Comparative expression analyses of bone morphogenetic protein 4 ( BMP4 ) expressions in muscles of tilapia and common carp indicate that BMP4 plays a role in the intermuscular bone distribution in a dose-dependent manner

Hormonal regulation and expression dynamics of Bmp4 in the reproductive cycle of Pampus argenteus

As a member of the bone morphogenetic protein (BMP) family, Bmp4 plays a crucial role in bone formation, early developmental stage and the regulation of gonadal development. This study aims to investigate the expression patterns and potential functions of the Bmp4 in Pampus argenteus during its reproductive cycle. A systematic evolutionary analysis of the Bmp4 was performed, and its expression was quantified and localized using real-time polymerase chain reaction (PCR), Western blotting and immunohistochemistry. Additionally, the effects of various hormones on hormone-related genes were analysed in vitro using cultured testes, ovaries and oocytes. The results revealed that Bmp4 is evolutionarily conserved and broadly expressed across tissues. Notably, its expression significantly increased at 4 and 13 days post-hatching (dph), with no significant differences observed at other developmental stages. Western blotting identified a specific Bmp4 target band in Stage III ovaries, and immunohistochemistry localized Bmp4 expression in oogonia, oocytes and spermatogonia. In vitro hormonal treatments demonstrated that oestradiol (E2) significantly upregulated bmp4 expression in both testes and ovaries, with expression levels being notably higher in ovaries. In immature vitellogenic oocytes cultured in vitro, sex hormone treatments did not significantly affect the expression of bmp4, lhr, fshr and lhβ. However, under LH + hCG treatment (50 ng/mL and 5 IU/mL), the expression of fshβ was upregulated. In summary, our findings reveal that Bmp4 serves as a pivotal factor in the early development of the gonads and germ cells in P. argenteus. The expression of Bmp4 within the ovary is likely regulated by E2. During the early-stage development of the ovary, E2 and Bmp4 may jointly promote the early-stage development and differentiation of germ cells. This study offers a valuable theoretical foundation for addressing challenges in the breeding process.

Transforming growth factor-beta gene family in Labeo rohita: Genome-wide molecular characterization and phylogenetic relationship with other vertebrates

Recent advancements in animal genetics, biotechnology, and bioinformatics can potentially contribute to the required improvement in fish production and quality. Current study explored for the first-time, various genes from Transforming growth factor-beta (TGF-β) gene family which could play vital role in growth and development of Labeo rohita, an economically important freshwater fish. A number of tools and analysis like characterizing the selected genes, multiple alignment and clade-wise phylogeny, dual Synteny analysis and chromosomal distribution, characterization of proteins, secondary structure and 3D models of proteins, PROSITE scan analysis, and transcription factor binding sites (TFBSs) of selected genes were performed to explore the relationship between selected genes from Labeo rohita and referenced species (Homo sapiens, Danio rerio, Oreochromis niloticus, Chelonia mydas, and Parus major). The study evaluated 27 genes from TGF-β gene family. The results suggested that physicochemical characteristics of studied genes exhibit a basic nature with the few exceptions. Two main clades (BPM like and GDF like) were obtained by the phylogenetic analysis across six vertebrate species. Homogeneity was observed in the gene structure for all selected genes of TGF-β gene superfamily. TGF-β family and TGF-β propeptide family were dominant in domain regions of studied genes. Gene structure comparisons suggested that the TGF-β gene superfamily has arisen by gene duplications events. The study identified five pairs of duplicated gene (segmental duplications) with the Ka/Ks < 1, indicating the negative selection pressure of these genes. The length of selected TFBSs (GATA, HOXD, STAT, HNF-1A, and YY1) ranged from 5 to 9 bp, with the HOXD having maximum bp. This study explored the molecular characterization for TGF-β gene family and related proteins in L. rohita and will potentially serve as basis of development of novel strategies in improvement of fish culture.

