Development and application of biological technologies in fish genetic breeding

The Effects of Humic Acids on the Early Developmental Stages of African Cichlids during Artificial Breeding

The aim of this study was to compare the effect of humic acid (HA) obtained by extraction from alginate on the incubation of roes and fry development in African cichlids, Labidochormis caeruleus, as well as their influence on the stabilization of the physicochemical parameters of water in an aquarium during artificial breeding. The roes were obtained by extruding from a female buccal cavity immediately after fertilization. For the experiment, 4 groups of 40 roes were formed in an incubator with an artificial hatchery. Groups 1-3 were exposed to 1%, 5%, and 10% concentrations of HA, respectively. The control group C was not exposed to HA. In all groups, the mortality and size differences of the fry, as well as the temperature, pH, hardness, nitrite, and nitrate levels in the tanks, were determined during a 30-day monitoring period until the resorption of the yolk sac. The results of this study indicated the ability of HA in 5% and 10% concentrations to reduce nitrite and nitrate levels in the aquatic environment, which significantly reduced the mortality of roes and the survivability of the fry. The determination of the morphological measurements of the fry revealed an increased body length in the groups exposed to 5% and 10% HA concentrations compared to the control group by the end of the monitored period. It was also noted that the yolk sac was resorbed two days earlier in the same groups than in the control. Thus, the results showed that HAs are suitable for use in the artificial aquarium incubation of roes and fry development, which are increasingly exposed to adverse environmental factors. The knowledge obtained in this study and its transfer into practice can allow even less experienced aquarists to successfully breed aquarium fish species that could not normally be bred under artificial conditions without the addition of HA.

Genome-wide analysis facilitates estimation of the amount of male contribution in meiotic gynogenetic three-spined stickleback (Gasterosteus aculeatus)

Gynogenetic embryos - those inheriting only maternal DNA - can be experimentally created by fertilizing eggs with radiation-treated sperm containing inactivated paternal chromosomes. Diploidy in the zygotes can be maintained through prevention of the second meiosis or restored by preventing the first mitosis after the maternal chromosome complement has been replicated. These gynogenetic organisms are useful in many fields including aquaculture, evolutionary biology and genomics. Although gynogenetic organisms have been created in numerous species, the completeness of uni-parental inheritance has often been assumed rather than thoroughly quantified across the genome. Instead, when tests of uni-parental inheritance occur, they typically rely on well-studied genetically determined phenotypes that represent a very small sub-set of the genome. Only assessing small genomic regions for paternal inheritance leaves the question of whether some paternal contributions to offspring might still have occurred. In this study, the authors quantify the efficacy of creating gynogenetic diploid three-spined stickleback fish (Gasterosteus aculeatus). To this end, the authors mirrored previous assessments of paternal contribution using well-studied genetically determined phenotypes including sex and genetically dominant morphological traits but expanded on previous studies using dense restriction site-associated DNA sequencing (RAD-seq) markers in parents and offspring to assess paternal inheritance genome-wide. In the gynogenetic diploids, the authors found no male genotypes underlying their phenotypes of interest - sex and dominant phenotypic traits. Using genome-wide assessments of paternal contribution, nevertheless, the authors found evidence of a small, yet potentially important, amount of paternally "leaked" genetic material. The application of this genome-wide approach identifies the need for more widespread assessment of paternal contributions to gynogenetic animals and promises benefits for many aspects of aquaculture, evolutionary biology and genomics.

Strengthening regulations, recent advances and remaining barriers in stem cell clinical translation in China: 2015-2021 in review

A new regulatory regime is being implemented under strict scrutiny for translation of stem cell medical practices since 2015 in China. The new mode of governance is strengthening to curb the marketing of unproven stem cell therapeutic products. This article begins with a brief historical overview of stem cell research and development and then focuses on the policies and country-level guidelines in the past years for stem cell translational research. This study reveals several key observations on the major progress made and the challenges associated with clinical translation of stem cells in China. Given that stem cells or stem cell-based therapeutic products are already considered as biological 'drugs', this study would be conducive to a better understanding of China's approach to stem cell translational research, marketisation and industrialization in progress.

