Identification of the Differentially Expressed Genes of Muscle Growth and Intramuscular Fat Metabolism in the Development Stage of Yellow Broilers

Multiple strategies association revealed functional candidate FASN gene for fatty acid composition in cattle

Fatty acid composition (FA) is an important indicator of meat quality in beef cattle. We investigated potential functional candidate genes for FA in beef cattle by integrating genomic and transcriptomic dataset through multiple strategies. In this study, we observed 65 SNPs overlapping with five candidate genes (CCDC57, FASN, HDAC11, ALG14, and ZMAT4) using two steps association based on the imputed sequencing variants. Using multiple traits GWAS, we further identified three significant SNPs located in the upstream of FASN and one SNP (chr19:50779529) was embedded in FASN. Of those, two SNPs were further identified as the cis-eQTL based on transcriptomic analysis of muscle tissues. Moreover, the knockdown of FASN yielded a significant reduction in intracellular triglyceride content in preadipocytes and impeded lipid droplet accumulation in adipocytes. RNA-seq analysis of preadipocytes with FASN interference revealed that the differentially expressed genes were enriched in cell differentiation and lipid metabolic pathway. Our study underscored the indispensable role of FASN in orchestrating adipocyte differentiation, and fatty acid metabolism. The integrative analysis with multiple strategies may contribute to the understanding of the genetic architecture of FA in farm animals.

Circumpolar Population Structure, Diversity and Recent Evolutionary History of the Bearded Seal in Relation to Past and Present Icescapes

The Arctic environment plays a critical role in the global climate system and marine biodiversity. The region's ice-covered expanses provide essential breeding and feeding grounds for a diverse assemblage of marine species, who have adapted to thrive in these harsh conditions and consequently are under threat from global warming. The bearded seal (Erignathus barbatus), including two subspecies (E. barbatus nauticus-Pacific and E. barbatus barbatus-Atlantic), is an ice-obligate Arctic species using sea ice for many aspects of its life history, rendering it particularly vulnerable to sea ice loss. It is one of the least studied and hence enigmatic of the Arctic marine mammals, with little knowledge regarding genetic structure, diversity, adaptations, and demographic history, consequently hampering management and conservation efforts. Here, we sequenced 70 whole nuclear genomes from across most of the species' circumpolar range, finding significant genetic structure between the Pacific and the Atlantic subspecies, which diverged during the Penultimate Glacial Period (~200 KYA). Remarkably, we found fine-scale genetic structure within both subspecies, with at least two distinct populations in the Pacific and three in the Atlantic. We hypothesise sea-ice dynamics and bathymetry had a prominent role in shaping bearded seal genetic structure and diversity. Our analyses of highly differentiated genomic regions can be used to complement the health, physiological, and behavioural research needed to conserve this species. In addition, we provide recommendations for management units that can be used to more specifically assess climatic and anthropogenic impacts on bearded seal populations.

Temperature manipulation during incubation: effect on embryo development and incidence of white striping and expression of related genes in broiler chickens from two commercial breeds

1. This study evaluated the effects of cyclic eggshell temperature between 10 and 14 d of embryogenesis on traits viz. the expression of MYOZ2, PPARγ and GPx7 in breast muscle, meat quality and incidence of white striping at slaughter age.2. Eggs were obtained from Cobb and Ross broiler breeders to investigate the response of breeds to eggshell temperature, which regulated air temperature. A total of 784 eggs were incubated at either the control eggshell temperature (37.8°C) from 0 to 18 d or exposed to cyclic high eggshell temperature (CHT) at 38.8°C for 6 h/d between 10 and 14 d of incubation. The temperature was 36.8°C between 18 and 21 d. Hatched chicks were reared under optimum rearing conditions. The birds were sampled at 19 d of incubation, at hatch and at 42 d post-hatch.3. There was no effect of eggshell temperature on yolk-free body weight and residual yolk sac weight. The CHT chicks had wider breasts on the day of hatching.4. At hatch and 42d post-hatch, PPARγ expression in Cobb-CHT was upregulated 4.78-fold and downregulated 3.28-fold, respectively, compared to the Cobb-control. At slaughter age, chickens from Ross-CHT had 1.98- and 2.33-fold upregulated PPARγ and GPX7 expressions, respectively, compared to Ross-control. The CHT increased GPx7 expression in the Cobb-CHT day-old chicks compared to the Cobb-control. On ED19, MYOZ2 expression was upregulated in Cobb and downregulated in Ross by CHT.5. The effects of breed and eggshell temperature on pH15, L*, a*, expressible juice and cooking loss were not significant. The CHT increased the incidence of severe white striping lesions in Ross chickens.6. It was concluded eggshell temperature modulated embryo development, incidence of white striping and expression of related genes differently in the two commercial breeds.

