Elevated expressions of GH/IGF axis genes in triploid crucian carp

Role of Phytobiotics in Modulating Transcriptomic Profile in Carps: A Mini-Review

Carp is a key aquaculture species worldwide. The intensification of carp farming, aimed at meeting the high demand for protein sources for human consumption, has resulted in adverse effects such as poor water quality, increased stress, and disease outbreaks. While antibiotics have been utilized to mitigate these issues, their use poses risks to both public health and the environment. As a result, alternative and more sustainable practices have been adopted to manage the health of farmed carp, including the use of probiotics, prebiotics, phytobiotics, and vaccines to prevent disease outbreaks. Phytobiotics, being both cost-effective and abundant, have gained widespread acceptance. They offer various benefits in carp farming, such as improved growth performance, enhanced immune system, increased antioxidant capacity, stress alleviation from abiotic factors, and enhanced disease resistance. Currently, a focal point of research involves employing molecular approaches to assess the impacts of phytobiotics in aquatic animals. Gene expression, the process by which genetic information encoded is translated into function, along with transcription profiling, serves as a crucial tool for detecting changes in gene expression within cells. These changes provide valuable insights into the growth rate, immune system, and flesh quality of aquatic animals. This review delves into the positive impacts of phytobiotics on immune responses, growth, antioxidant capabilities, and flesh quality, all discerned through gene expression changes in carp species. Furthermore, this paper explores existing research gaps and outlines future prospects for the utilization of phytobiotics in aquaculture.

Growth performance, health status, gut microbiome, and expression of immune and growth-related genes of rainbow trout (Oncorhynchus mykiss) fed diets with pea protein replacement of fish meal

The need for fish meal constrains fish farming and significantly impacts sustainability of the aquaculture industry. Hence, it is important to investigate the use of plant-based protein sources in fish diets. The present study was conducted to determine the effects of different levels of fish meal (FM) replacement by pea protein (PP) in a 60-day feeding experiment in rainbow trout, Oncorhynchus mykiss. Effects on growth performance, body composition, hematology, serum biochemistry and immunology, and immune (TNF-α, IL1-ß and Il-8) and growth-related (GH and IGFI) gene expression were investigated. Five experimental diets (45% protein and 20% lipid) differed in replacement level of FM by PP at rates of 0% (control (PP0)), 25% (PP25), 50%(PP50), 75%(PP75) and 100%(PP100). Fish were fed with experimental diets in triplicate twice daily. The best growth performance was obtained in PP0 and PP25 groups. While fat ratios of fish fillets significantly differed (p < 0.05), there was no significant effects on protein ratios (p < 0.05). There was no significant change in the hematological values of fish, except those fed the PP100 diets, which displayed a reduction in eyrthocyte counts, hemoglobin content and hematocrit. As PP supplementation increased fish showed elevated serum glucose, total protein, cholesterol and myeloperoxidase activity and decreased glutamic pyruvic transaminase and alkaline phosphatase activity. Fish fed diets with between 25 and 75% replacement showed a decline in lactic acid bacteria in the gut. Significant increases in expression were observed in the liver of the PP25 fish relative to the 0% control for all immune and growth-related genes except for IL1-ß. These data suggest that up to 25% of FM can be replaced by PP without any adverse effects on rainbow trout.

A comparative study of dietary amino acid patterns: unveiling growth, composition, and molecular signatures in juvenile Onychostoma macrolepis

The wild Onychostoma macrolepis, a species under national class II protection in China, lacks a specific compound feed for captive rearing. Understanding the dietary amino acid pattern is crucial for optimal feed formulation. This study aimed to investigate the effects of the four different dietary amino acid patterns, i.e., anchovy fishmeal protein (FMP, control group) and muscle protein (MP), whole-body protein (WBP), fish egg protein (FEP) of juvenile Onychostoma macrolepis, on the growth performance, body composition, intestinal morphology, enzyme activities, and the expression levels of gh, igf, mtor genes in juveniles. In a 12-week feeding trial with 240 juveniles (3.46±0.04g), the MP group demonstrated superior outcomes in growth performance (FBW, WGR, SGR), feed utilization efficiency (PER, PRE, FCR). Notably, it exhibited higher crude protein content in whole-body fish, enhanced amino acid composition in the liver, and favorable fatty acid health indices (AI, TI, h/H) in muscle compared to other groups (P < 0.05). Morphologically, the MP and FMP groups exhibited healthy features. Additionally, the MP group displayed significantly higher activities of TPS, ALP, and SOD, along with elevated expression levels of gh, igf, mtor genes, distinguishing it from the other groups (P < 0.05). This study illustrated that the amino acid pattern of MP emerged as a suitable dietary amino acid pattern for juvenile Onychostoma macrolepis. Furthermore, the findings provide valuable insights for formulating effective feeds in conserving and sustainably farming protected species, enhancing the research's broader ecological and aquacultural significance.

Behavioral transcriptomic effects of triploidy and probiotic therapy (Bifidobacterium, Lactobacillus, and Lactococcus mixture) on juvenile Chinook salmon (Oncorhynchus tshawytscha)

Aquaculturists use polyploid fish to maximize production albeit with some unintended consequences including compromised behaviors and physiological function. Given benefits of probiotic therapies (e.g., improved immune response, growth, and metabolism), we explored probiotic supplementation (mixture of Bifidobacterium, Lactobacillus, and Lactococcus), to overcome drawbacks. We first examined fish gut bacterial community composition using 16S metabarcoding (via principal coordinate analyses and PERMANOVA) and determined probiotics significantly impacted gut bacteria composition (p = 0.001). Secondly, we examined how a genomic disruptor (triploidy) and diet supplements (probiotics) impact gene transcription and behavioral profiles of hatchery-reared Chinook salmon (Oncorhynchus tshawytscha). Juveniles from four treatment groups (diploid-regular feed, diploid-probiotic feed, triploid-regular feed, and triploid-probiotic feed; n = 360) underwent behavioral assays to test activity, exploration, neophobia, predator evasion, aggression/sociality, behavioral sensitivity, and flexibility. In these fish, transcriptional profiles for genes associated with neural functions (neurogenesis/synaptic plasticity) and biomarkers for stress response and development (growth/appetite) were (i) examined across treatments and (ii) used to describe behavioral phenotypes via principal component analyses and general linear mixed models. Triploids exhibited a more active behavioral profile (p = 0.002), and those on a regular diet had greater Neuropeptide Y transcription (p = 0.02). A growth gene (early growth response protein 1, p = 0.02) and long-term neural development genes (neurogenic differentiation factor, p = 0.003 and synaptysomal-associated protein 25-a, p = 0.005) impacted activity and reactionary profiles, respectively. Overall, our probiotic treatment did not compensate for triploidy. Our research highlights novel applications of behavioral transcriptomics for identifying candidate genes and dynamic, mechanistic associations with complex behavioral repertoires.

