zebrafish species Danio rerio has become one of the major vertebrate model organisms used in biomedical research. However, there are aspects of the model that need to be improved. One of these is the ability to identify individual fish and fish lines by DNA profiling. Although many dinucleotide short tandem repeat (diSTR) markers are available for this and similar purposes, they have certain disadvantages such as an excessive polymerase slippage ("stutter") that causes difficulties in automated genotyping and cross-laboratory comparisons. Here we report on the development of a 13-plex of tetranucleotide and pentanucleotide STRs (tetraSTRs and pentaSTRs, respectively) that have low stutter. The system uses an inexpensive universal primer labelling system, which can easily be converted to a direct labeling system if desired. This 13-plex was examined in three zebrafish lines (NHGRI-1, kca33Tg, and kca66Tg, originally obtained from ZIRC). The average observed heterozygosity (Ho) and expected heterozygosity (He) in these highly inbred lines were 0.291 and 0.359, respectively, which is very similar to what has been found with diSTRs. The probability of identity (PI) for all fish tested was 2.1 × 10^-5 and the PI for siblings (PIsib) was 6.4 × 10^-3, as calculated by the Genalex package. Ninety percent of the fish tested were correctly identified with their respective strains. It is also demonstrated that this panel can be used to confirm doubled-haploid cell lines. This multiplex should find multiple uses for improving the accuracy and reproducibility of studies using the zebrafish model.

Triploidy in zebrafish larvae: Effects on gene expression, cell size and cell number, growth, development and swimming performance

There is renewed interest in the regulation and consequences of cell size adaptations in studies on understanding the ecophysiology of ectotherms. Here we test if induction of triploidy, which increases cell size in zebrafish (Danio rerio), makes for a good model system to study consequences of cell size. Ideally, diploid and triploid zebrafish should differ in cell size, but should otherwise be comparable in order to be suitable as a model. We induced triploidy by cold shock and compared diploid and triploid zebrafish larvae under standard rearing conditions for differences in genome size, cell size and cell number, development, growth and swimming performance and expression of housekeeping genes and hsp70.1. Triploid zebrafish have larger but fewer cells, and the increase in cell size matched the increase in genome size (+ 50%). Under standard conditions, patterns in gene expression, ontogenetic development and larval growth were near identical between triploids and diploids. However, under demanding conditions (i.e. the maximum swimming velocity during an escape response), triploid larvae performed poorer than their diploid counterparts, especially after repeated stimuli to induce swimming. This result is consistent with the idea that larger cells have less capacity to generate energy, which becomes manifest during repeated physical exertion resulting in increased fatigue. Triploidy induction in zebrafish appears a valid method to increase specifically cell size and this provides a model system to test for consequences of cell size adaptation for the energy budget and swimming performance of this ectothermic vertebrate.

Effects of homozygosity on sex determination in zebrafish Danio rerio

Gynogenetic zebrafish Danio rerio were obtained by activating D. rerio oocytes with UV irradiated common carp Cyprinus carpio sperm and then applying one of four different shocks [two (early) meiotic and two (late) mitotic shocks]. Gynogens produced by three of the shocks survived to maturity. All adult gynogens (n = 52) except one were found to be male. There was no difference in growth rate between the biparental controls and gynogens produced through the most effective shock, thereby eliminating growth rate as a possible cause of the skewed sex ratio. Gynogen males had reduced fertility compared to biparental controls, with about half of gynogens being unable to reproduce through natural spawning (all controls reproduced successfully). Gynogen males that did reproduce gave lower fertilization rates compared with controls. This demonstrates the negative effects of increased homozygosity on male reproductive function. Families sired by meiotic gynogen males were more likely to be female biased (33% of families) compared with families sired by biparental control males (11%). In addition to confirming the polygenic nature of sex determination in D. rerio, these observations suggest that recessive or over-dominant male-determining alleles are present in domesticated D. rerio populations.