Unraveling the genetic and epigenetic landscape governing intramuscular fat deposition in rabbits: Insights and implications

Intramuscular fat (IMF) content is a predominant factor recognized to affect rabbit meat quality, directly impacting flavor, juiciness, and consumer preference. Despite its significance, the major interplay of genetic and epigenetic factors regulating IMF in rabbits remains largely unexplored. This review sheds light on this critical knowledge gap, offering valuable insights and future directions. We delve into the potential role of established candidate genes from other livestock (e.g. PPARγ, FABP4, and SCD) in rabbits, while exploring the identified novel genes of IMF in rabbits. Furthermore, we explored the quantitative trait loci studies in rabbit IMF and genomic selection approaches for improving IMF content in rabbits. Beyond genetics, this review unveils the exciting realm of epigenetic mechanisms modulating IMF deposition. We explored the potential of DNA methylation patterns, histone modifications, and non-coding RNA-mediation as fingerprints for selecting rabbits with desirable IMF levels. Additionally, we explored the possibility of manipulating the epigenetic landscape through nutraceuticals interventions to promote favorable IMF depositions. By comprehensively deciphering the genomic and epigenetic terrain of rabbit intramuscular fat regulation, this study aims to assess the existing knowledge regarding the genetic and epigenetic factors that control the deposition of intramuscular fat in rabbits. By doing so, we identified gaps in the current research, and suggested potential areas for further investigation that would enhance the quality of rabbit meat. This can enable breeders to develop targeted breeding strategies, optimize nutrition, and create innovative interventions to enhance the quality of rabbit meat, meet consumer demands and increase market competitiveness.

Comparative transcriptomic analysis revealed potential mechanisms regulating the hypertrophy of goose pectoral muscles

Pectoral muscle development is an important economic trait. According to the different essence, muscle development can be divided into 2 processes: embryonic muscle fiber generation and postnatal muscle fiber hypertrophy, and postnatal muscle fiber hypertrophy has a greater impact on muscle development than the number of muscle fibers formed during the embryonic phase in poultry. However, the underlying mechanisms regulating the hypertrophy of goose pectoral muscles have not been elucidated. Therefore, the purpose of the present study was to conduct transcriptome sequencing in pectoral muscles of both Landes (LD) and Sichuan White (SW) geese at 6, 10, and 30 weeks of age to reveal the molecular mechanisms regulating pectoral muscle hypertrophy through intra-breed and inter-breed bioinformatics analyses. Phenotypically, the pectoral muscle weight/index of LD and SW geese increased from 6 to 30 weeks of age, and except for the pectoral muscle index at 10 weeks of age (P = 0.962), at the same age, the pectoral muscle weight/index of LD geese were significantly higher than that of SW geese (P < 0.05). In transcriptional regulation, intra-breed bioinformatics analysis identified 3331 genes whose expression levels were opposite to the trend of pectoral muscle hypertrophy both in LD and SW geese, and the 3331 genes were mainly enriched into abundant KEGG pathways related to lipid metabolism, proliferation/apoptosis, and immune response. Moreover, 23 genes (including SLC2A10, TNFRSF1A, PRKAA1, SLC27A4, ITGB2, THY1, RHOA, MYL10, ACTB, PRKCB, PIK3R2, RAC2, DMD, LATS2, YAP1, WWTR1, SMAD7, CTGF, FGF1, AXIN2, GLI2, ID2, and CCND2) who were enriched in 6 crosstalk pathways named viral myocarditis, insulin resistance, sphingolipid signaling pathway, hippo signaling pathway, chemokine signaling pathway, and leukocyte transendothelial migration were identified as the key candidate genes regulating the hypertrophy of goose pectoral muscles. In inter-breed bioinformatics analysis, abundant different expression genes (DEGs) related to lipid metabolism, immune response, and proliferation/apoptosis were identified between LD and SW geese too, and compared with SW geese, the expression level of MYL10 in LD geese was lower, while the expression levels of GLI2/CTGF/SMAD7 in LD geese were higher. These results suggested that the hypertrophy of goose pectoral muscles might be achieved through more lipid deposition and less leukocyte infiltration to promote the proliferation of cells within the muscles, and the low expression of MYL10 and high expressions of GLI2/CTGF/SMAD7 might the keys to induce the pectoral muscle hypertrophy of LD geese from 6 to 30 weeks of age over that of SW geese. All data the present study obtained will provide new insights into the molecular mechanisms regulating the hypertrophy of goose pectoral muscles.