Efficacy of Utilization of All-Plant-Based and Commercial Low-Fishmeal Feeds in Two Divergently Selected Strains of Rainbow Trout (Oncorhynchus mykiss): Focus on Growth Performance, Whole-Body Proximate Composition, and Intestinal Microbiome

The present study aimed to investigate the growth performance, whole-body proximate composition, and intestinal microbiome of rainbow trout strains when selected and non-selected for weight gain on all-plant protein diets. A 2x2 factorial design was applied, where a selected (United States) and a non-selected (ITA) rainbow trout strain were fed using either an all-plant protein (PP) or a commercial low-FM diet (C). Diets were fed to five replicates of 20 (PP) or 25 (C) fish for 105 days. At the end of the trial, growth parameters were assessed, and whole fish (15 pools of three fish/diet) and gut samples (six fish/diet) were collected for whole-body proximate composition and gut microbiome analyses, respectively. Independent of the administered diet, the United States strain showed higher survival, final body weight, weight gain, and specific growth rate when compared to the ITA fish (p < 0.001). Furthermore, decreased whole-body ether extract content was identified in the PP-fed United States rainbow trout when compared to the ITA strain fed the same diet (p < 0.001). Gut microbiome analysis revealed the Cetobacterium probiotic-like genus as clearly associated with the United States rainbow trout, along with the up-regulation of the pathway involved in starch and sucrose metabolism. In summary, the overall improvement in growth performance and, to a lesser extent, whole-body proximate composition observed in the selected rainbow trout strain was accompanied by specific, positive modulation of the intestinal microbiome.

Robust strategy for disease resistance and increasing production breeding in red swamp crayfish (Procambarus clarkii)

Red swamp crayfish (Procambarus clarkii) is an important aquaculture species in China. With increasing crayfish culture, a number of outbreaks of various diseases have been identified in crayfish. Despite this, there are no reports on the application of disease resistance genes in the molecular breeding of crayfish. In this study, transcriptome analysis was performed to explore the disease resistance genes in crayfish, with a focus on investigating the genetic variations in the open reading frames of these genes, for subsequent haplotype analysis. Furthermore, pathogen-challenge experiments were carried out in the crayfish, to identify the favoured haplotypes. A novel disease resistance gene, R (Resistance), was identified by means of transcriptome analysis. In total, two, four, and five haplotypes of the three disease resistance genes, ALF, R, and crustin2, respectively, were detected. ALF1, R1, and Cru1 were the favoured haplotypes of ALF, R, and crustin2, respectively. Subsequently, the favoured haplotype combinations of the different genes were obtained, and a series of molecular markers were developed to identify them. Finally, we propose a molecular breeding strategy to enhance the disease resistance of crayfish, and thus, improve its production.

Transcriptomic Analysis Reveals Functional Interaction of mRNA-lncRNA-miRNA in Steroidogenesis and Spermatogenesis of Gynogenetic Japanese Flounder (Paralichthys olivaceus)

Teleost fishes exhibit extraordinary diversity, plasticity and adaptability with their sex determination and sexual development, and there is growing evidence that non-coding RNAs (ncRNAs) are emerging as critical regulators of reproduction. Japanese flounder (Paralichthys olivaceus) is an important marine cultured fish that presents significant sexual dimorphism with bigger females, in which gynogenesis has been applied for aquaculture industry. In order to reveal the regulatory mechanisms of sexual development in gynogenetic female and sex-reversed neo-male P. olivaceus, the lncRNA-miRNA-mRNA interactions were investigated using high-throughput sequencing. A total of 6772 differentially expressed mRNAs (DEmRNAs), 2284 DElncRNAs, and 244 DEmiRNAs were obtained between gynogenetic female ovaries and sex-reversed neo-male testes. Genes in the steroid hormone biosynthesis and secretion pathway were enriched and mostly significantly upregulated in neo-male testes. Subsequently, network analysis uncovered high functional specificity for gynogenetic P. olivaceus sperm motility, as co-expressed DEmRNAs were significantly enriched in microtubule and cytoskeleton-related biological processes. Clustered miRNAs were characterized in the P. olivaceus genome with examples of the largest conserved let-7 clusters. The 20 let-7 members are distributed in 11 clusters and may not transcribe together with their neighboring miR-125b, with let-7 repressing cyp11a and miR-125b repressing esr2b, both as key steroidogenesis pathway genes. In summary, this study provides comprehensive insights into the mRNA-miRNA-lncRNA functional crosstalk in teleost sexual development and gametogenesis and will expand our understanding of ncRNA biology in teleost gynogenesis.