Gene expression analyses of GH/IGF axis in triploid crucian carp with growth heterosis

Hybridization and polyploid breeding are the main approaches used to obtain new aquaculture varieties. Allotriploid crucian carp (3n) with rapid growth performance was generated by mating red crucian carp (RCC) with allotetraploids (4n). Fish growth is controlled by the growth hormone (GH)/insulin-like growth factor (IGF) axis. In the present study, we examined the expression characteristics of GH/IGF axis genes in hybrids F1, 4n, 3n, RCC and common carp (CC). The results showed that GHRa, GHRb, IGF1, IGF2, and IGF-1Ra were highly expressed in 3n compared with RCC and CC, whereas IGF3 was undetectable in the liver in RCC, CC and 3n. GHRa and GHRb had low expression in the 4n group. In hybrid F1, GHRa expression was low, whereas GHRb was highly expressed compared to the levels in RCC and CC. Moreover, in hybrid F1, the expression of IGF3 was higher, and the expression of IGF1 and IGF2 was lower than that in the RCC and CC, whereas the expression of IGF-1Ra was similar to that in RCC and CC. For the IGFBP genes, IGFBP1 had higher expression in 3n compared than that in RCC and CC, while other IGFBP genes were not high expressed in 3n. Among the genes detected in this study, 11 genes were nonadditively expressed in 3n, with 5 genes in the transgressive upregulation model. We proposed that the 11 nonadditive expression of GH/IGF axis genes is related to growth heterosis in 3n. This evidence provides new insights into hybridization and polyploid breeding from the perspective of hormone regulation.

Combination of metabolome and proteome analyses provides insights into the mechanism underlying growth differences in Acipenser dabryanus

To analyze the differences between different-sized Acipenser dabryanus, we randomly selected 600 3-month-old A. dabryanus juveniles. Four months later, the blood and white muscle of these fish were analyzed. The results showed no significant difference in the length-weight relationship (LWR) b value between the large and small A. dabryanus. The levels of serum growth hormone (gh) and insulin-like growth factor 1 (igf1) in the large A. dabryanus were significantly lower than those in the small, whereas the activity levels of Total superoxide dismutase (T-sod) and catalase (cat) were opposite to the results of gh and igf1. A total of 212 and 245 metabolites showed significant changes in the positive and negative polarity mode, respectively. Among 3,308 proteins identified, 69 proteins showed upregulated expression, and 185 proteins showed downregulated expression. These results indicated that the growth advantage of A. dabryanus was closely related to glycolysis, protein synthesis, and antioxidant function.

Telomerase Activity in Somatic Tissues and Ovaries of Diploid and Triploid Rainbow Trout (Oncorhynchus mykiss) Females

Telomerase activity has been found in the somatic tissues of rainbow trout. The enzyme is essential for maintaining telomere length but also assures homeostasis of the fish organs, playing an important role during tissue regeneration. The unique morphological and physiological characteristics of triploid rainbow trout, when compared to diploid specimens, make them a promising model for studies concerning telomerase activity. Thus, in this study, we examined the expression of the Tert gene in various organs of subadult and adult diploid and triploid rainbow trout females. Upregulated Tert mRNA transcription was observed in all the examined somatic tissues sampled from the triploid fish when compared to diploid individuals. Contrastingly, Tert expression in the ovaries was significantly decreased in the triploid specimens. Within the diploids, the highest expression of Tert was observed in the liver and in the ovaries of the subadult individuals. In the triploids, Tert expression was increased in the somatic tissues, while the ovaries exhibited lower activity of telomerase compared to other organs and decreased compared to the ovaries in the diploids. The ovaries of triploid individuals were underdeveloped, consisting of only a few oocytes. The lack of germ cells, which are usually characterized by high Tert expression, might be responsible for the decrease in telomerase activity in the triploid ovaries. The increase in Tert expression in triploid somatic tissues suggests that they require higher telomerase activity to cope with environmental stress and maintain internal homeostasis.

Protective effects of the fructooligosaccharide on the growth performance, biochemical indexes, and intestinal morphology of blunt snout bream (Megalobrama amblycephala) infected by Aeromonas hydrophila

The purpose of the study was to investigate the effects of dietary fructooligosaccharide (FOS) on growth performance, biochemical indexes, intestinal morphology, and growth-related gene expression of blunt snout bream (Megalobrama amblycephala) infected by Aeromonas hydrophila (AH). Two hundred twenty-five healthy blunt snout bream with an initial body weight of 38.41 ± 0.88 g were randomly divided into five groups with three replicates: control (basal diet), model (AH + basal diet), SFOS (AH + 2 g/kg FOS), MFOS (AH + 4 g/kg FOS), LFOS (AH + 6 g/kg FOS). After 9 weeks of feeding, the results showed that the FOS-added diet abrogated AH-induced retardation, hemorrhage, and inflammatory infiltration. FOS supplementation enhanced the growth performance degradation caused by AH, and the highest growth performance was observed at MFOS. Meanwhile, the addition of FOS to feed improved the blood immunity reduced by AH. In expansion, the mucosal epithelium of intestinal villi exfoliated, exposing the lamina propria, and a few villi were genuinely harmed in the model group. Fish fed with MFOS ameliorated the damaged intestine, evidenced by well-preserved intestine architecture. Furthermore, the model group downregulated the expression of growth-related genes (growth hormone receptor (GHR), insulin-like growth factor 1 (IGF-1)). Fish fed with 2 g/kg or 4 g/kg FOS upregulated the genes specified above expressions in the liver compared with the model group. In conclusion, the results mentioned above suggested that the dietary FOS could relieve the pressure to elevate the immune damage and intestine injury induced by AH and enhance the hepatic expression of IGF-1 and GHR.

Effects of dietary nutmeg (Myristica fragrans) seed meals on growth, non-specific immune indices, antioxidant status, gene expression analysis, and cold stress tolerance in zebrafish (Danio rerio)

Introduction

A medicinal plant, Myristica fragrans seed meal (nutmeg), was utilized to evaluate its impact on the growth, immunity, and antioxidant defense of zebrafish (Danio rerio).

Methods

In this regard, zebrafish (0.47 ± 0.04 g) (mean ± S.D.) were fed with 0% (control), 1% (T1-nutmeg), 2% (T2-nutmeg), and 3% (T3-nutmeg) of powdered nutmeg for 70 days. At the end of the feeding trial, growth performance, survival rate of fish, and temperature-challenge effects were recorded. Immune and antioxidant parameters were also assessed through the collection of serum and skin mucus samples.

Results

The results indicated that nutmeg supplementation did not significantly influence the growth of zebrafish (P > 0.05); however, the survival rate of fish fed with 2 and 3% of nutmeg supplementation significantly decreased (P < 0.05). The skin mucus and serum total protein, total immunoglobulin (Ig), and lysozyme activity were significantly increased in T3-nutmeg treatment in comparison to the control (P < 0.05). Superoxide dismutase (SOD) and catalase (CAT) activities were also enhanced in the T3-nutmeg group (P < 0.05). Nutmeg supplementation significantly upregulated the mRNA expression of growth hormone (gh) and insulin growth factor-1 (igf-1). Moreover, the nutmeg inclusion upregulated the expression of interleukin-1β (IL-1β), lysozyme, sod, and cat. The dietary supplementation of nutmeg significantly increased the resistance of zebrafish against cold-water shock and survivability afterward (P < 0.05).

Discussion

In conclusion, the supplementation of 3% powdered nutmeg in zebrafish diets could be suggested as an effective immune stimulator that improves antioxidant defense and stress tolerance.