Analysis of genetic structure and identification of important genes associated with muscle growth in Fujian Muscovy duck

Fujian Muscovy duck is a well-known meat waterfowl in Fujian Province due to its high meat production, superior breeding potential, and strong resistance. To fully explore the genetic characteristics of these advantages, Fujian black Muscovy duck and white Muscovy duck were used for whole-genome re-sequencing and transcriptome analyses. Population structure analysis showed significant differentiation between the two feather strains. Runs of homozygosity analysis indicated a stronger artificial influence on the black-feathered strain, with ROH island genes notably enriched in muscle tissue-related terms and pathways. Selective sweep and transcriptome analysis revealed a significant enrichment of genes linked to muscle tissue and muscle fiber-related terms and pathways. Key candidate genes identified, such as MEF2C, MYOZ2, and METTL21C, are believed to play crucial roles in meat production in Fujian Muscovy duck. This study offers a new perspective on improving meat production in Fujian Muscovy duck, which can benefit breeding strategies and production management.

Association of CETP Gene Polymorphisms and Haplotypes with Acute Heart Rate Response to Exercise

Polymorphisms in the cholesteryl ester transfer protein (CETP) gene are known to be strongly associated with increased cardiovascular risk, primarily through their effects on the lipid profile and consequently on atherosclerotic risk. The acute heart rate response (AHRR) to physical activity is closely related to individual cardiovascular health. This study aimed to investigate the effect of CETP gene polymorphisms on AHRR. Our analysis examines the association of five single nucleotide polymorphisms (SNPs; rs1532624, rs5882, rs708272, rs7499892, and rs9989419) and their haplotypes (H) in the CETP gene with AHRR in 607 people from the Hungarian population. Individual AHRR in the present study was assessed using the YMCA 3-min step test and was estimated as the difference between resting and post-exercise heart rate, i.e., delta heart rate (ΔHR). To exclude the direct confounding effect of the CETP gene on the lipid profile, adjustments for TG and HDL-C levels, next to conventional risk factors, were applied in the statistical analyses. Among the examined five SNPs, two showed a significant association with lower ΔHR (rs1532624-Cdominant: B = -8.41, p < 0.001; rs708272-Gdominant: B = -8.33, p < 0.001) and reduced the risk of adverse AHRR (rs1532624-Cdominant: OR = 0.44, p = 0.004; rs708272-Gdominant: OR = 0.43, p = 0.003). Among the ten haplotypes, two showed significant association with lower ΔHR (H3-CAGCA: B = -6.81, p = 0.003; H9-CGGCG: B = -14.64, p = 0.015) and lower risk of adverse AHRR (H3-CAGCA: OR = 0.58, p = 0.040; H9-CGGCG: OR = 0.05, p = 0.009) compared to the reference haplotype (H1-AGACG). Our study is the first to report a significant association between CETP gene polymorphisms and AHRR. It also confirms that the association of the CETP gene with cardiovascular risk is mediated by changes in heart rate in response to physical activity, in addition to its effect on lipid profile.

Genetic characteristics and selection signatures between Southern Chinese local and commercial chickens

The introduction of exotic breeds and the cultivation of new lines by breeding companies have posed challenges to native chickens in South China, including loss of breed characteristics, decreased genetic diversity, and declining purity. Understanding the population genetic structure and genetic diversity of native chickens in South China is crucial for further advancements in breeding efforts. In this study, we analyzed the population genetic structure and genetic diversity of 321 individuals from 10 different breeds in South China. By comparing commercial chickens with native ones, we identified selection signatures occurring between local chickens and commercial breeds. The analysis of population genetic structure revealed that the native chicken populations in South China exhibited a considerable level of genetic diversity. Moreover, the commercial lines of Xiaobai chicken and Huangma chicken displayed even higher levels of genetic diversity, which distinguished them from other native varieties at the clustering level. However, certain individuals within these commercial varieties showed a discernible genetic relationship with the native populations. Notably, both commercial varieties also retained a significant degree of genetic similarity to their respective native counterparts. In order to investigate the genomic changes occurring during the commercialization of native chickens, we employed 4 methods (Fst, ROD, XPCLR, and XPEHH) to identify potential candidate regions displaying selective signatures in Southern Chinese native chicken population. A total of 168 (identified by Fst and ROD) and 86 (identified by XPCLR and XPEHH) overlapping genes were discovered. Functional annotation analysis revealed that these genes may be associated with reproduction and growth (SAMSN1, HYLS1, ROBO3, FGF14, PRSS23), musculoskeletal development (DNER, MYBPC1, DGKB, ORC1, KLF10), disease resistance and environmental adaptability (PUS3, CRB2, CALD1, USP15, SGCD, LTBP1), as well as egg production (ADGRB3, ACSF3). Overall, native chickens in South China harbor numerous selective sweep regions compared to commercial chickens, enriching valuable genomic resources for future genetic research and breeding conservation.