Linkage mapping and QTL analysis of growth traits in Rhopilema esculentum

R. esculentum is a popular seafood in Asian countries and an economic marine fishery resource in China. However, the genetic linkage map and growth-related molecular markers are still lacking, hindering marker assisted selection (MAS) for genetic improvement of R. esculentum. Therefore, we firstly used 2b-restriction site-associated DNA (2b-RAD) method to sequence 152 R. esculentum specimens and obtained 9100 single nucleotide polymorphism (SNP) markers. A 1456.34 cM linkage map was constructed using 2508 SNP markers with an average interval of 0.58 cM. Then, six quantitative trait loci (QTLs) for umbrella diameter and body weight were detected by QTL analysis based on the new linkage map. The six QTLs are located on four linkage groups (LGs), LG4, LG13, LG14 and LG15, explaining 9.4% to 13.4% of the phenotypic variation. Finally, 27 candidate genes in QTLs regions of LG 14 and 15 were found associated with growth and one gene named RE13670 (sushi, von Willebrand factor type A, EGF and pentraxin domain-containing protein 1-like) may play an important role in controlling the growth of R. esculentum. This study provides valuable information for investigating the growth mechanism and MAS breeding in R. esculentum.

A New Type of Allodiploid Hybrids Derived From Female Megalobrama amblycephala × Male Gobiocypris rarus

Distant hybridization can combine whole genomes from parent species and result in changes in the phenotypes and genotypes in hybrids. The characteristics of many hybrid fishes with even number of chromosomes have been reported, but the hybrids with odd number chromosomes are rarely reported. Blunt snout bream (Megalobrama amblycephala, BSB, 2n = 48) and rare gudgeon (Gobiocypris rarus, RG, 2n = 50) belong to two different subfamilies and have quite different biological characteristics. In this study, we obtain the hybrids (BR) derived from the inter-subfamily hybridization of female BSB and male RG. We investigate the fertilization rate, hatching rate, morphological traits, chromosomal numbers, DNA content, growth rates, and 5S rDNA in the BR. The results show that the BR is an allodiploid fish with 49 chromosomes, and all the measurable traits are significantly different (p < 0.05) among BR, BSB, and BR. Interestingly, the upper part of the BR body color is similar to BSB (gray), the lower part of the BR body color is similar to RG (light yellow), and the BR inherits a unique light yellow wide longitudinal band from the RG. Furthermore, the BR has a fast growth rate compared with RG. The 5S rDNA of the BR inherits the specific bands of its parental 5S rDNA respectively and has some mutations, which show obvious recombination, heredity, and variability in BR. This study will be of great significance in fish genetic breeding.

Rapid Genomic and Epigenetic Alterations in Gynogenetic Carassius auratus Red Var. Derived from Distant Hybridization

Gynogenesis is an important reproductive mode in fish and is used fairly widely in genetic breeding. Gynogenetic offspring (2n = 100, abbreviated as GRCC) were generated through the distant hybridization of Carassius auratus red var. (2n = 100, RCC) (♀) × Megalobrama amblycephala (2n = 48, BSB) (♂), in which male and female individual both had normal gonadal development. To better understand genomic and epigenetic consequences of GRCC, fluorescence in situ hybridization, amplified fragment length polymorphism, and methylation-sensitive amplification polymorphism analysis were performed on GRCC and RCC. GRCC possess two sets of RCC-derived chromosomes and one to three microchromosomes, in which 30.44% of bands inherit these patterns from red crucian carp and blunt snout bream, and 24.12% of novel bands were found by amplified fragment length polymorphism analysis. In terms of methylation, the DNA methylation level of GRCC was lower than that of their parents, and 45.29% of methylation patterns in GRCC were altered compared with their parents. GRCC show a special genetic composition in the genome, in which genome-wide changes and the adjustment of DNA methylation levels and patterns occurred. The result revealed that genetic and epigenetic changes were rapidly triggered in gynogenetic fish that were derived from distant hybridization, showing a special genetic composition in the genome. This study provides new insights into fish genetic breeding and the evolutionary patterns of the vertebrate genome.