Decoding the fish genome opens a new era in important trait research and molecular breeding in China

Aquaculture represents the fastest-growing global food production sector, as it has become an essential component of the global food supply. China has the world's largest aquaculture industry in terms of production volume. However, the sustainable development of fish culture is hindered by several concerns, including germplasm degradation and disease outbreaks. The practice of genomic breeding, which relies heavily on genome information and genotypephenotype relationships, has significant potential for increasing the efficiency of aquaculture production. In 2014, the completion of the genome sequencing and annotation of the Chinese tongue sole signified the beginning of the fish genomics era in China. Since then, domestic researchers have made dramatic progress in functional genomic studies. To date, the genomes of more than 60 species of fish in China have been assembled and annotated. Based on these reference genomes, evolutionary, comparative, and functional genomic studies have revolutionized our understanding of a wide range of biologically and economically important traits of fishes, including growth and development, sex determination, disease resistance, metamorphosis, and pigmentation. Furthermore, genomic tools and breeding techniques such as SNP arrays, genomic selection, and genome editing have greatly accelerated genetic improvement through the incorporation of functional genomic information into breeding activities. This review aims to summarize the current status, advances, and perspectives of the genome resources, genomic study of important traits, and genomic breeding techniques of fish in China. The review will provide aquaculture researchers, fish breeders, and farmers with updated information concerning fish genomic research and breeding technology. The summary will help to promote the genetic improvement of production traits and thus will support the sustainable development of fish aquaculture.

Functional modularity and mechanical stress shape plastic responses during fish development

The adaptive potential of plastic phenotypes relies on combined developmental responses. We investigated how manipulation of developmental conditions related to foraging mode in the fish Megaleporinus macrocephalus induces plastic responses at different levels: (a) functional modularity of skull bones, (b) biomechanical properties of the chondrocranium using finite element models, (c) bmp4 expression levels, used as a proxy for molecular pathways involved in bone responses to mechanical load. We identified new modules in experimental groups, suggesting increased integration in specific head bone elements associated with the development of subterminal and upturned mouths, which are major features of Megaleporinus plastic morphotypes released in the lab. Plastic responses in head shape involved differences in the magnitude of mechanical stress, which seem restricted to certain chondrocranium regions. Three bones represent a "mechanical unit" related to changes in mouth position induced by foraging mode, suggesting that functional modularity might be enhanced by the way specific regions respond to mechanical load. Differences in bmp4 expression levels between plastic morphotypes indicate associations between molecular signaling pathways and biomechanical responses to load. Our results offer a multilevel perspective of epigenetic factors involved in plastic responses, expanding our knowledge about mechanisms of developmental plasticity that originate novel complex phenotypes.

Screening for IBs-relative genes by transcriptome analysis and generation IBs-less mutants in Culter alburnus

Intermuscular bones (IBs), distributed specifically in the myosepta on both sides of lower teleosts, negatively affect palatability and processing. Recent research in zebrafish and several economically important farmed fishes has led to the breakthrough discovery of the mechanism of IBs formation and generation of IBs-loss mutants. This study explored the ossification patterns of IBs in juvenile Culter alburnus. Besides, some key genes and bone-related signaling pathways were identified by transcriptomic data. Furthermore, PCR microarray validation revealed that claudin1 could potentially regulate IBs formation. Additionally, we created several IBs-reduced mutants of C. alburnus by loss of the function of bone morphogenetic proteins 6 (bmp6) gene using CRISPR/Cas9 editing. These results suggested that CRISPR/Cas9-mediated bmp6 knockout was promising approach for breeding IBs-free strain in other cyprinids.

QNZ exposure induces development toxicity and mechanisms of hatching inhibition in large-scale loach (Paramisgurnus dabryanus) embryos

QNZ is a quinazoline-type NF-κB inhibitor and is one of the hot anti-inflammatory drug candidates in recent years. With its development and application, QNZ will inevitably enter the aquatic environment posing a threat to aquatic organisms. To investigate the potential toxicity of QNZ in the early life stages of the organism, this study exposed embryos of large-scale loach (Paramisgurnus dabryanus) to 0, 20, 40, 60, and 80 nM of QNZ. The hatching of embryos was significantly inhibited and hatching time was delayed. We explored the mechanism of hatching delay and failure. The results suggested that QNZ exposure reduced the number of hatching gland cells (HGCs) and hatching enzyme activity. Also, the frequency of spontaneous movements was inhibited by interfering with the expression of genes related to the cholinergic system and skeletal muscle development. Further, QNZ exposure induces a series of morphological changes (spine deformation, pericardial edema, tail deformation, and yolk sac edema) in embryos and newly-hatched larvae, and finally increased the deformity rate and mortality rate of newly-hatched larvae. The information presented in this study will provide a scientific basis for further studies into the potential toxicity of QNZ on aquatic organisms.