Muscle Transcriptome Analysis of Mink at Different Growth Stages Using RNA-Seq

Mink is a kind of small and precious fur animal resource. In this study, we employed transcriptomics technology to analyze the gene expression profile of mink pectoral muscle tissue, thereby elucidating the regulatory mechanisms underlying mink growth and development. Consequently, a total of 25,954 gene expression profiles were acquired throughout the growth and development stages of mink at 45, 90, and 120 days. Among these profiles, 2607 genes exhibited significant differential expression (|log2(fold change)| ≥ 2 and p_adj < 0.05). GO and KEGG enrichment analyses revealed that the differentially expressed genes were primarily associated with the mitotic cell cycle process, response to growth factors, muscle organ development, and insulin resistance. Furthermore, GSEA enrichment analysis demonstrated a significant enrichment of differentially expressed genes in the p53 signaling pathway at 45 days of age. Subsequent analysis revealed that genes associated with embryonic development (e.g., PEG10, IGF2, NRK), cell cycle regulation (e.g., CDK6, CDC6, CDC27, CCNA2), and the FGF family (e.g., FGF2, FGF6, FGFR2) were all found to be upregulated at 45 days of age in mink, which suggested a potential role for these genes in governing early growth and developmental processes. Conversely, genes associated with skeletal muscle development (PRVA, TNNI1, TNNI2, MYL3, MUSTN1), a negative regulator of the cell cycle gene (CDKN2C), and IGFBP6 were found to be up-regulated at 90 days of age, suggesting their potential involvement in the rapid growth of mink. In summary, our experimental data provide robust support for elucidating the regulatory mechanisms underlying the growth and development of mink.

Characterizing structural variants based on graph-genotyping provides insights into pig domestication and local adaption

Structural variants (SVs), such as deletions (DELs) and insertions (INSs), contribute substantially to pig genetic diversity and phenotypic variation. Using a library of SVs discovered from long-read primary assemblies and short-read sequenced genomes, we map pig genomic SVs with a graph-based method for re-genotyping SVs in 402 genomes. Our results demonstrate that those SVs harboring specific trait-associated genes may greatly shape pig domestication and local adaptation. Further characterization of SVs reveals that some population-stratified SVs may alter the transcription of genes by affecting regulatory elements. We identify that the genotypes of two DELs (296-bp DEL, chr7: 52,172,101-52,172,397; 278-bp DEL, chr18: 23,840,143-23,840,421) located in muscle-specific enhancers are associated with the expression of target genes related to meat quality (FSD2) and muscle fiber hypertrophy (LMOD2 and WASL) in pigs. Our results highlight the role of SVs in domestic porcine evolution, and the identified candidate functional genes and SVs are valuable resources for future genomic research and breeding programs in pigs.

Identification of key differentially methylated genes in regulating muscle development and intramuscular fat deposition in chickens

Muscle development and intramuscular fat (IMF) deposition are intricate physiological processes characterized by multiple gene expressions and interactions. In this research, the phenotypic variations in the breast muscle of Jingyuan chickens were examined at three different time points: 42, 126, and 180 days old. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were performed to identify differentially methylated genes (DMGs) responsible for regulating muscle development and IMF deposition. The findings indicate a significant increase in breast muscle weight (BMW), myofiber diameter, and cross-sectional area, as well as IMF content, in correlation with the progressive number of growing days in Jingyuan chickens. The findings also revealed that 380 hypo-methylated and 253 hyper-methylated DMGs were identified between the three groups of breast muscle. Module gene and DMG association analysis identified m6A methylation-mediated multiple DMGs associated with muscle development and fat metabolism. In vitro cell modeling analysis reveals stage-specific differences in the expression of CUBN, MEGF10, BOP1, and BMPR2 during the differentiation of myoblasts and intramuscular preadipocytes. Cycloleucine treatment significantly inhibited the expression levels of CUBN, BOP1, and BMPR2, and promoted the expression of MEGF10. These results suggest that m6A methylation-mediated CUBN, MEGF10, BOP1, and BMPR2 can serve as potential candidate genes for regulating muscle development and IMF deposition, and provide an important theoretical basis for further investigation of the functional mechanism of m6A modification involved in adipogenesis.

Molecular analysis to identify novel potential biomarkers as drug targets in colorectal cancer therapy: an integrated bioinformatics analysis

Colorectal cancer (CRC) is a heterogeneous disease that requires new diagnostic and prognostic markers. Integrated bioinformatics approach to identify novel therapeutic targets associated with CRC. Using GEO2R identified DEGs in CRC, and Funrich software facilitated the visualization of DEGs through Venn diagrams. From a total of 114 enhanced DEGs, potential hub genes were further filtered based on their nodal strength and edges using STRING database. To gain insights into the functional roles of these hub genes, gene ontology and pathway enrichment were conducted thorough g: profiler web server. Subsequently, overall survival plots from GEPIA and oncogenic predictive functions like mRNA expressions for stages and nodal metastasis were employed to identify hub genes in CRC patient samples. Additionally, the cBioPortal and HPA databases also revealed genetic alterations and expression levels in these hub genes in CRC patients, further supporting their involvement in colorectal cancer. Gene expression by RT-PCR shows upregulation of hub genes in HT-29 cells. Finally, our integrated bioinformatic analysis revealed that ABCE1, AURKA, HSPD1, PHKA1, CDK4, and YWHAE as hub genes with potential oncogenic roles in CRC. These genes hold promise as diagnostic and prognostic markers for colorectal tumorigenesis, providing insights into targeted therapies for improved patient outcomes.

