Gene Expression Profiling of Grass Carp (Ctenopharyngodon idellus) and Crisp Grass Carp

Comparative genome-wide methylation analysis reveals epigenetic regulation of muscle development in grass carp (Ctenopharyngodon idellus) fed with whole faba bean

Crisp grass carp (CGC), the most representative improved varieties of grass carp (GC), features higher muscle hardness after feeding faba bean (Vicia faba L.) for 90-120 days. DNA methylation, a most widely studied epigenetic modification, plays an essential role in muscle development. Previous studies have identified numerous differentially expressed genes (DEGs) between CGC and GC. However, it remains unknown if the expression levels of these DEGs are influenced by DNA methylation. In the present study, we performed a comprehensive analysis of DNA methylation profiles between CGC and GC, and identified important candidate genes related to muscle development coupled with the transcriptome sequencing data. A total of 9,318 differentially methylated genes (DMGs) corresponding to 155,760 differentially methylated regions (DMRs) were identified between the two groups under the CG context in promoter regions. Combined with the transcriptome sequencing data, 14 key genes related to muscle development were identified, eight of which (gsk3b, wnt8a, wnt11, axin2, stat1, stat2, jak2, hsp90) were involved in muscle fiber hyperplasia, six of which (tgf-β1, col1a1, col1a2, col1a3, col4a1, col18a1) were associated with collagen synthesis in crisp grass carp. The difference of methylation levels in the key genes might lead to the expression difference, further resulting in the increase of muscle hardness in crisp grass carp. Overall, this study can help further understand how faba bean modulates muscle development by the epigenetic modifications, providing novel insights into the texture quality improvement in other aquaculture fish species by nutritional programming.

Effects of faba bean (Vicia faba L.) on fillet quality of Yellow River carp (Cyprinus carpio) via the oxidative stress response

In order to further explain the fillet texture improvement of Yellow River carp (Cyprinus carpio) fed with faba bean (Vicia faba L.), a three-month rearing trial was conducted to investigate fatty acid composition, antioxidant capacity, myofiber development, collagen deposition and transcriptome in white muscle of two farmed carp groups (One was fed only faba bean, the other was fed commercial diet). As a strong oxidant, faba bean changed fatty acids composition in white muscle, especially DHA and EPA, up-regulated the levels of reactive oxygen species (ROS) and down-regulated major antioxidant enzyme activities in the hepatopancreas and white muscle. Through the analysis of transcriptome and subsequent verification analysis, we speculated that the increase of ROS led to the decrease of myofiber diameter and collagen metabolism. This study provides a theoretical basis for further understanding the regulation of faba bean on fillet texture characteristic of Yellow River carp.

Size Effects of Microplastics on Embryos and Observation of Toxicity Kinetics in Larvae of Grass Carp (Ctenopharyngodon idella)

Microplastics have caused great concern in recent years. However, few studies have compared the toxicity of different sizes of microplastics in fishes, especially commercial fishes, which are more related to human health. In the present study, we revealed the effects of varying sizes of microplastics on grass carp embryos and larvae using scanning electron microscopy (SEM) and fluorescence imaging. Embryos were exposed to 80 nm and 8 μm microplastics at concentrations of 5, 15, and 45 mg/L. Toxicity kinetics of various sizes of fluorescent microplastics were analyzed through microscopic observation in the larvae. Results found that nanoplastics could not penetrate the embryo’s chorionic membrane, instead they conglutinated or aggregated on the chorion. Our results are the first to explore the defense mechanisms of commercial fish embryos against microplastics. Larvae were prone to ingesting their own excrement, resulting in microplastic flocculants winding around their mouth. For the first time, it was found that excreted microplastics could be reconsumed by fish and reaccumulated in the oral cavity. Microplastics of a certain size (1 μm) could be accumulated in the nasal cavity. We speculate that the presence of a special groove structure in the nasal cavity of grass carp larvae may manage to seize the microplastics with a particular size. As far as we know, this is the first report of microplastics being found in the nasal passages of fish. Fluorescence images clearly recorded the toxicity kinetics of microplastics in herbivorous fish.

Effects of Dietary Paper Mulberry (Broussonetia papyrifera) on Growth Performance and Muscle Quality of Grass Carp (Ctenopharyngodon idella)

Simple Summary

The quality of muscle plays an important role in improving the economic benefit of aquatic products. The paper mulberry (Broussonetia papyrifera, BP) grows wildly in the south of Asia. In this experiment, grass carps (initial weight: 50.0 ± 0.5 g) were fed diets with the addition of 0%, 5%, 10%, 15% and 20% BP in a control diet (crude protein: 31%, crude fat: 3.8%) for 8 weeks. In conclusion, adding 5% BP did not affect the growth of grass carp. However, the supplementation of 10% BP could improve muscle quality through improving muscle hardness, reducing fat accumulation and muscle fiber diameter, at the cost of reducing growth performance.