Advances in understanding the mitogenic, metabolic, and cell death signaling in teleost development: the case of greater amberjack (Seriola dumerili, Risso 1810)

Cell growth and differentiation signals of insulin-like growth factor-1 (IGF-1), a key regulator in embryonic and postnatal development, are mediated through the IGF-1 receptor (IGF-1R), which activates several downstream pathways. The present study aims to address crucial organogenesis and development pathways including Akt, MAPKs, heat shock response, apoptotic and autophagic machinery, and energy metabolism in relation to IGF-1R activation during five developmental stages of reared Seriola dumerili: 1 day prior to hatching fertilized eggs (D-1), hatching day (D0), 3 days post-hatching larvae (D3), 33 (D33) and 46 (D46) days post-hatching juveniles. During both the fertilized eggs stage and larval-to-juvenile transition, IGF-1R/Akt pathway activation may mediate the hypertrophic signaling, while p44/42 MAPK phosphorylation was apparent at S. dumerili post-hatching processes and juvenile organs completion. On the contrary, apoptosis was induced during embryogenesis and autophagy at hatching day indicating a potential involvement in morphogenetic rearrangements and yolk-sac reserves depletion. Larvae morphogenesis was accompanied by a metabolic turnover with increased substantial energy consumption. The findings of the present study demonstrate the developmental stages-specific shift in critical signaling pathways during the ontogeny of reared S. dumerili.

Correlations of expression of nuclear and mitochondrial genes in triploid fish

The expression of nuclear and mitochondrial genes, as well as their coordinated control, regulates cell proliferation, individual development, and disease in animals. However, the potential coregulation between nuclear and mitochondrial genes is unclear in triploid fishes. The two triploids (R2C and RC2) with distinct mitochondrial genomes but similar nuclear genomes exhibit different embryonic development times and growth rates. They are an excellent model for studying how nuclear and mitochondrial genes coordinate. Here, we performed the mRNA-seq of four stages of embryonic development (blastula, gastrula, segmentation, and hatching periods) in the two triploids (R2C and RC2) and their diploid inbred parents (red crucian carp and common carp). After establishing the four patterns of mitochondrial and nuclear gene expression, 270 nuclear genes regulated by mitochondrial genes were predicted. The expression levels of APC16 and Trim33 were higher in RC2 than in R2C, suggesting their potential effects on regulating embryonic development time. In addition, 308 differentially expressed genes filtered from the list of nuclear-encoded mitochondrial genes described by Mercer et al. in 2011 were considered potential genes for which nuclear genes regulate mitochondrial function. The findings might aid in our understanding of the correlation between mitochondrial and nuclear genomes as well as their synergistic effects on embryonic development.

Chronic exposure to tralopyril induced abnormal growth and calcium regulation of turbot (Scophthalmus maximus)

Tralopyril is an emerging marine antifouling agent with limited data on its effects on fish growth and calcium regulation. To determine the changes induced by long-term exposure to tralopyril, multi-levels (such as molecular, biochemical, and individual levels) responses were measured in turbot at different concentrations (1 μg/L, 20 μg/L). The results showed that 1 μg/L mainly affected the immune response, while 20 μg/L affected the synthesis and metabolism of steroids and fat. However, different concentrations of tralopyril affected the synthesis, secretion and action of parathyroid hormone and growth hormone. The expression of GH/IGF axis gene and the level of growth hormone increased significantly, leading to abnormal growth. The energy tradeoff between immunity and growth at 1 μg/L tralopyril pressure may inhibit growth. The change of Ca²⁺ level was accompanied by the disturbance of PTH-related gene expression. The results of molecular docking showed that the disturbance of Ca²⁺ regulation might be attributed to the inhibition of vitamin D receptor by tralopyril, which affected the vitamin D signaling pathway. This study provides scientific data for the in-depth understanding and risk assessment of the toxicological effects of tralopyril and reveals the potential threat of tralopyril to environmental health.

Heterosis of growth trait regulated by DNA methylation and miRNA in allotriploid fish

Background

Heterosis of growth traits in allotriploid fish has benefited the production of aquaculture for many years, yet its genetic and molecular basis has remained obscure. Now, an allotriploid complex, including two triploids and their diploid inbred parents, has provided an excellent model for investigating the potential regulatory mechanisms of heterosis.

Results

Here, we performed a series of analyses on DNA methylation modification and miRNA expression in combination with gene expression in the allotriploid complex. We first established a model of cis- and trans-regulation related to DNA methylation and miRNA in allotriploids. Then, comparative analyses showed that DNA methylation contributed to the emergence of a dosage compensation effect, which reduced gene expression levels in the triploid to the diploid state. We detected 31 genes regulated by DNA methylation in the subgenomes of the allotriploids. Finally, the patterns of coevolution between small RNAs and their homoeologous targets were classified and used to predict the regulation of miRNA expression in the allotriploids.

Conclusions

Our results uncovered the regulatory network between DNA methylation and miRNAs in allotriploids, which not only helps us understand the regulatory mechanisms of heterosis of growth traits but also benefits the study and application of epigenetics in aquaculture.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13072-022-00455-6.

Combined effects of polystyrene microplastics and cadmium on oxidative stress, apoptosis, and GH/IGF axis in zebrafish early life stages

The toxicological interactions of microplastics (MPs) and heavy metals have been paid much attention in aquatic organism. The mechanisms are not fully clear, particularly in fish early life stages. To the end, zebrafish embryos were exposed to 500 μg/L MPs, 5 μg/L cadmium (Cd), and their combination for 30 days. Body weight, adsorption characteristics of Cd onto MPs, Cd accumulation, oxidative stress, apoptosis, and growth hormone/insulin-like growth factor-I (GH/IGF) axis were examined. Exposure to MPs and Cd alone reduced body weight, which was aggravated by co-exposure. An increase in reactive oxygen species (ROS) levels was observed in larvae exposed to Cd or MPs + Cd, suggesting an induction of oxidative stress. Lipid peroxidation levels were not affected by exposure to MPs and Cd alone but dramatically enhanced by co-exposure, which may be explained by the reduction of total antioxidant capacity (TAOC) and activity levels of Mn-superoxide dismutase (Mn-SOD) and catalase (CAT) after co-exposure. Increased apoptotic cells were observed in the vertebral body of larvae exposed to Cd, the esophagus of larvae exposed to MPs, and both organs of larvae exposed to MPs + Cd, which was further confirmed by changes in the activities of Caspase-3, Caspase-8 and Caspase-9. PCR array on the transcription of genes related to growth, oxidative stress and apoptosis was examined, showing that the combined exposure resulted in greater magnitude of changes than MPs and Cd alone. The results indicate that MPs can enhance the negative effects of Cd on growth, oxidative damage and apoptosis in early life stages of zebrafish. However, the adsorption of Cd onto MPs was not observed and the combined exposure did not increase the Cd content in larvae compared to the single Cd exposure, implying that vector role of MPs in Cd uptake is negligible.

Particles rather than released Zn2+ from ZnO nanoparticles aggravate microplastics toxicity in early stages of exposed zebrafish and their unexposed offspring

Knowledge on the interaction between microplastics (MPs) and zinc oxide nanoparticles (ZnO NPs) is limited. Here, we investigated effects of embryo-larvae exposure to 500 μg/L polystyrene MPs (5 µm), 1200 μg/L ZnO NPs (< 100 nm), 500 μg/L dissolved Zn²⁺ from ZnSO4^, and the mixtures of MPs and ZnO NPs or ZnSO4 on exposed F0 larvae and unexposed F1 larvae. Consequently, ZnO particles adhered to MPs surfaces rather than Zn²⁺, and increased Zn transport into larvae. Growth inhibition, oxidative stress, apoptosis, and disturbance of growth hormone and insulin-like growth factor (GH/IGF) axis were induced by MPs and ZnO NPs alone, which were further aggravated by their co-exposure in F0 larvae. MPs + ZnO increased apoptotic cells in the gill and esophagus compared with MPs and ZnO NPs alone. Reduced growth and antioxidant capacity and down-regulated GH/IGF axis were merely observed in F1 larvae from F0 parents exposed to MPs + ZnO. Contrary to ZnO NPs, dissolved Zn²⁺ reversed MPs toxicity, suggesting the protective role of Zn²⁺ may be not enough to ameliorate thfie negative effects of ZnO particles. To summarize, we found that particles rather than released Zn²⁺ from ZnO nanoparticles amplified MPs toxicity in early stages of exposed zebrafish and their unexposed offspring.