Transcriptomic analysis of intermuscular bone development in barbel steed (Hemibarbus labeo)

Intermuscular bones (IBs), which are little, bony spicules in muscle, are embedded in lower teleosts' myosepta. Despite the importance of studying IB development in freshwater aquaculture species, the genes associated with IB development need to be further explored. In the present study, we identified four stages of IB development in barbel steed (Hemibarbus labeo), namely stage 1: IBs have not emerged, stage 2: a few small IBs have emerged in the tail, stage 3: longer IBs gradually emerged in the tail and stage 4: all of the IBs in the tail are mature and long, via Alizarin red staining. Subsequently, we used the HiseqXTen platform to sequence and de novo assemble the transcriptome of epaxial muscle (between 35th and 40th myomere) of barbel steed at 29 days (stage 1) and 42 days (stage 3) after hatching. A total of 190,814 unigenes were obtained with an average length and N50 of 648 bp and 1027 bp, respectively. We found 2174 differentially expressed genes (DEGs) between stages 1 and 3, of which 378 and 1796 were up- and down-regulated, respectively. Functional enrichment analysis showed that several DEGs functioned in ossification, positive regulation of osteoblast differentiation, osteoblast differentiation, and BMP signaling pathway, and were further enriched in signal pathway, including osteoclast differentiation, TGF-β signaling pathway, cytokine-cytokine receptor interaction, Jak-STAT signaling pathway, and other KEEG pathways. In conclusion, we identified genes that may be related to IB development, such as kazal type serine peptidase inhibitor domain 1 (KAZALD1), extracellular matrix protein 1 (ECM1), tetranectin, bone morphogenetic protein 1 (bmp1), acid phosphatase 5 (ACP5), collagen type XI alpha 1 chain (COL11A1), matrix metallopeptidase 9 (MMP9), pannexin-3 (PANX3), sp7 transcription factor (Sp7), and c-x-c motif chemokine ligand 8 (CXCL8), by comparing the transcriptomes of epaxial muscle before and after IB ossification. This study provided a theoretical basis for identifying the molecular mechanisms underlying IB development in fish.

Hydroxytyrosol-rich extract from olive juice as an additive in gilthead sea bream juveniles fed a high-fat diet: Regulation of somatic growth

The dietary inclusion of plant-based products in fish feeds formulation is required for the sustainable development of aquaculture. Moreover, considering functional diets, hydroxytyrosol, one of the major phenolic compounds found in olives (Olea europaea), has been identified as a potential candidate to be used in the aquafeeds industry due to its health promoting abilities. The aim of this study was to evaluate the effects of the inclusion of an olive juice extract rich in hydroxytyrosol as an additive (0.52 g HT/kg feed) in a high-fat (24% lipids) diet in gilthead sea bream (Sparus aurata) juveniles. Moreover, the experimental diets, with or without the extract, were administered daily at a standard (3% of total biomass in the tank) or restricted ration (40% reduction) for 8–9 weeks. Growth and biometric parameters, insulin-like growth factor 1 (IGF-1) plasma levels and growth hormone/IGF axis-, myogenic- and osteogenic-related genes expression in liver, white muscle and/or bone were analyzed. Moreover, in vitro cultures of vertebra bone-derived cells from fish fed the diets at a standard ration were performed at weeks 3 and 9 to explore the effects of hydroxytyrosol on osteoblasts development. Although neither body weight or any other biometric parameter were affected by diet composition after 4 or 8 weeks, the addition of the hydroxytyrosol-rich extract to the diet increased IGF-1 plasma levels, regardless of the ration regime, suggesting an anabolic condition. In muscle, the higher mRNA levels of the binding protein igfbp-5b and the myoblast fusion marker dock5 in fish fed with the hydroxytyrosol-rich diet suggested that this compound may have a role in muscle, inducing development and a better muscular condition. Furthermore in bone, increased osteogenic potential while delayed matrix mineralization after addition to the diet of the olive juice extract was supported by the upregulated expression of igf-1 and bmp4 and reduced transcript levels of osteopontin. Overall, this study provides new insights into the beneficial use of hydroxytyrosol as a dietary additive in gilthead sea bream functional diets to improve muscle-skeletal condition and, the aquaculture industry.