Abstract

The present study investigated the effects of dietary paper mulberry (Broussonetia Papyrifera, BP) on growth performance, muscle quality and muscle growth-related mRNA expressions of grass carp. Fish (initial weight: 50.0 ± 0.5 g) were fed diets supplemented with 0% (control diet), 5%, 10%, 15% and 20% BP for 8 weeks. The results showed that increasing levels of paper mulberry linearly and quadratically decreased the special gain rate (SGR) and increased the feed conversion rate (FCR) of grass carp (p < 0.05). Significantly positive quadratic trends were found between paper mulberry levels and muscle crude fat or crude protein of grass carp (p < 0.05). In comparison to the control diet, the 10%BP and 15%BP groups had significantly decreased muscle crude fat and increased crude protein (p < 0.05). The levels of paper mulberry resulted in a linear and quadratic increase in water loss of grass carp muscle (p < 0.05), and all groups with paper mulberry supplementation were significantly higher than the control group (p < 0.05). Significant positive linear and quadratic trends were found between the paper mulberry levels and muscle fiber diameter or density of grass carp (p < 0.05). In comparison to the control diet, the significant differences were found in the 15%BP and 20%BP groups (p < 0.05). The muscle adhesiveness and hardness linearly and quadratically increased with the increasing levels of paper mulberry (p < 0.05), and both of which increased significantly when the level of paper mulberry reached 10% (p < 0.05). In addition, the increase in paper mulberry linearly and quadratically improved the expressions of myoblast determination protein (MyoD), myogenin (MyoG), paired box protein 7 (Pax7) and myostatin 1 (MSTN1) (p < 0.05). When the supplementation of paper mulberry reached 15%, the expressions of all these mRNAs were significantly higher than those of the control group (p < 0.05). In summary, adding 5% paper mulberry did not affect the growth of grass carp. However, the supplementation of 10% paper mulberry could improve muscle quality through improving muscle hardness, reducing fat accumulation and muscle fiber diameter, at the cost of reducing growth performance.

Increased accuracy of genomic predictions for growth under chronic thermal stress in rainbow trout by prioritizing variants from GWAS using imputed sequence data

Through imputation of genotypes, genome‐wide association study (GWAS) and genomic prediction (GP) using whole‐genome sequencing (WGS) data are cost‐efficient and feasible in aquaculture breeding schemes. The objective was to dissect the genetic architecture of growth traits under chronic heat stress in rainbow trout (Oncorhynchus mykiss) and to assess the accuracy of GP based on imputed WGS and different preselected single nucleotide polymorphism (SNP) arrays. A total of 192 and 764 fish challenged to a heat stress experiment for 62 days were genotyped using a customized 1 K and 26 K SNP panels, respectively, and then, genotype imputation was performed from a low‐density chip to WGS using 102 parents (36 males and 66 females) as the reference population. Imputed WGS data were used to perform GWAS and test GP accuracy under different preselected SNP scenarios. Heritability was estimated for body weight (BW), body length (BL) and average daily gain (ADG). Estimates using imputed WGS data ranged from 0.33 ± 0.05 to 0.55 ± 0.05 for growth traits under chronic heat stress. GWAS revealed that the top five cumulatively SNPs explained a maximum of 0.94%, 0.86% and 0.51% of genetic variance for BW, BL and ADG, respectively. Some important functional candidate genes associated with growth‐related traits were found among the most important SNPs, including signal transducer and activator of transcription 5B and 3 (STAT5B and STAT3, respectively) and cytokine‐inducible SH2‐containing protein (CISH). WGS data resulted in a slight increase in prediction accuracy compared with pedigree‐based method, whereas preselected SNPs based on the top GWAS hits improved prediction accuracies, with values ranging from 1.2 to 13.3%. Our results support the evidence of the polygenic nature of growth traits when measured under heat stress. The accuracies of GP can be improved using preselected variants from GWAS, and the use of WGS marginally increases prediction accuracy.