Effects of early low temperature exposure on the growth, glycolipid metabolism and growth hormone (gh) gene methylation in the late stage of Chinese perch (Siniperca chuatsi)

Temperature is an important factor affecting the early development, growth and physiology of fish, as well as on aspects of feeding and metabolism. Here, we investigated the impact of low temperature on the growth, glycolipid metabolism and growth hormone (gh) gene methylation in the late stage of Chinese perch (Siniperca chuatsi). Chinese perch larvae were exposed to temperatures with 21 °C (low temperature group (LT)) and 25 °C (control group) for 7 days, and then the LT group was slowly heated to 25 °C and raised at this temperature for two months. Results indicated that the LT group exhibited significantly lower growth rate and weight gain rate than the control group (p < 0.05), but no obvious food intake (FI) were detected yet between LT group and control group. The larvae exposed at 21 °C relative to the 25 °C group had significant decreased transcript levels of GH-IGF axis genes (gh, igf1 and igf2) in Chinese perch juvenile (p < 0.05). Further analysis of the DNA methylation levels of gh showed that the LT group had higher at the CpG sites of -3029 and - 3032 than the control group in larvae (p < 0.05), whereas the DNA methylation levels at CpG sites of -2982 and - 3039 of gh were significantly lower compared with the control group in juveniles (p < 0.05). In addition, the plasma glucose was significantly increased in the LT group (p < 0.05), suggesting the metabolism of blood glucose slowed at low temperature. In larvae, the expressions of glycolipid metabolism genes (ins-ra and ins-rb) in LT group were significantly up-regulated compared to control group in larvae (p < 0.05), while down-regulated in juveniles (p < 0.05). The expression level of ucp2 mRNA was continuously up-regulated under low temperature stress. All these data demonstrate that early exposure to low temperature affected the growth and glycolipid metabolism of Chinese perch.

Comparative Transcriptome Analysis Revealed Genes Involved in Sexual and Polyploid Growth Dimorphisms in Loach (Misgurnus anguillicaudatus)

Simple Summary

Misgurnus anguillicaudatus not only exhibits sexual size dimorphism, but also shows polyploid size dimorphism. Here, we performed comparative transcriptome integration analysis of multiple tissues of diploid and tetraploid M. anguillicaudatus of both sexes. We found that differences in energy metabolism and steroid hormone synthesis levels may be the main causes of sexual and polyploidy growth dimorphisms of M. anguillicaudatus. Fast-growing M. anguillicaudatus (tetraploids, females) have higher levels of energy metabolism and lower steroid hormone synthesis and fatty acid degradation abilities than slow-growing M. anguillicaudatus (diploids, males).

Abstract

Sexual and polyploidy size dimorphisms are widespread phenomena in fish, but the molecular mechanisms remain unclear. Loach (Misgurnus anguillicaudatus) displays both sexual and polyploid growth dimorphism phenomena, and are therefore ideal models to study these two phenomena. In this study, RNA-seq was used for the first time to explore the differentially expressed genes (DEGs) between both sexes of diploid and tetraploid loaches in four tissues (brain, gonad, liver, and muscle). Results showed that 21,003, 17, and 1 DEGs were identified in gonad, liver, and muscle tissues, respectively, between females and males in both diploids and tetraploids. Regarding the ploidy levels, 4956, 1496, 2187, and 1726 DEGs were identified in the brain, gonad, liver, and muscle tissues, respectively, between tetraploids and diploids of the same sex. When both sexual and polyploid size dimorphisms were considered simultaneously in the four tissues, only 424 DEGs were found in the gonads, indicating that these gonadal DEGs may play an important regulatory role in regulating sexual and polyploid size dimorphisms. Regardless of the sex or ploidy comparison, the significant DEGs involved in glycolysis/gluconeogenesis and oxidative phosphorylation pathways were upregulated in faster-growing individuals, while steroid hormone biosynthesis-related genes and fatty acid degradation and elongation-related genes were downregulated. This suggests that fast-growing loaches (tetraploids, females) have higher energy metabolism levels and lower steroid hormone synthesis and fatty acid degradation abilities than slow-growing loaches (diploids, males). Our findings provide an archive for future systematic research on fish sexual and polyploid dimorphisms.

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.

Tris(1,3-dichloro-2-propyl)phosphate Reduces Growth Hormone Expression via Binding to Growth Hormone Releasing Hormone Receptors and Inhibits the Growth of Crucian Carp

Tris(1,3-dichloro-2-propyl)phosphate (TDCIPP) has commonly been used as an additive flame retardant and frequently detected in the aquatic environment and in biological samples worldwide. Recently, it was found that exposure to TDCIPP inhibited the growth of zebrafish, but the relevant molecular mechanisms remained unclear. In this study, 5 day-old crucian carp (Carassius auratus) larvae were treated with 0.5, 5, or 50 μg/L TDCIPP for 90 days; the effect on growth was evaluated; and related molecular mechanisms were explored. Results demonstrated that 5 or 50 μg/L TDCIPP treatment significantly inhibited the growth of crucian carp and downregulated the expression of growth hormones (ghs), growth hormone receptor (ghr), and insulin-like growth factor 1 (igf1). Molecular docking, dual-luciferase reporter gene assay, and in vitro experiments demonstrated that TDCIPP could bind to the growth hormone releasing hormone receptor protein of crucian carp and disturb the stimulation of growth hormone releasing hormone to the expression of ghs, resulting in the decrease of the mRNA level of gh1 and gh2 in pituitary cells. Our findings provide new perceptions into the molecular mechanisms of developmental toxicity of TDCIPP in fish.

The linkage of cell cycle and DNA replication with growth difference in female Chinese tongue sole (Cynoglossus semilaevis): Analysis from transcriptomic study and WGCNA

In addition to the typical sexual size dimorphism, considerable size differences within the female population of the Chinese tongue sole (Cynoglossus semilaevis) have become a further bottleneck of the improvement of sole aquaculture. To identify the internal mechanism, transcriptomic analysis and weighted gene co-expression network analysis (WGCNA) were employed simultaneously. Transcriptomic analyses of brain, pituitary gland, liver, gonad, and muscle tissues from two female groups with size differences identified 109, 698, 1325, 2299, and 2141 differentially expressed genes (DEGs), respectively. The results of these enrichment analyses suggest that the up-regulation of neuroactive ligand-receptor interaction, cell cycle, DNA replication, and MAPK signaling pathway in the group with larger females may be involved in the regulation of the observed growth differences. WGCNA of DEGs showed that cell cycle and DNA replication might be crucial pathways for accelerating cell growth in the groups with larger females. Finally, a series of hub genes including 6-phosphofructokinase type C (pfkp), ribosome biogenesis protein (wdr12), bleomycin hydrolase (blmh), and semaphorin-3A (sema3a) were recognized by the illustrated network map of modules. The linkage of cell cycle, DNA replication, and hub genes in the growth regulation of C. semilaevis provides further information for a better understanding of growth differences in fish.