Effects of Shigella flexneri exposure on development of Xenopus Tropicals embryo and its immune response

Shigella sp. is a highly infectious intestinal pathogen worthy of serious attention that is widely present in aquaculture water and some other polluted water types and might inhibit embryonic development as a biological pollutant. In this study, acute toxicity tests in which Xenopus tropical embryos were exposed to Shigella flexneri at subpathogenic concentrations (10⁶, 10⁷, and 10⁸ CFU·mL^-1) for 96 h were carried out to evaluate toxicity indicators such as mortality, hatching rate, malformation rate and enzyme activity. Meanwhile, the expression of related genes was also studied to reveal the toxicity and mechanism of S. flexneri involved in embryonic development. Under S. flexneri exposure, embryo mortality, heart rate and malformation rate increased, but the hatching rate decreased and even led to embryonic gene misexpression, oxidative stress and immune responses. The results showed that S. flexneri might affect the growth and development of embryos by causing differences in the expression of genes related to embryonic development, oxidative stress and immune disorders. Its target organs are the intestine and heart, whose toxic effects are positively correlated with exposure concentration. This result provides a certain theoretical reference for rational evaluation of the influence of Shigella on the early embryos of amphibians.

Bulked Segregant Analysis and Association Analysis Identified the Polymorphisms Related to the Intermuscular Bones in Common Carp (Cyprinus carpio)

Simple Summary

Many widely cultured freshwater fish species, such as common carp, belong to the Cyprinidae family. However, most cyprinids have numerous and complex intermuscular bones (IBs), resulting in an adverse effect on cyprinid fish meat processing and consumption. Numerous studies have been trying to understand the development mechanism of IBs and to identify the SNPs associated with the total IB number. However, the SNPs associated with different forms of IBs have been studied less thoroughly. The joint effects of the SNPs on IB development also remain poorly understood. The common carp has numerous geographical populations and domesticated strains, diversifying its phenotypes. The question of whether consensus IB-related SNPs or genes exist among multiple strains of common carp has also not yet been answered. Selective breeding of IB-reduced common carp has been hindered due to a lack of effective molecular markers. To answer these questions, we performed bulked segregant analysis (BSA) to detect the consensus SNPs in three strains. The consensus BSA-SNPs and the other SNPs in their flanking regions were validated in additional individuals. The SNPs associated with the frequency of different IB types were identified. We examined the joint effects of significant SNPs on the numbers of different types of IBs. The identified genetic markers may benefit future selective breeding and reduce the IB number in common carp.

Abstract

The allotetraploid common carp is one of the most important freshwater food fish. However, the IBs found in allotetraploid common carp increase the difficulty in fish meat processing and consumption. Although candidate genes associated with the total IB number have been identified, the SNPs associated with the numbers of the total IBs and different forms of IBs have not yet been identified, hindering the breeding of IB-reduced common carp. Herein, the numbers of different types of IBs in three common carp strains were measured. Using whole-genome resequencing and bulked segregant analysis in three pairs of IB-more and IB-less groups, we identified the consensus nonsynonymous SNPs in three strains of common carp. Screening the flanking regions of these SNPs led to the detection of other SNPs. Association study detected 21 SNPs significantly associated with the number of total IBs, epineural-IBs, and ten detailed types of IBs. We observed the joint effects of multiple SNPs on each associated IB number with an improved explained percentage of phenotypic variation. The resulting dataset provides a resource to understand the molecular mechanisms of IB development in different common carp strains. These SNPs are potential markers for future selection to generate IB-reduced common carp.

Comparison of Myosepta Development and Transcriptome Profiling between Blunt Snout Bream with and Tilapia without Intermuscular Bones

Simple Summary

The presence or absence of intermuscular bones (IBs) is directly related to the economic and edible value of fish. The specific regulatory mechanism of IB formation is not completely known yet. Here, we explored the molecular mechanisms that regulate the formation of IBs based on histological analysis, transcriptome profiling, and gene expression quantification using M. amblycephala (with IBs) and O. niloticus (without IBs) as models. As a result, we identified several bone-related genes and elucidated their regulatory roles in the development of IBs.