Evaluating the genetic structure of wild and commercial red cusk-eel (Genypterus chilensis) populations through the development of novel microsatellite markers from a reference transcriptome

The red cusk-eel (Genypterus chilensis) is a native Chilean species with a high-value market, with the potential to diversify Chilean aquaculture. The objective of this study was to develop a set of microsatellite markers, estimate genetic parameters, determine population differentiation, and identify the population structure of wild and commercial populations of G. chilensis. We discovered 6427 microsatellites markers from RNA-seq data, of which 54.9%, 20.2% and 16.8% were di-, tri-, and tetranucleotides, respectively. We used 12 of these markers to genotype two sets of broodstock, one group from commercial fish, and one group from wild fish from the Coquimbo Region of G. chilensis. We estimate the genetic parameters of the markers, selecting ten polymorphic markers (PIC > 0.5). We observed differences in the inbreeding coefficient among populations, with high values of inbreeding in one broodstock set and lower values in the other groups. The evaluation of population differentiation using Fst showed small (0.0195) to large (0.1888) genetic differentiation between the groups. The structure analysis showed that commercial and wild groups were formed by three clusters, without relevant evidence of admixture process, suggesting that groups evaluated in this study are formed of at least three subpopulations of G. chilensis, which could be explained by the low or lack of migration suggested for this species. This is the first study that identifies a high number of molecular markers in G. chilensis, providing relevant information of the genetic structure of commercial and wild population of this species.

Zebrafish breeding program: genetic parameters estimates for growth traits

The objective of this study was to evaluate the genetic parameters of two generations of zebrafish breeding program. The base population was formed by crossing individuals of six commercial stocks of zebrafish, resulting in a nucleus with 60 families. Two generations were evaluated, with a total of 780 and 781 individuals for the first and second generation, respectively. The selection was made based on the mean genetic value of each family, followed by mass selection of the breeders. Mathematical models that considered the fixed (age, density in the larval stage, sex, and generation) and random (animal additive genetics, common to full-sibs, and residual) effects were evaluated using BLUPF90 program family. Weight and total length were used as response variables. Total length was the best selection criterion because it had a higher heritability (0.30) than weight (0.22). There was a high common to full-sib effect, especially in the first generation of animals. For second-generation data, the heritability was 0.26 for total length, as well as a lower common to full-sib effect for length. The best model obtained for this evaluation was considering all effects, being age and density as first and second polynomial, respectively. The genetic and phenotypic correlations for weight and length were 0.87 and 0.75, respectively. These results indicate that genetic breeding using total length as the selection criterion may produce a larger and heavier zebrafish strain.

Insertional mutagenesis in ChordinA induced by endogenous ΔTgf2 transposon leads to bifurcation of axial skeletal systems in grass goldfish

The grass goldfish appeared early in the evolutionary history of goldfish, and shows heritable stability in the development of the caudal fin. The twin-tail phenotype is extremely rare, however, some twin-tail individuals were produced in the process of breeding for ornamental value. From mutations in the twin-tail goldfish genome, we identified two kinds of Tgf2 transposons. One type was completely sequenced Tgf2 and the other type was ΔTgf2, which had 858 bp missing. We speculate that the bifurcation of the axial skeletal system in goldfish may be caused by an endogenous ΔTgf2 insertion mutation in Chordin A, as ΔTgf2 has no transposition activity and blocks the expression of Chordin A. The twin-tail showed doubled caudal fin and accumulation of red blood cells in the tail. In addition, in situ hybridization revealed that ventral embryonic tissue markers (eve1, sizzled, and bmp4) were more widely and strongly expressed in the twin-tail than in the wild-type embryos during the gastrula stage, and bmp4 showed bifurcated expression patterns in the posterior region of the twin-tail embryos. These results provide new insights into the artificial breeding of genetically stable twin-tail grass goldfish families.

Targeted disruption of tyrosinase causes melanin reduction in Carassius auratus cuvieri and its hybrid progeny

The white crucian carp (Carassius auratus cuvieri, WCC) not only is one of the most economically important fish in Asia, characterized by strong reproductive ability and rapid growth rates, but also represents a good germplasm to produce hybrid progenies with heterosis. Gene knockout technique provides a safe and acceptant way for fish breeding. Achieving gene knockout in WCC and its hybrid progeny will be of great importance for both genetic studies and hybridization breeding. Tyrosinase (TYR) is a key enzyme in melanin synthesis. Depletion of tyr in zebrafish and mice results in mosaic pigmentation or total albinism. Here, we successfully used CRISPR-Cas9 to target tyr in WCC and its hybrid progeny (WR) derived from the cross of WCC (♀) and red crucian carp (Carassius auratus red var., RCC, ♂). The level of TYR protein was significantly reduced in mutant WCC. Both the mutant WCC and the mutant WR showed different degrees of melanin reduction compared with the wild-type sibling control fish, resulting from different mutation efficiency ranging from 60% to 90%. In addition, the transcriptional expression profiles of a series of pivotal pigment synthesis genes, i.e. tyrp1, mitfa, mitfb, dct and sox10, were down-regulated in tyr-CRISPR WCC, which ultimately caused a reduction in melanin synthesis. These results demonstrated that tyr plays a key role in melanin synthesis in WCC and WR, and CRISPR-Cas9 is an effective tool for modifying the genome of economical fish. Furthermore, the tyr-CRISPR models could be valuable in understanding fundamental mechanisms of pigment formation in non-model fish.