Differential modulation of oxidative stress, antioxidant defense, histomorphology, ion-regulation and growth marker gene expression in goldfish (Carassius auratus) following exposure to different dose of virgin microplastics

Goldfish (Carassius auratus) juveniles were exposed to virgin polyvinyl chloride microplastics (PVC-MPs) in triplicate at 0, 0.1 or 0.5 mg/L for four days. Afterwards, the histopathology of the gills, liver and intestines were examined, along with various antioxidant enzymes and indicators of oxidative damage (malondialdehyde (MDA) and hydrogen peroxide (H₂O₂)), in the brain, liver and gills. In addition, we also studied the expression of hepatic insulin-like growth factor-1 (IGF-1), insulin-like growth factor binding protein 1 (IGFBP-1) and growth hormone (GH) receptor, while cortisol receptor (CR) and cytochrome P450 1A (CYP1A) gene expression were assayed in both the liver and gills. Histological analysis revealed PVC-MPs in the intestines at 0.1 and 0.5 mg/L, along with substantially shorter villi. The gills appeared undamaged by PVC-MPs exposure and had limited or no effect to antioxidant activity, Na⁺/K⁺-ATPase and H⁺-ATPase activity or plasma ion levels, but there was a prominent upsurge of the detoxification enzymes glutatione S-transferase (GST) activity and CYP1A expression. Livers showed inflammation and some occurrences of hemorrhaging and necrosis at 0.5 mg/L. While the brain showed some evidence of oxidative damage, the liver was the most susceptible to oxidative damage, based on increased MDA, H₂O₂ and various antioxidant enzymes. Hepatic expression of IGFBP-1 and GH receptor were significantly downregulated at 0.5 mg/L while CR was upregulated. Results indicate that exposure to environmentally relevant PVC-MP can cause oxidative damage in the brain and liver, adverse histomorphological changes to the intestine and liver and alter the gene expression in goldfish.

Identification of the cDNA Encoding the Growth Hormone Receptor (GHR) and the Regulation of GHR and IGF-I Gene Expression by Nutritional Status in Reeves' Turtle (Chinemys reevesii)

Chinemys reevesii (Reeves’ turtle) is a slow-growing reptile that is distributed widely across China. Prior to this study, the cDNA sequence of the growth hormone receptor (GHR) in the Reeve’s turtle, or how periods of starvation might influence the gene expression of GHR and insulin-like growth factor I (IGF-I) in this species, were unknown. Here, we identified the full-length sequence of the cDNA encoding GHR in Reeves’ turtle by using RT-PCR and RACE. The full-length GHR cDNA was identified to be 3936 base-pairs in length, with a 1848 base-pair open reading frame (ORF) that encodes a 615 amino acid protein. Analysis showed that GHR mRNA was detectable in a wide range of tissues; the highest and lowest levels of expression were detected in the liver and the gonad, respectively. IGF-I was also expressed in a range of tissues, but not in the gonad; the highest levels of IGF-I expression were detected in the liver. After 4 weeks of fasting, the expression levels of GHR and IGF-I in the liver had decreased significantly; however, these gradually returned to normal after refeeding. We report the first cloned cDNA sequence for the GHR gene in the Reeve’s turtle. Our findings provide a foundation from which to investigate the specific function of the GHR in Reeve’s turtle, and serve as a reference for studying the effects of different nutrient levels on GHR expression in this species.

GH and GHR gene cloning, expression and their associations with growth-related traits of the barbel chub (Squaliobarbus curriculus)

Growth hormone (ScGH) and growth hormone receptor (ScGHR) genes from the barbel chub (Squaliobarbus curriculus), in addition to their cDNAs, were cloned. The associations between their mRNA expression levels and growth-related traits were analysed, and the differences in the levels of expression of growth regulation-related genes between the largest and smallest individuals were compared. The full-length 1182-bp cDNA of ScGH contained a 633-bp open reading frame (ORF), and the length of the gene had 2492 bp. The full-length 2825-bp cDNA of ScGHRa contained a 1818-bp ORF, and the gene had 6970 bp. The full-length 2822-bp cDNA of ScGHRb contained a 1737-bp ORF, and the gene had 8149 bp. Quantitative real-time PCR revealed that ScGH was only expressed in the pituitary. ScGHRa was expressed predominantly in muscle, and the expression level of ScGHRb was the highest in the liver. The ScGHRa mRNA levels in the muscle were significantly negatively correlated with the caudal peduncle length. However, no correlation between growth-related traits and ScGH and ScGHRb expression levels were found. Pituitary ScGH, liver GHRb and liver insulin-like growth factor I (igf-1) expression levels were significantly higher in the largest individuals than those in the smallest S. curriculus individuals. Contrarily, the largest individuals had significantly lower expression levels of muscle igf-1 and liver myog than the smallest individuals. Overall, our results provide novel molecular information for growth-regulation study of S. curriculus.

Genomic structure and characterization of growth hormone receptors from golden pompano Trachinotus ovatus and their expression regulation by feed types

In this study, sequence analysis showed that ToGHR1 and ToGHR2 encoded polypeptides of 577 and 588 amino acids, respectively. Bioinformatics analysis showed that both ToGHR1 and ToGHR2 contain FN3 domains and transmembrane domains, which have glycosylation and phosphorylation sites. The exons of ToGHR1 and exons 4-10 of ToGHR2 are homologous to exons 2 and 4-9 in Homo sapiens genes, respectively. Only 3 SSR sites in ToGHR1 have SSR polymorphisms, and ToGHR2 has no SSR polymorphisms. ToGHR1 and ToGHR2 have high homology with GHR1 and GHR2 of many fish by BLAST. qRT-PCR was used to examine the expression profile of ToGHR mRNA in 12 normal liver and intestine tissue samples from 3 feed-type groups. The results showed that ToGHR is expressed in all 12 tissues, especially liver and muscle tissues, which showed higher ToGHR expression than that in other tissues (p < 0.05). Experiments on feed-type groups may indicate that high levels of LC-PUFA in squid bait can promote ToGHR1 expression and simultaneously inhibit ToGHR2 expression in the liver tissue. In addition, the high levels of LC-PUFA in food could inhibit intestinal ToGHR1 expression, and the intermediate levels may promote intestinal ToGHR1 expression. However, the unsaturated fatty acid content in the food does not affect the expression of intestinal ToGHR2.

Combined effects of dosage compensation and incomplete dominance on gene expression in triploid cyprinids

Hybridization and polyploidy are pervasive evolutionary features of flowering plants and frequent among some animal groups, such as fish. These processes always lead to novel genotypes and various phenotypes, including growth heterosis. However, its genetic basis in lower vertebrate is still poorly understood. Here, we conducted transcriptome-level analyses of the allopolyploid complex of Carassius auratus red var. (R) (♀) × Cyprinus carpio L. (C) (♂), including the allodiploid and allotetraploid with symmetric subgenomes, and the two allotriploids with asymmetric subgenomes. The gradual changes of gene silencing and novel gene expression suggested the weakening of the constraint of polymorphic expression in genotypic changes. Then, analyses of the direction and magnitude of homoeolog expression exhibited various asymmetric expression patterns, which supported that R incomplete dominance and dosage compensation were co-regulated in the two triploids. Under these effects, various magnitudes of R-homoeolog expression bias were observed in growth-regulated genes, suggesting that they might contribute to growth heterosis in the two triploids. The determination of R incomplete dominance and dosage compensation, which might be led by asymmetric subgenomes and multiple sets of homologous chromosomes, explained why various expression patterns were shaped and their potential contribution to growth heterosis in the two triploids.