Proteomic and metabolomic basis for improved textural quality in crisp grass carp (Ctenopharyngodon idellus C.et V) fed with a natural dietary pro-oxidant

Reactive oxygen species (ROS) regulate metabolism and chemical composition of various tissues. To understand how ROS affect the textural quality of fish muscle, we performed a multi-omics analysis on an established crisp grass carp model fed with a natural pro-oxidant faba bean. ROS levels were systemically and significantly increased up to three-fold in crisp grass carp, improving the muscle texture. Lipid metabolism was significantly enhanced up to five-fold in muscle and liver possibly to compensate the impaired carbohydrate metabolism of these tissues, but this caused further local ROS production. Mitochondrial damage associated with autophagy was evident in crisp grass carp. Proteomics revealed that elevated ROS likely disturbed the actin-myosin interaction and collagen turnover inducing fragmentation of myofibrillar proteins, all of which could have positively impacted the textural quality. The systemic metabolic changes that lead to the partial collapse of redox regulation likely underlie the ROS-induced improvement of textural quality.

Transcriptome analysis revealed changes of multiple genes involved in muscle hardness in grass carp (Ctenopharyngodon idellus) fed with faba bean meal

An 8-week feeding trial and transcriptome analysis were conducted to investigate the potential mechanism of muscle-hardening caused by faba bean in grass carp (Ctenopharyngodon idellus). Ordinary grass carp (fed with practical diet) and crisp grass carp (fed with faba bean meal) groups were designed. Lower water holding capacity and higher some texture parameters were observed in the muscle of crisp grass carp compared with another group. 19.62 GB clean reads were generated, and total 1354 genes exhibiting differentially expression were identified (FDR < 0.05). Genes function enrichment revealed up-regulated genes in crisp grass carp mainly in response to myofibroblast proliferation, while down-regulated genes in response to immune regulation. Consistent with this, the tight junction pathway and the NF-κB signaling pathway were likewise significantly enriched. In summary, this study identified several candidate genes and putative signaling pathways deserving further investigation to the mechanism of muscle-hardening in fish fed with faba bean.

Intestinal Microbiota of Grass Carp Fed Faba Beans: A Comparative Study

Many reports of the intestinal microbiota of grass carp have addressed the microbial response to diet or starvation or the effect of microbes on metabolism; however, the intestinal microbiota of crisp grass carp has yet to be elucidated. Moreover, the specific bacteria that play a role in the crispiness of grass carp fed faba beans have not been elucidated. In the present study, 16S sequencing was carried out to compare the intestinal microbiota in the fore-, mid- and hind-intestine segments of grass carp following feeding with either faba beans or formula feed. Our results showed that (1) the hind-intestine presented significant differences in diversity relative to the fore- or midintestine and (2) faba beans significantly increased the diversity of intestinal microbiota, changed the intestinal microbiota structure (Fusobacteria was reduced from 64.26% to 18.24%, while Proteobacteria was significantly increased from 17.75% to 51.99%), and decreased the metabolism of energy, cofactors and vitamins in grass carp. Furthermore, at the genus and species levels, Acinetobacter accounted for 15.09% of the microbiota, and Acinetobacter johnsonii and Acinetobacter radioresistens constituted 3.41% and 2.99%, respectively, which indicated that Acinetobacter of the family Moraxellaceae contributed to changes in the intestinal microbiota structure and could be used as a potential biomarker. These results may provide clues at the intestinal microbiota level to understanding the mechanism underlying the crispiness of grass carp fed faba beans.

Lipid accumulation in grass carp (Ctenopharyngodon idellus) fed faba beans (Vicia faba L.)

Feeding faba beans (Vicia faba L.) to grass carp (Ctenopharyngodon idellus) increases muscle compactness but decreases growth and motility. The lipid metabolism of grass carp was examined to assess potential effects of feeding faba beans on physiological properties using a total of 180 fish. The treatment group was fed faba beans for 120 days and a commercial diet for another 30 days. The control group received a commercial diet for 150 days. Fish were sampled every month. Weight gain was significantly lower in the treatment group than in the control. Hardness, springiness, chewiness, cohesiveness, and gumminess of the dorsal muscle increased significantly with the feeding faba beans from 30 to 120 days, which was not reversed by the subsequent feeding of commercial diet. Fat accumulation increased significantly in the treatment group as suggested by the condition factor, viscera index, hepatopancreatic index, and intraperitoneal fat index (IPFI), hepatopancreas, and muscle fat content but was not affected by subsequent feeding with the commercial diet. Serum triglyceride and total cholesterol levels were significantly reduced in the experimental diet group. In the hepatopancreas and intraperitoneal fat IPF, monounsaturated fatty acids showed significantly higher content in faba bean feeding fish, whereas polyunsaturated fatty acid content showed the reversed pattern. In the hepatopancreas, the activities of the lipogenic enzymes malate dehydrogenase and glucose 6-phosphate dehydrogenase were higher in the treatment than in the control group. Moreover, the treatment group showed lower mRNA levels of carnitine palmitoyltransferase-1. Overall, our results clearly demonstrate increasing lipid accumulation in the viscera of faba bean-fed grass carp.