Genomic Insights into Molecular Regulation Mechanisms of Intramuscular Fat Deposition in Chicken

Intramuscular fat (IMF) plays an important role in the tenderness, water-holding capacity, and flavor of chicken meat, which directly affect meat quality. In recent years, regulatory mechanisms underlying IMF deposition and the development of effective molecular markers have been hot topics in poultry genetic breeding. Therefore, this review focuses on the current understanding of regulatory mechanisms underlying IMF deposition in chickens, which were identified by multiple genomic approaches, including genome-wide association studies, whole transcriptome sequencing, proteome sequencing, single-cell RNA sequencing (scRNA-seq), high-throughput chromosome conformation capture (HiC), DNA methylation sequencing, and m6A methylation sequencing. This review comprehensively and systematically describes genetic and epigenetic factors associated with IMF deposition, which provides a fundamental resource for biomarkers of IMF deposition and provides promising applications for genetic improvement of meat quality in chicken.

Validation of protein biological markers of lamb meat quality characteristics based on the different muscle types

This work investigated the ability of 8 potential biomarkers (phosphoglycerate kinase-1 (PGK1), pyruvate kinase-M2 (PKM2), phosphoglucomutase-1 (PGM1), β-enolase (ENO3, myosin-binding protein-C (MYBPC1), myosin regulatory light chain-2 (MYLPF), troponin C-1 (TNNC1) and troponin I-1 (TNNI1)) to characterize meat quality by analyzing their relative abundance and enzymatic activity. Two different meat quality groups (Quadriceps femoris (QF) and Longissimus thoracis (LT) muscles) were selected at 24 h postmortem from 100 lamb carcasses. The relative abundance of PKM2, PGK1, PGM1, ENO3, MYBPC1, MYLPF, and TNNI1 was significantly different between LT and QF muscle groups (P < 0.01). Moreover, PKM, PGK, PGM, and ENO activity in LT muscle group was significantly lower than that in QF muscle (P < 0.05). Suggesting that PKM2, PGK1, PGM1, ENO3, MYBPC1, MYLPF, and TNNI1 can be used as robust biomarkers of lamb meat quality, providing the reference for understanding the molecular mechanism of postmortem meat quality formation in future.

RNA N6-methyladenosine profiling reveals differentially methylated genes associated with intramuscular fat metabolism during breast muscle development in chicken

Intramuscular fat (IMF) is an important indicator for determining meat quality, and IMF deposition during muscle development is regulated by a complex molecular network involving multiple genes. The N⁶-methyladenosine (m⁶A) modification of mRNA plays an important regulatory role in muscle adipogenesis. However, the distribution of m⁶A and its role in IMF metabolism in poultry has not been reported. In the present study, a transcriptome-wide m⁶A profile was constructed using methylated RNA immunoprecipitation sequence (MeRIP-seq) and RNA sequence (RNA-seq) to explore the potential mechanism of regulating IMF deposition in the breast muscle based on the comparative analysis of IMF differences in the breast muscles of 42 (group G), 126 (group S), and 180-days old (group M) Jingyuan chickens. The findings revealed that the IMF content in the breast muscle increased significantly with the increase in the growth days of the Jingyuan chickens (P < 0.05). The m⁶A peak in the breast muscles of the 3 groups was highly enriched in the coding sequence (CDS) and 3' untranslated regions (3' UTR), which corresponded to the consensus motif RRACH. Moreover, we identified 129, 103, and 162 differentially methylated genes (DMGs) in the breast muscle samples of the G, S, and M groups, respectively. Functional enrichment analyses revealed that DMGs are involved in many physiological activities of muscle fat anabolism. The m⁶A-induced ferroptosis pathway was identified in breast muscle tissue as a new target for regulating IMF metabolism. In addition, association analysis demonstrated that LMOD2 and its multiple m⁶A negatively regulated DMGs are potential regulators of IMF differential deposition in muscle. The findings of the present study provide a solid foundation for further investigation into the potential role of m⁶A modification in regulating chicken fat metabolism.