Nonadditive and Asymmetric Allelic Expression of Growth Hormone in Hybrid Tilapia

Hybridization is a common breeding technique that can improve germplasm through heterosis in aquaculture. However, the regulation of key gene expression, including the details of transcriptional level changes at the beginning of hybridization events, remains largely undefined, especially in teleosts. In this study, by interspecies crossing between two pure lines of Nile tilapia and blue tilapia, we obtained a hybrid tilapia population as a model to elucidate heterosis, and we traced the molecular outcomes of growth hormone (GH) expression and allele-specific expression (ASE) in hybrids. The hybrids display growth vigor compared to their parents in the 120-day growth trial. GH mRNA expression was uniquely expressed in the pituitary. Higher GH expression was found in the hybrid than the midparent value, in both males and females, showing a nonadditive pattern. We identified four single-nucleotide polymorphism sites between Nile tilapia and blue tilapia. Subsequently, by pyrosequencing, we found asymmetric allelic expression in hybrids with higher maternal allelic transcript ratios in both males and females. Fasting significantly increased GH expression in hybrids, but asymmetric allelic expression was not affected by feeding or fasting conditions. Finally, we identified cis and trans effects via overall expression and ASE values in the hybrid, which showed that the cis and trans effects promoted the expression of maternal subgenome in the hybrid, contributing to the expression superiority of GH in hybrid tilapia. Taken together, the results of our study first illustrated the concept of GH expression superiority and its formation mechanism in hybrid fish with growth vigor.

Growth and survival of Takifugu rubripes larvae cultured under different light conditions

We assessed the effects of light intensity and spectrum on the growth and survival of Takifugu rubripes larvae from 30 to 69 days after hatching. Five lighting regimes were applied using 0.5, 1.5, and 3.0 W m^-2 full spectrum white (W0.5, W1.5, W3.0), 0.5 W m^-2 yellow (Y0.5), and 0.5 W m^-2 blue light (B0.5). At the end of the experiment, body length, wet weight, and specific growth rate from day 0 to day 39 were significantly greater in larvae reared under W3.0 than under B0.5 (P ˂ 0.05). No significant differences were observed among W0.5, W1.5, and W3.0, or among W0.5, Y0.5, and B0.5 (P > 0.05). Survival rate was significantly higher in larvae reared under W1.5 than W0.5 (P ˂ 0.05), but no significant differences were observed among W0.5, Y0.5, and B0.5 (P > 0.05). Additionally, light conditioning did not affect the total thickness of the retina. Although the ratio of the thickness of the retinal pigment epithelium layer/total thickness (TT) was significantly higher in larvae exposed to W3.0 compared with those exposed to other light conditions, and the thickness of the outer nuclear layer/TT was significantly lower in larvae exposed to W3.0 compared with those exposed to W0.5 (P < 0.05), no relationship was confirmed between the structure of the retina and the growth performance of the T. rubripes larvae. Expression patterns of two stress-related and seven growth-related genes were also compared with the biometric parameters investigated in the experimental groups. No significant differences in the aanat1a, crh, ss1, igf1, or igf2 expression were observed among the five treatments. Pomc expression was significantly lower in larvae exposed to W1.5 than the larvae exposed to W0.5, and it was significantly lower in larvae exposed to Y0.5 than in larvae exposed to W0.5 or B0.5 (P < 0.05). Significant differences were also found in the expression of gh, with the highest levels being observed under W3.0, while the lowest levels were observed in B0.5 (P < 0.05). Ghrh expression was significantly higher in W3.0 (P < 0.05). These results should be considered when designing rearing protocols for fugu larvae in aquaculture systems.

Expression Patterns of Growth Related Genes in Juvenile Red Spotted Grouper (Epinephelus akaara) with Different Growth Performance after Size Grading

Fish shows great difference in growth rate between individuals during larval development and early growth. This difference seriously reduces the production efficiency in fish culture. Growth hormone (GH)/Insulin-like growth factor 1 (IGF1) system is said to play some pivotal roles in fish growth. In this study, we investigated differences of GH, IGF1 and GHR gene expressions in juvenile red spotted grouper (Epinephelus akaara) with different growth performance. Red spotted groupers were reared under the same environmental condition (water temperature 24±1℃, natural light) for 96 days after hatching. They were divided into 3 groups by size (fast growing, middle growing and slow growing groups: FGG, MGG, and SGG, respectively). RNA was extracted from the brain, liver and muscle tissues from each group, and target gene expression was examined by real-time PCR. In the brain with pituitary gland, expression of GH gene in FGG was significantly higher than the expression in SGG, but the expression of IGF1 and GHR genes in the muscle was highest in SGG. Difference of GHR and IGF1 mRNA in the liver between groups with different growth performance was less clear than that in other tissues, although level of IGF1 mRNA was higher in SGG than in MGG. These results suggest that hormonal governing of growth is not the same in fast growing and slow growing fish, and size grading could cause a shift of hormonal state and growth pattern in this species.

Nutrient Regulation of Endocrine Factors Influencing Feeding and Growth in Fish

Endocrine factors regulate food intake and growth, two interlinked physiological processes critical for the proper development of organisms. Somatic growth is mainly regulated by growth hormone (GH) and insulin-like growth factors I and II (IGF-I and IGF-II) that act on target tissues, including muscle, and bones. Peptidyl hormones produced from the brain and peripheral tissues regulate feeding to meet metabolic demands. The GH-IGF system and hormones regulating appetite are regulated by both internal (indicating the metabolic status of the organism) and external (environmental) signals. Among the external signals, the most notable are diet availability and diet composition. Macronutrients and micronutrients act on several hormone-producing tissues to regulate the synthesis and secretion of appetite-regulating hormones and hormones of the GH-IGF system, eventually modulating growth and food intake. A comprehensive understanding of how nutrients regulate hormones is essential to design diet formulations that better modulate endogenous factors for the benefit of aquaculture to increase yield. This review will discuss the current knowledge on nutritional regulation of hormones modulating growth and food intake in fish.

The growth hormone signaling system: Insights into coordinating the anabolic and catabolic actions of growth hormone

Although growth hormone (GH) is a multifunctional factor that coordinates various aspects of feeding, reproduction, osmoregulation, and immune system function, perhaps two of its most studied actions are the regulation of growth and metabolism, particularly lipid metabolism. In this review, we describe the major growth-promoting and lipid metabolic actions of GH and then discuss how the GH system regulates these actions. Numerous intrinsic and extrinsic factors provide information about the metabolic status of the organism and influence the production of release of GH. The actions of GH are mediated by GH receptors (GHR), which are widely distributed among tissues. Teleosts possess multiple forms of GHRs that arose through the evolution of this group. Modulation of tissue responsiveness to GH is regulated by molecular and functional expression of GHRs, and in teleosts GHR subtypes, by various factors that reflect the metabolic and growth status of the organism, including nutritional state. The action of GH is propagated by the linkage of GHRs to several cellular effector systems, including JAK-STAT, ERK, PI3K-Akt, and PKC. The differential activation of these pathways, which is governed by nutrient status, underlies GH stimulation of growth or GH stimulation of lipolysis. Taken together, the multi-functional actions of GH are determined by the distribution and abundance of GHRs (and GHR subtypes in teleosts) as well as by the GHR-effector system linkages.