Developmental competence of eggs produced by rainbow trout Doubled Haploids (DHs) and generation of the clonal lines

Poor quality eggs produced by the fully homozygous doubled haploids (DHs) may impair generation of clonal lines in fish species. In the present research, gynogenetic development of rainbow trout (Oncorhynchus mykiss) was induced in eggs originated from the DH females. Eggs were activated with the UV-irradiated grayling (Thymallus thymallus) spermatozoa and subjected to the high hydrostatic pressure (HHP) shock to provide diploid clonal individuals. Only two of four DH females produced eggs that were successfully activated by the irradiated spermatozoa and subsequently developed into the gynogenetic embryos. Survival rates of rainbow trout from the clonal lines equalled 21.5% and 19.8% during embryogenesis and decreased after hatching to 18.6% and 14.9%, respectively. Some of the dead rainbow trout clones collected between hatching and swim-up stage were emaciated and exhibited spinal deformities including scoliosis. Provided results confirmed limited developmental competences of eggs produced by rainbow trout DH females. Clonal rainbow trout developing in such eggs exhibited reduced survival and increased frequency of the body abnormalities.

Adult zebrafish in CNS disease modeling: a tank that's half-full, not half-empty, and still filling

The zebrafish (Danio rerio) is increasingly used in a broad array of biomedical studies, from cancer research to drug screening. Zebrafish also represent an emerging model organism for studying complex brain diseases. The number of zebrafish neuroscience studies is exponentially growing, significantly outpacing those conducted with rodents or other model organisms. Yet, there is still a substantial amount of resistance in adopting zebrafish as a first-choice model system. Studies of the repertoire of zebrafish neural and behavioral functions continue to reveal new opportunities for understanding the pathobiology of various CNS deficits. Although some of these models are well established in zebrafish, including models for anxiety, depression, and addiction, others are less recognized, for example, models of autism and obsessive-compulsive states. However, mounting data indicate that a wide spectrum of CNS diseases can be modeled in adult zebrafish. Here, we summarize recent findings using zebrafish CNS assays, discuss model limitations and the existing challenges, as well as outline future directions of research in this field.

Improved Procedure for Induction of the Androgenetic Doubled Haploids in Zebrafish

Androgenesis is useful for induction of doubled haploids from male genetic resources and contributes to the restoration of individuals from cryopreserved sperm. Here, we determined the suitable conditions for egg in vitro preservation and the suitable dose of UV irradiation for genetic inactivation of the egg nucleus, and established an improved procedure for induction of androgenetic-doubled haploids in zebrafish. The suitable solution for egg preservation was evaluated by the fertilization rate using different types of solutions or conditions. Hank's solution with 0.5% bovine serum albumin (pH8.0) was suitable for the preservation of zebrafish eggs. In addition, we discovered an improvement of fertilization rates by temporal preservation of ovulated eggs in the suitable solution. UV irradiation of eggs at 50-75 mJ/cm² induced haploid embryos. Microsatellite genotyping using eight loci revealed the paternity and homozygosity of the putative androgenetic doubled haploids. The yield rate of androgenetic doubled haploids, which were induced by UV irradiation and heat shock, ranged from 0.4% to 10.7%.

Production and verification of a 2nd generation clonal group of Japanese flounder, Paralichthys olivaceus

Clonal fishes are useful tools in biology and aquaculture studies due to their isogenicity. In Japanese flounder (Paralichthys olivaceus), a group of homozygous clones was created by inducing meiogynogenesis in eggs from a mitogynogenetic homozygous diploid. As the clones reached sexual maturity, meiogynogenesis was again induced in order to produce a 2^nd generation clonal group of Japanese flounder. After 3 months, there were 611 healthy, surviving individuals. Twenty-four microsatellite markers, that covered all the linkage groups of Japanese flounder, were used to identify the homozygosity of the 2^nd generation clones; no heterozygous locus was detected. This indicates that the production of a 2^nd generation clonal group of Japanese flounder was successful. Restriction-site DNA associated sequencing at the genomic level also confirmed the homozygosity and clonality of the 2^nd generation clonal group. Furthermore, these 2^nd generation clones had a small coefficient of variation for body shape indices at 210 days of age and showed a high degree of similarity in body characteristics among individuals. The successful production of 2^nd generation clones has laid the foundation for the large-scale production of clonal Japanese flounder.