Transcriptome analysis reveals candidate genes of the synthesis of branched-chain fatty acids related to mutton flavor in the lamb liver using Allium Mongolicum Regel extract

The objective of this study was to identify candidate genes via which Allium mongolicum Regel ethanol extract (AME) affects the synthesis of branched-chain fatty acids (BCFAs) related to mutton flavor by transcriptome analysis in the lamb liver. Thirty male Small-tailed Han sheep (3 mo old; 33.6 ± 1.2 kg) were randomly divided into two groups and fed for 75 d with a basal diet containing no AME (CON, control group) or 2.8 g·lamb⁻¹·d⁻¹ AME (AME group). Twelve sheep, CON (n = 6) and AME (n = 6), were selected for slaughter at the end of the trial period, and liver samples were subsequently collected. There was no difference in 4-ethyloctanoic acid content among treatments. The 4-methyloctanoic acid and 4-methylnonanoic acid levels were significantly lower in the AME group than in the CON group (P < 0.05). Furthermore, 461 differentially expressed genes (DEGs) were identified between the CON and AME groups, of which 182 were upregulated and 279 were downregulated in the AME group. The DEGs were enriched in three pathways, namely, glutathione metabolism, ECM–receptor interaction, and steroid hormone biosynthesis, as determined by the Kyoto Encyclopedia of Genes and Genomes pathway analysis. Finally, CYP2B6, ACOT12, THEM4, ACSF2, LPIN1, and ADCY4 were identified as candidate genes that might be involved in regulating the BCFAs synthesis in the sheep liver.

The mechanism of Megalobrama amblycephala muscle injury repair based on RNA-seq

Skeletal muscle myogenesis and injury-induced muscle regeneration contribute to muscle formation. Skeletal muscle stem cells, termed satellite cells (SCs), proliferate to repair injured muscle. To identify the molecular mechanism of regeneration after muscle injury as well as the genes related to muscle development in fish, in this study, the immunohistochemistry and the high-throughput RNA sequencing (RNA-seq) analysis were performed after Megalobrama amblycephala muscle was injured by needle stab. The results showed that paired box7-positive (Pax7⁺) SCs increased, and peaked at 96 to 144 h-post injury (hpi). The 6729 differentially expressed genes (DEGs), including 2125 up-regulated and 4604 down-regulated genes were found. GO terms significantly enriched by DEGs contained intercellular connections, signaling transduction and enzyme activity. KEGG enrichment analysis showed that most of the pathways were related to immunity, metabolism and cells related molecules, including actin skeleton regulation, Epstein Barr virus infection and plaque adhesion. The WGCNA results revealed that actin cytoskeleton and lipid metabolism related genes probably played crucial roles during repair after muscle injury. Collectively, all these results will provide new insights into the molecular mechanisms underlying muscle injury repair of fish.

Effects of physical exercise on muscle metabolism and meat quality characteristics of Mongolian sheep

The objective of this study was to investigate the effects of exercise training on muscle metabolism, fatty acid composition, carcass traits, and meat quality characteristics of Mongolian sheep. Fourteen Mongolian sheep were randomly divided into two groups (7 sheep in each) and placed in two adjacent livestock pens. One group of sheep was kept in the pen (Control [C] group) and the other group of sheep (Training [T] group) were driven away in a field to walk twice a day. The results showed a reduction in pH measured 45 min post mortem, L*, a*, and b* value, intramuscular fat, and carcass length, and an increase in the ultimate pH value and shear force in the meat of T group in comparison with that of C group (p < .050). Also, exercise training moderately affected the fatty acid composition of LT muscle. Compared with C group, the concentrations of myristoleic acid (C14:1) and stearic acid (C18:0) were increased (p < .050), while the concentrations of C20:3 n‐6, neurolic acid (C24:1), and n‐3 polyunsaturated fatty acid (PUFA) were decreased in T group (p < .050). Transcriptome analysis highlighted 621 genes differentially expressed in two groups, including 385 were up‐regulated (e.g., GLUT4 and PGC‐1α) and 236 were down‐regulated (e.g., PLIN1 and ACSL3) in T with respect to C group. Besides, considering these genes, a number of enrichment pathways related to muscle metabolic processes, involving carbohydrate metabolism, lipid metabolism, oxidation reduction process, and muscle tissue development, were highlighted. In conclusion, these results contributed to a better understanding of the possible biological and molecular processes underlying the effects of exercise training on muscle metabolism and meat quality in Mongolian sheep, and provide useful information for contributing to understand the phenotypic and functional differences in meat quality of sheep.

Hepatic Proteomic Analysis Reveals That Enhanced Carboxylic Acid Metabolism and Oxidoreduction Promote Muscle and Fat Deposition in Muscovy Duck

Simple Summary

Liver plays an important role in lipid synthesis and muscle growth in poultry. The current study measured the growth traits and the proteome of Muscovy duck liver at 14, 28, 42, and 56 days, aiming at exploring the key regulatory proteins for intramuscular fat deposition and muscle growth. The results showed that Muscovy duck grew most rapidly at 28 vs. 42 days of age, subcutaneous and abdominal fat were deposited rapidly, but intramuscular fat content decreased. At the same time, the abundance of liver proteins regarding the tricarboxylic acid cycle and oxidoreduction increased significantly. This study provides a profile of the fat deposition and liver proteome for Muscovy duck.