A comparative study of distant hybridization in plants and animals

Distant hybridization refers to crosses between two different species, genera, or higher-ranking taxa, which can break species limits, increase genetic variation, and combine the biological characteristics of existing species. It is an important way of creating genetic variation, fertile strains, and excellent characteristics in new strains and populations. Combining analyses and summaries from many inter-related documents in plants and animals, both domestic and international, including examples and long-standing research on distant hybridization in fish from our laboratory, we summarize and compare the similarities and differences in plant and animal distant hybridization. In addition, we analyze and review the biological characteristics of their different ploidy progenies and the possible causes of disparity in survival rates. Mechanisms of sterility in animal and plant distant hybrids are also discussed, and research methods for the study of biological characteristics of hybrids, including morphology, cytology, and molecular cytogenetics are presented. This paper aims to provide comprehensive research materials and to systematically compare the general and specific characteristics of plant and animal hybrids with regards to reproduction, genetics, growth traits, and other biological characteristics. It is hoped that this paper will have great theoretical and practical significance for the study of genetic breeding and biological evolution of plant and animal distant hybridization.

Characterization of pax3a and pax3b genes in artificially induced polyploid and gynogenetic olive flounder (Paralichthys olivaceus) during embryogenesis

Although chromosome set manipulation techniques including polyploidy induction and gynogentic induction in flatfish are becoming increasingly mature, there exists a poor understanding of their effects on embryonic development. PAX3 plays crucial roles during embryonic myogenesis and neurogenesis. In olive flounder (Paralichthys olivaceus), there are two duplicated pax3 genes (pax3a, pax3b), and both of them are expressed in the brain and muscle regions with some subtle regional differences. We utilized pax3a and pax3b as indicators to preliminarily investigate whether chromosome set manipulation affects embryonic neurogenesis and myogenesis using whole-mount in situ hybridization. In the polyploid induction groups, 94 % of embryos in the triploid induction group had normal pax3a/3b expression patterns; however, 45 % of embryos in the tetraploid induction group showed abnormal pax3a/3b expression patterns from the tailbud formation stage to the hatching stage. Therefore, the artificial induction of triploidy and tetraploidy had a small or a moderate effect on flounder embryonic myogenesis and neurogenesis, respectively. In the gynogenetic induction groups, 87 % of embryos in the meiogynogenetic diploid induction group showed normal pax3a/3b expression patterns. However, almost 100 % of embryos in the gynogenetic haploid induction group and 63 % of embryos in the mitogynogenetic diploid induction group showed abnormal pax3a/3b expression patterns. Therefore, the induction of gynogenetic haploidy and mitogynogenetic diploidy had large effects on flounder embryonic myogenesis and neurogenesis. In conclusion, the differential expression of pax3a and pax3b may provide new insights for consideration of fish chromosome set manipulation.

Recent Major Advances of Biotechnology and Sustainable Aquaculture in China

Background:

Global aquaculture production has increased continuously over the last five decades, and particularly in China. Its aquaculture has become the fastest growing and most efficient agri-sector, with production accounting for more than 70% of the world’s aquaculture output. In the new century, with serious challenges regarding population, resources and the environment, China has been working to develop high-quality, effective, healthy, and sustainable blue agriculture through the application of modern biotechnology. Sound knowledge related to the biology and ecology of aquatic organisms has laid a solid foundation and provided the innovation and technology for rapid development of the aquaculture industry. Marine biotechnology, which is enabling solutions for ocean productivity and sustainability, has been promoted since the last decades of the 20th Century in China.

Objective:

In this article, priority areas of research, mainly genetic breeding, omics studies, novel production systems, biosecurity, bioprocesses and biorefinery, as well as the major progress of marine biotechnology R&D in China are reviewed.

Conclusion:

Current innovative achievements in China are not enough and the level and frequency of academic advancements must be improved. International cooperation and assistance remain crucial for the success of marine biotechnology.