Diet Affects Muscle Quality and Growth Traits of Grass Carp (Ctenopharyngodon idellus): A Comparison Between Grass and Artificial Feed

Fish muscle, the main edible parts with high protein level and low fat level, is consumed worldwide. Diet contributes greatly to fish growth performance and muscle quality. In order to elucidate the correlation between diet and muscle quality, the same batch of juvenile grass carp (Ctenopharyngodon idellus) were divided into two groups and fed with either grass (Lolium perenne, Euphrasia pectinata and Sorghum sudanense) or artificial feed, respectively. However, the different two diets didn't result in significant differences in all the detected water quality parameters (e.g., Tm, pH, DO, NH3/[Formula: see text]-N, [Formula: see text]-N, [Formula: see text], TN, TP, and TOC) between the two experimental groups. After a 4-month culture period, various indexes and expression of myogenic regulatory factor (MRFs) and their related genes were tested. The weight gain of the fish fed with artificial feed (AFG) was nearly 40% higher than the fish fed with grass (GFG). Significantly higher alkaline phosphatase, total cholestrol, high density cholestrol and total protein were detected in GFG as compared to AFG. GFG also showed increased hardness, resilience and shear force in texture profile analysis, with significantly bigger and compact muscle fibers in histologic slices. The fat accumulation was most serious in the abdomen muscle of AFG. Additionally, the expression levels of MyoG, MyoD, IGF-1, and MSTNs were higher, whereas Myf-5, MRF4, and IGF-2 were lower in most positional muscles of GFG as compared to AFG. Overall, these results suggested that feeding grass could promote muscle growth and development by stimulating muscle fiber hypertrophy, as well as significantly enhance the expression of CoL1As. Feeding C. idellus with grass could also improve flesh quality by improving muscle characteristics, enhancing the production of collagen, meanthile, reducing fat accumulation and moisture in muscle, but at the cost of a slower growth.

Proteomic signature of muscle fibre hyperplasia in response to faba bean intake in grass carp

Fish muscle growth is important for the rapidly developing global aquaculture industry, particularly with respect to production and quality. Changes in muscle fibre size are accomplished by altering the balance between protein synthesis and proteolysis. However, our understanding regarding the effects of different protein sources on fish muscle proteins is still limited. Here we report on the proteomic profile of muscle fibre hyperplasia in grass carp fed only with whole faba bean. From the results, a total of 99 significantly changed proteins after muscle hyperplasia increase were identified (p < 0.05, ratio <0.5 or >2). Protein–protein interaction analysis demonstrated the presence of a network containing 56 differentially expressed proteins, and muscle fibre hyperplasia was closely related to a protein–protein network of 12 muscle component proteins. Muscle fibre hyperplasia was also accompanied by decreased abundance in the fatty acid degradation and calcium signalling pathways. In addition, metabolism via the pentose phosphate pathway decreased in grass carp after ingestion of faba bean, leading to haemolysis. These findings could provide a reference for the prevention and treatment of human glucose-6-phosphate dehydrogenase deficiency (“favism”).

Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella)

Characterization of the transcriptomic response to infection is an effective approach to understanding the immune mechanisms. Herein we challenged grass carp (Ctenopharyngodon idella) with grass carp reovirus (GCRV) and sequenced four cDNA libraries obtained from head-kidney and spleen by using Illumina Miseq. As a result, we gained a total of 21.52 Gb clean data with 107.96 million reads, and de novo assembled 55,199 unigenes with an average length of 1,470 bp. Comparative transcriptome analysis reveals that 217 unigenes are differentially expressed (fold-change of at least 4) between resistant and susceptible fish in both head-kidney and spleen, and of which 36 unigenes were validated by RT-qPCR experiment. The expression profile of immune-related genes demonstrates that the immune response of spleen is more intense than that of head-kidney. Remarkably, 11,811 unigenes contain multiple transcripts, of which 322 unigenes possess notably differentially expressed transcripts between the four transcriptomic datasets. Furthermore, the splicing transcripts of IL-12p40 and IL-1R1 are firstly found to play diverse roles in the antiviral response of fishes. This study provides a complete transcriptome dataset of C. idella, which is valuable for the studies of immune complexity and, moreover, throws light on the regulatory role of AS in antiviral immunity.