Abstract

Liver is responsible for 90% of lipid synthesis in poultry; thus, it plays an important role in the growth of Muscovy ducks, which have a high fat deposition ability in a time-dependent manner. Therefore, male Muscovy ducks at 14, 28, 42, and 56 days were selected for body weight (BW), carcass weight (CW), subcutaneous fat thickness (SFT), abdominal fat weight (AFW), intramuscular fat content (IMF), and breast muscle fiber (BMF) diameter and density determination. Two-dimensional electrophoresis (2-DE) combining liquid chromatography linked to tandem mass spectrometry (LC-MS/MS) was used to analyze proteomic changes in liver at each stage. The BW, CW, AFW, SFT, and BMF diameter and density were significantly increased, while IMF content was significantly decreased at 28 to 42 days of age (p < 0.05). There were 57 differentially abundant protein (DEP) spots representing 40 proteins identified among the ages, in which 17, 41 and 4 spots were differentially abundant at 14 vs. 28, 28 vs. 42, and 42 vs. 56, respectively. Gene Ontology enrichment analysis found that DEPs were mostly enriched in the oxidation-reduction process, carboxylic acid metabolism, etc. Protein–protein interaction showed that catalase (CAT), triosephosphate isomerase (TPI), and protein disulfide-isomerase (PDI) were the key proteins responsible for the growth of Muscovy duck. In conclusion, 28 to 42 days of age is the crucial period for Muscovy ducks, and the ability of metabolism and antioxidants were significantly enhanced in liver.

TMT-based quantitative proteomics analysis reveals the key proteins related with the differentiation process of goat intramuscular adipocytes

Background

Intramuscular adipocytes differentiation is a complex process, which is regulated by various transcription factor, protein factor regulators and signal transduction pathways. However, the proteins and signal pathways that regulates goat intramuscular adipocytes differentiation remains unclear.

Result

In this study, based on nanoscale liquid chromatography mass spectrometry analysis (LC-MS/MS), the tandem mass tag (TMT) labeling analysis was used to investigate the differentially abundant proteins (DAPs) related with the differentiation process of goat intramuscular adipocytes. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes enrichment and protein-protein interaction network analyses were performed for the characterization of the identified DAPs. The candidate proteins were verified by parallel reaction monitoring analysis. As a result, a total of 123 proteins, 70 upregulation proteins and 53 downregulation proteins, were identified as DAPs which may be related with the differentiation process of goat intramuscular adipocytes. Furthermore, the cholesterol metabolism pathway, glucagon signaling pathway and glycolysis / gluconeogenesis pathway were noticed that may be the important signal pathways for goat Intramuscular adipocytes differentiation.

Conclusions

By proteomic comparison between goat intramuscular preadipocytes (P_IMA) and intramuscular adipocytes (IMA), we identified a series protein that might play important role in the goat intramuscular fat differentiation, such as SRSF10, CSRP3, APOH, PPP3R1, CRTC2, FOS, SERPINE1 and AIF1L, could serve as candidates for further elucidate the molecular mechanism of IMF differentiation in goats.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07730-y.

Dietary Enteromorpha Polysaccharides Supplementation Improves Breast Muscle Yield and Is Associated With Modification of mRNA Transcriptome in Broiler Chickens

The present study evaluated the effects of dietary supplementation of Enteromorpha polysaccharides (EP) on carcass traits of broilers and potential molecular mechanisms associated with it. This study used RNA-Sequencing (RNA-Seq) to detect modification in mRNA transcriptome and the cognate biological pathways affecting the carcass traits. A total of 396 one-day-old male broilers (Arbor Acres) were randomly assigned to one of six dietary treatments containing EP at 0 (CON), 1000 (EP_1000), 2500 (EP_2500), 4000 (EP_4000), 5500 (EP_5500), and 7000 (EP_7000) mg/kg levels for a 35-d feeding trial with 6 replicates/treatment. At the end of the feeding trial, six birds (one bird from each replicate cage) were randomly selected from each treatment and slaughtered for carcass traits analysis. The results showed that the dietary supplementation of EP_7000 improved the breast muscle yield (p < 0.05). Subsequently, six breast muscle samples from CON and EP_7000 groups (three samples from each group) were randomly selected for RNA-Seq analysis. Based on the RNA-Seq results, a total of 154 differentially expressed genes (DEGs) were identified (p < 0.05). Among the DEGs, 112 genes were significantly upregulated, whereas 42 genes were significantly down-regulated by EP_7000 supplementation. Gene Ontology enrichment analysis showed that the DEGs were mainly enriched in immune-related signaling pathways, macromolecule biosynthetic, DNA-templated, RNA biosynthetic, and metabolic process (p < 0.05). Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the DEGs were enriched in signaling pathways related to viral infectious diseases and cell adhesion molecules (p < 0.05). In conclusion, dietary inclusion of EP_7000 improves the breast muscle yield, which may be involved in improving the immunity and the cell differentiation of broilers, thus promoting the muscle growth of broilers. These findings could help understand the molecular mechanisms that enhance breast muscle yield by dietary supplementation of EP in broilers.