Essential roles of stat5.1/stat5b in controlling fish somatic growth

Signal transducer and activator of transcription 5b (STAT5b) has been identified as a key downstream mediator of growth hormone (GH) signaling in somatic growth of mammalian. However, the corresponding homologue gene of Stat5b is unknown in fish species. In this study, we generated loss-of-function mutants in stat5.1 and stat5.2, two stat5 homologues existing in zebrafish. In stat5.1-deficient zebrafish, a significant reduction of body length and body weight was detected in the embryos/larvae and adults compared with the wild-type control fish, and sexual size dimorphism in adult zebrafish was also eliminated. However, the stat5.2-deficient zebrafish displayed a normal developmental phenotype during all lifespan. Chromatin immunoprecipitation combined with deep sequencing (ChIP-seq) method was adopted to further investigate the potential transcriptional targets of Stat5 protein and cast much light upon the biological function of Stat5. We identified more than 800 genes as transcriptional targets of Stat5 during zebrafish embryogenesis. KEGG analysis indicated that the Stat5 target gene network is predominantly linked to the metabolic pathways, neuroactive ligand-receptor interaction and JAK-STAT signaling pathways. Further validation studies suggested that Stat5.1 protein could directly regulate the expression of gh1, and stat5.1-mutated zebrafish showed a reduction of gh1 mRNA level. In the present study, stat5.1 was revealed as the corresponding homologue gene of Stat5b in fish species. Additionally, we found a novel molecular interaction between Stat5.1/Stat5b and GH, and unraveled a positive feedback loop Stat5.1-GH-Stat5.1 which is necessary for somatic growth and body development in zebrafish.

Analyzing homoeolog expression provides insights into the rediploidization event in gynogenetic hybrids of Carassius auratus red var. × Cyprinus carpio

Rediploidization is considered to be a part of the evolutionary history of allotetraploids, and resulted in the emergence of novel epigenetic regulatory activities. To study the changing patterns of gene expression following the reduction of a genome by 50%, we used RNA-seq and quantitative real-time PCR (qPCR) to investigate total gene expression and homoeolog expression in three hybrids of a C. auratus red var. (2n = 100, ♀) (R) and C. carpio (2n = 100, ♂) (C) (i.e., F1, F18, and G4) and their original parents. A comparison of homoeolog expression between G4 and F18 identified 7 genes (0.22%) that exhibited novel R/C homoeolog expression patterns in G4, while 4 genes (0.12%) were affected by R/C homoeolog silencing. We determined the direction and extent of the homoeolog expression bias (HEB). The C-HEB genes (i.e., nrp1a and igf1) and R-HEB genes (i.e., fgf23 and esm1) provided insights into the effects of the dominance of one parental homoeolog expression on growth regulation. This dominance may contribute to the rapid growth of G4 fish. Our findings may be relevant for clarifying the relationship between growth heterosis and differences in homoeolog expression patterns.

Acute exposure to tris (2-butoxyethyl) phosphate (TBOEP) affects growth and development of embryo-larval zebrafish

Tris (2-butoxyethyl) phosphate (TBOEP), is used as a flame retardant worldwide. It is an additive in materials and can be easily discharged into the surrounding environment. There is evidence linking TBOEP exposure to abnormal development and growth in zebrafish embryos/larvae. Here, using zebrafish embryo as a model, we investigated toxicological effects on developing zebrafish (Danio rerio) caused by TBOEP at concentrations of 0, 20, 200, 1000, 2000μg/L starting from 2h post-fertilization (hpf). Our findings revealed that TBOEP exposure caused developmental toxicity, such as malformation, growth delay and decreased heart rate in zebrafish larvae. Correlation analysis indicated that inhibition of growth was possibly due to down-regulation of expression of genes related to the growth hormone/insulin-like growth factor (GH/IGF) axis. Furthermore, exposure to TBOEP significantly increased thyroxine (T4) and 3,5,3'-triiodothyronine (T3) in whole larvae. In addition, changed expression of genes involved in the hypothalamic-pituitary-thyroid (HPT) axis was observed, indicating that perturbation of HPT axis might be responsible for the developmental damage and growth delay induced by TBOEP. The present study provides a new set of evidence that exposure of embryo-larval zebrafish to TBOEP can cause perturbation of GH/IGF axis and HPT axis, which could result in developmental impairment and growth inhibition.

De Novo Transcriptome Characterization and Growth-Related Gene Expression Profiling of Diploid and Triploid Bighead Catfish (Clarias macrocephalus Günther, 1864)

To enhance understanding of triploid gene expression, the transcriptome information from bighead catfish (Clarias macrocephalus Günther, 1864) was studied using the paired-end Illumina HiSeq™ 2000 sequencing platform. In total, 68,227,832 raw reads were generated from liver tissues and 53,149 unigenes were assembled, with an average length of 765 bp and N50 length of 1283 bp. Of these unigenes, 33,428 (62.89%) could be annotated according to their homology with matches in the NCBI non-redundant (Nr), NCBI nucleotide (Nt), Swiss-Prot, Clusters of Orthologous Groups (COG), gene ontology (GO), or Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Relative expression of liver genes between diploid and triploid bighead catfish revealed more than 90% of the annotated unigenes similarly expressed, regardless of ploidy, whereas 362 upregulated and 83 downregulated with at least a twofold change in triploid relative to diploid. Quantitative real-time PCR of 15 differentially expressed growth-related genes showed consistency between the expression profiles of those genes with the results from RNA-seq analysis. Our results showed that genes in C. macrocephalus liver responded independently to triploidy with the majority showing similar expression levels between diploid and triploid (a dosage compensation phenomenon). The underlying mechanism of the varying gene expression patterns was discussed. Notably, 5 of the top 20 upregulated genes associated with stress response and thus may reflect stress caused by triploidy. The present study adds a substantial contribution to the sequence data available for C. macrocephalus and hence provides valuable resources for further studies. Furthermore, it gives information that may enhance understanding of triploid physiology.

Determination of dosage compensation and comparison of gene expression in a triploid hybrid fish

Background

Polyploidy and hybridization are both recognized as major forces in evolution. Most of our current knowledge about differences in gene regulation in polyploid hybrids comes from plant studies. The gene expression of diverged genomes and regulatory interactions are still unclear in lower vertebrates.

Results

We generated 229 million cleaned reads (42.23 Gbp) from triploid of maternal grass carp (Ctenopharyngodon idellus, Cyprininae, 2n = 48) × paternal blunt snout bream (Megalobrama amblycephala, Cultrinae, 2n = 48) and their diploid parents using next-generation sequencing. In total, 157,878 contigs were assembled and 15,444 genes were annotated. We examined gene expression level changes among the parents and their triploid offspring. The mechanisms of dosage compensation that reduced triploid expression levels to the diploid state were determined in triploid fish. In this situation, novel gene expression and gene silencing were observed. Then, we established a model to determine the extent and direction of expression level dominance (ELD) and homoeolog expression bias (HEB) based on the relative expression level among the parents and their triploid offspring.

Conclusions

Our results showed that the genome-wide ELD was biased toward maternal genome in triploid. Extensive alterations in homoeolog expression suggested a combination of regulatory and epigenetic interactions through the transcriptome network. Additionally, the expression patterns of growth genes provided insights into the relationship between the characteristics of growth and underlying mechanisms in triploids. Regulation patterns of triploid state suggest that various expression levels from the initial genomic merger have important roles in adaptation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3424-5) contains supplementary material, which is available to authorized users.