Abstract

Intermuscular bones (IBs) are small spicule-like bones located in the myosepta of basal teleosts, which negatively affect the edibleness and economic value of fish. Blunt snout bream (Megalobrama amblycephala, with epineural and epipleural IBs) and tilapia (Oreochromis niloticus, without epineural and epipleural IBs) are two major aquaculture species and ideal models for studying the formation mechanisms of fish IBs. Here, we compared myosepta development between M. amblycephala and O. niloticus, based on histological analysis, transcriptome profiling, and expression analysis of bone-related genes. The histological results showed that dye condensation began to appear in the myosepta 20 days post hatching (dph) in M. amblycephala, and IBs could be clearly observed 50 dph in the myosepta, based on different staining methods. However, in O. niloticus, dye condensation was not observed in the myosepta from 10 to 60 dph. Differentially expressed genes (DEGs) at different developmental stages were screened by comparing the transcriptomes of M. amblycephala and O. niloticus, and KEGG analysis demonstrated that these DEGs were enriched in many bone-related pathways, such as focal adhesion, calcium, and Wnt signaling pathways. Quantitative PCR was performed to further compare the expression levels of some bone-related genes (scxa, scxb, runx2a, runx2b, bgp, sp7, col1a2, entpd5a, entpd5b, phex, alpl, and fgf23). All the tested genes (except for alpl) exhibited higher expression levels in M. amblycephala than in O. niloticus. A comparison of the dorsal and abdominal muscle tissues between the two species also revealed significant expression differences for most of the tested genes. The results suggest that scxa, scxb, runx2a, runx2b, entpd5a, col1a2, and bgp may play important roles in IB development. Our findings provide some insights into the molecular mechanisms of IB formation, as well as clues for further functional analysis of the identified genes to better understand the development of IBs.

Toxicity of 2-methyl-4-chlorophenoxy acetic acid alone and in combination with cyhalofop-butyl to Cyprinus carpio embryos

Herbicides may pose considerable danger to non-target aquatic organisms and further threaten human health. The present investigation was aimed to assess the effects of 2-methyl-4-chlorophenoxy acetic acid (MCPA-Na) on Cyprinus carpio embryos. Embryos were exposed to six concentrations of MCPA-Na (0, 52, 54, 56, 58 and 60 mg/L) for 96 h. A series of symptoms were observed in developmental embryos during MCPA-Na exposure, including increased death, hatching inhibited and morphological deformities. Further, MCPA-Na exposure leading to a series of morphological changes (pericardial edema, tail deformation, and spine deformation) in embryos, which were consistent with modifications in the associated genes. In this work, we also investigated the joint toxicity of herbicides (MCPA-Na and cyhalofop-butyl) commonly used in paddy fields on carp embryos, using the 96 h-LC₅₀ of herbicides (59.784 mg/L MCPA-Na and 1.472 mg/L cyhalofop-butyl) and confirmed that a synergistic effect existing in the binary mixtures.

Molecular mechanisms of intermuscular bone development in fish: a review

Intermuscular bones (IBs) are slender linear bones embedded in muscle, which ossify from tendons through a process of intramembranous ossification, and only exist in basal teleosts. IBs are essential for fish swimming, but they present a choking risk during human consumption, especially in children, which can lead to commercial risks that have a negative impact on the aquaculture of these fish. In this review, we discuss the morphogenesis and functions of IBs, including their underlying molecular mechanisms, as well as the advantages and disadvantages of different methods for IB studies and techniques for breeding and generating IB-free fish lines. This review reveals that the many key genes involved in tendon development, osteoblast differentiation, and bone formation, e.g., scxa, msxC, sost, twist, bmps, and osterix, also play roles in IB development. Thus, this paper provides useful information for the breeding of new fish strains without IBs via genome editing and artificial selection.

Effects of antidepressants with different modes of action on early life stages of fish and amphibians

Drugs are excreted from the human body as both original substances and as metabolites and enter aquatic environment through waste water. The aim of this study was to widen the current knowledge considering the effects of waterborne antidepressants with different modes of action-amitriptyline, venlafaxine, sertraline-on embryos of non-target aquatic biota-fish (represented by Danio rerio) and amphibians (represented by Xenopus tropicalis). The tested concentrations were 0.3; 3; 30; 300 and 3000 μg/L in case of amitriptyline and venlafaxine and 0.1; 1; 10; 100 and 1000 μg/L for sertraline. Test on zebrafish embryos was carried out until 144 h post fertilization, while test on Xenopus embryos was terminated after 48 h. Lethal and sublethal effects as well as swimming alterations were observed at higher tested concentrations that are not present in the environment. In contrast, mRNA expression of genes related to heart, eye, brain and bone development (nkx2.5, otx 2, bmp4 and pax 6) seems to be impacted also at environmentally relevant concentrations. In a wider context, this study reveals several indications on the ability of antidepressants to affect non target animals occupying environments which may be contaminated by such compounds.