Characterization and Comparative Transcriptomic Analysis of Skeletal Muscle in Pekin Duck at Different Growth Stages Using RNA-Seq

Simple Summary

Skeletal muscle is an important tissue and its development is strictly regulated by genes. In this study, in order to understand the muscle-related gene expression in Pekin duck, RNA-seq was performed to analyze and compare skeletal muscle at different growth stages. Alternative splicing, single nucleotide polymorphisms and insertion–deletions were detected, and 299 novel genes were discovered. MYL4, IGF2BP1, CSRP3, SPP1, KLHL31, LAMB2, LAMA2, ITGB1 and OPN played crucial roles in skeletal muscle development. Oxidative phosphorylation, ECM-receptor interaction, focal adhesion, carbon metabolism, and biosynthesis of amino acids participated in the regulation of skeletal muscle development in Pekin duck. This study provides an important reference for revealing the developmental mechanisms of pectoral and leg muscles in duck.

Abstract

Skeletal muscle, accounting for approximately 50% of body weight, is the largest and most important tissue. In this study, the gene expression profiles and pathways in skeletal muscle of Pekin duck were investigated and compared at embryonic day 17, 21, and 27 and postnatally at 6 months of age. An average of 49,555,936 reads in each sample was obtained from the transcriptome libraries. Over 70.0% of alternative splicing (AS) in each sample was mainly alternative 5′ first exon (transcription start site)—the first exon splicing (TSS) and alternative 3′ last exon (transcription terminal site)—the last exon splicing (TTS), indicating that TSS and TTS were the most common AS event in Pekin ducks, and these AS events were closely related to the regulation of muscle development at different growth stages. The results provided a valuable genomic resource for selective breeding and functional studies of genes. A total of 299 novel genes with ≥2 exons were obtained. There were 294 to 2806 differentially expressed genes (DEGs) in each pairwise comparison of Pekin duck. Notably, 90 DEGs in breast muscle and 9 DEGs in leg muscle were co-expressed at all developmental points. DEGs were validated by qPCR analysis, which confirmed the tendency of the expression. DEGs related to muscle development were involved in biological processes such as “endodermal cell differentiation”, “muscle cell cellular homeostasis”, “skeletal muscle tissue growth” and “skeletal muscle cell differentiation”, and were involved in pathways such as oxidative phosphorylation, ECM-receptor (extracellular matrix receptor) interaction, focal adhesion, carbon metabolism, and biosynthesis of amino acids. Some DEGs, including MYL4, IGF2BP1, CSRP3, SPP1 and KLHL31, as well as LAMB2, LAMA2, ITGB1 and OPN, played crucial roles in muscle growth and development. This study provides valuable information about the expression profile of mRNAs and pathways from duck skeletal muscle at different growth stages, and further functional study of these mRNAs and pathways could provide new ideas for studying the molecular networks of growth and development in duck skeletal muscle.

Transcriptome landscapes of differentially expressed genes related to fat deposits in Nandan-Yao chicken

Nandan-Yao chicken is a Chinese native chicken with lower fat deposition and better meat quality. Fat deposition is a quite complex and important economic trait. However, its molecular mechanism is still unknown in chickens. In the current study, Nandan-Yao chicken was divided into two groups based on the rate of abdominal fat at 120 days old, namely the high-fat group and low-fat group. The total RNAs were isolated and sequenced by RNA sequencing (RNA-seq). After quality control, we gained 1222, 902, 784, 624, and 736 differentially expressed genes (DEGs) in abdominal fat, back skin, liver, pectoral muscle, and leg muscle, respectively. Analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that significantly enriched GO term and KEGG signaling pathway mainly involved cytosolic ribosome, growth development, PPAR signaling pathway, Wnt signaling pathway, and linoleic acid metabolism in abdominal fat, back skin, and liver. While in pectoral muscle and leg muscle, it is mainly enriched in phosphatidylinositol signaling system, adrenergic signaling in cardiomyocytes, cytosolic ribosome, and cytosolic part. Sixteen genes were differentially expressed in all five tissues. Among them, PLA2G4A and RPS4Y1 might be the key regulators for fat deposition in Nandan-Yao chicken. The protein-protein interaction (PPI) network analysis of DEGs showed that PCK1 was the most notable genes. The findings in the current study will help to understand the regulation mechanism of abdominal fat and intramuscular fat in Nandan-Yao chicken and provide a theoretical basis for Chinese local chicken breeding.