Homoeologue expression insights into the basis of growth heterosis at the intersection of ploidy and hybridity in Cyprinidae

Hybridization and polyploidization are considered important driving forces that form new epigenetic regulations. To study the changing patterns of expression accompanying hybridization and polyploidization, we used RNA-seq and qRT-PCR to investigate global expression and homoeologue expression in diploid and tetraploid hybrids of Carassius auratus red var. (♀) (R) and Cyprinus carpio (♂) (C). By comparing the relative expression levels between the hybrids and their parents, we defined the expression level dominance (ELD) and homoeologue expression bias (HEB) in liver tissue. The results showed that polyploidization contributed to the conversion of homoeologue ELD. In addition, hybridization had more effect on the change in HEB than polyploidization, while polyploidization had more effect on the change of global gene expression than hybridization. Meanwhile, similar expression patterns were found in growth-related genes. The results suggested that hybridization and polyploidization result in differential degrees of maternal HEB in three tissues (liver, muscle and ovary) tested. The results of this study will increase our understanding of the underlying regulation mechanism of rapid growth in diploid hybrids and allotetraploids. The differential degrees of global expression and homoeologue expression contribute to growth heterosis in newly formed hybrids, ensuring the on-going success of allotetraploid speciation.

Feeding rates affect growth, intestinal digestive and absorptive capabilities and endocrine functions of juvenile blunt snout bream Megalobrama amblycephala

This study aimed to investigate the optimal feeding rate for juvenile blunt snout bream (average initial weight 23.74 ± 0.09 g) based on the results on growth performance, intestinal digestive and absorptive capabilities and endocrine functions. A total of 840 fish were randomly distributed into 24 cages and fed a commercial feed at six feeding rates ranging from 2.0 to 7.0% body weight (BW)/day. The results indicated that weight gain rate increased significantly (P < 0.05) as feeding rates increased from 2.0 to 5.0% BW/day, but decreased with the further increasing feeding rates (P > 0.05). Protein efficiency ratio and nitrogen and energy retention all showed a similar trend. However, feed conversion ratio increased significantly (P < 0.05) with increasing feeding rates. Feeding rates have little effects (P > 0.05) on whole-body moisture, ash and protein contents, but significantly (P < 0.05) affect both lipid and energy contents with the highest values both observed in fish fed 4.0% BW/day. In addition, moderate ration sizes (2.0-4.0% BW/day) resulted in the enhanced activities of intestinal enzymes, including lipase, protease, Na(+), K(+)-ATPase, alkaline phosphatase and creatine kinase. Furthermore, the mRNA levels of growth hormone, insulin-like growth factors-I, growth hormone receptor and neuropeptide all increased significantly (P < 0.05) as feeding rates increased from 2.0 to 5.0% and 6.0% BW/day, but decreased significantly (P < 0.05) with the further increase in feeding rates, whereas both leptin and cholecystokinin expressions showed an opposite trend. Based on the broken-line regression analysis of SGR against feeding rates, the optimal feeding rate for juvenile blunt snout bream was estimated to be 4.57% BW/day.

A feedback regulatory loop involving p53/miR-200 and growth hormone endocrine axis controls embryo size of zebrafish

In vertebrates, growth hormone/insulin-like growth factor (GH/IGF) axis signaling plays a critical role in regulating somatic growth. Understanding the direct upstream regulators of GH/IGF axis remains a major challenge. Our studies of the zebrafish reveal that the conserved miR-200 family members are critical regulators of embryo size by targeting several GH/IGF axis genes, including GH, GHRa, GHRb and IGF2a. Overexpression of miR-200s led to cell cycle arrest in the G1 phase and induced apoptotic responses during embryo development, thereby inhibiting somatic growth of zebrafish embryos. Intriguingly, GH induced expression of both p53 and miR-200s, and miR-200s is a potential p53 transcriptional target, thus forming a negative feedback loop. Significantly, the up-regulation of miR-200s associated with GH activation is abolished in embryos with p53 mutation. By integrating these studies, we conclude that p53/miR-200 and GH/IGF signaling pathway form a negative regulatory loop to control embryo size, that provide critical insights into the long-standing puzzle of how body growth is determined during early development of teleosts.

Effect of acute ammonia exposure on expression of GH/IGF axis genes GHR1, GHR2 and IGF-1 in pufferfish (Takifugu obscurus)

Waterborne ammonia has become a persistent pollutant of aquatic habitats. The exposure to ammonia stress can reduce growth in a wide range of aquatic organisms. To assess the effect of ammonia exposure on the growth hormone/insulin-like growth factors (GH/IGF) axis, we identified and characterized GHR1, GHR2 and IGF-1 from pufferfish. Comparative analysis showed that these genes shared high identity and similarity with corresponding genes in other fish species. The transcripts of these genes were widely expressed in all tested tissues. The highest level of GHR1 mRNA was found in the brain, whereas GHR2 and IGF-1 mRNA levels were the highest in the liver. Following acute ammonia exposure (100 mg/L total ammonia-nitrogen), GHR2 expression in the liver did not change at 6 h and then significantly decreased at 12, 24 and 48 h, whereas GHR1 and IGF-1 expressions were significantly down-regulated at 6, 12, 24 and 48 h, respectively. These results indicated that ammonia stress decreased the expression of GH/IGF axis genes, which might have negative effect on the growth and development of pufferfish.

Ploidy effects on genes regulating growth mechanisms during fasting and refeeding in juvenile rainbow trout (Oncorhynchus mykiss)

Diploid and triploid rainbow trout weighing approximately 3g were either fed for five weeks, or feed deprived for one week, followed by refeeding. During feed deprivation gastrointestinal somatic index decreased in diploids, but not triploids, and during refeeding, carcass growth rate recovered more quickly in triploids. Although not affected by ploidy, liver ghr2 and igfbp2b expression increased and igfbp1b decreased in fasted fish. Effects of ploidy on gene expression indicate potential mechanisms associated with improved recovery growth in triploids, which include decreased hepatic igfbp expression, which could influence IGF-I bioavailability, differences in tissue sensitivity to TGFbeta ligands due to altered tgfbr and smad expression, and differences in expression of muscle regulatory genes (myf5, mstn1a, and mstn1b). These data suggest that polyploidy influences the expression of genes critical to muscle development and general growth regulation, which may explain why triploid fish recover from nutritional insult better than diploid fish.

Growth and endocrine effect of growth hormone transgene dosage in diploid and triploid coho salmon

Growth-hormone transgene dosage, polyploidy, and parental effects on growth and endocrine responses have been assessed in coho salmon. Diploid fry with one or two transgene doses grew equally, whereas later-stage juvenile homozygotes grew faster than hemizygotes. In contrast, homozygotes and hemizygotes grew equally after smoltification, both in sea water and fresh water. Triploid transgenic salmon showed impaired growth which could not be fully overcome with additional transgene copies. Levels of muscle GH mRNA were elevated in two vs. one transgene dose diploids, but in triploids, a dosage effect was observed in muscle but not for animals carrying three transgene doses. IGF-I mRNA levels were elevated in transgenic vs. non-transgenic animals, but a dosage effect was not observed. Diploids and triploids with two transgenes had higher plasma GH levels than one-dose animals, but three-dose triploids showed no further elevation. Circulating IGF-I levels also showed a dosage effect in diploids, but not among any transgene doses in triploids. The present study reveals complex interactions among transgene dosage, maternal effects, developmental stage, and ploidy on growth and endocrine parameters in GH transgenic coho salmon. Specifically, GH transgenes do not always express nor have effects on growth that are directly correlated with the number of transgenes. Further, the reduced growth rate seen in triploid transgenic animals could not be fully overcome by increasing transgene dosage. The findings have relevance for understanding growth physiology, transgene function, and for environmental risk assessments that require understanding phenotypes of hemizygous vs. homozygous transgenic animals in populations.