Metabolomic, lipidomic, and proteomic profiles provide insights on meat quality differences between Shitou and Wuzong geese

A comprehensive comparison of metabolomic, lipidomic, and proteomic profiles was conducted between the breast and leg muscles of Shitou goose (STE) and Wuzhong goose (WZE), which exhibit significant variations in body size and growth rate, to evaluate their impact on meat quality. WZE had higher intramuscular fat content in their breast muscles, which were also chewier and had higher drip and cooking losses than STE. Metabolomic analysis revealed differential regulation of amino acid and purine metabolism between WZE and STE. Lipidomic analysis indicated a higher abundance of PE and PC lipid molecules in WZE. Integration of proteomic and metabolomic data highlighted purine metabolism and amino acid biosynthesis as the major distinguishing pathways between STE and WZE. The primary differential pathways between breast and leg muscles were associated with energy metabolism and fatty acid metabolism. This comprehensive analysis provides valuable insights into the distinct meat quality of STE and WZE.

MeRIP sequencing reveals the regulation of N6-methyladenosine in muscle development between hypertrophic and leaner broilers

Meat production performance is the most important economic trait in broilers, and skeletal muscle, as the largest organ in animals, is directly related to meat production during embryonic and postnatal growth and development. N6-Methyladenosine (m6A) is a chemical modification occurs on RNA adenosine that has been reported to participate in a variety of biological processes in all species. However, there are still few reports on the regulatory role of muscle growth and development in poultry after birth. This study aims to reveal the distribution of m6A modification sites in chicken pectoralis major muscle after birth and find out the regulatory relationship between m6A and muscle development. As representatives of leaner (Xinghua chicken [XH]) and hypertrophic (White Recessive Rock chicken [WRR]) broilers, there are significant differences in body weight, muscle fiber diameter, and muscle fiber cross-sectional area between XH and WRR chickens. RNA sequencing detected a total of 397 differentially expressed genes (DEG) in the pectoralis major muscle of XH and WRR chicken, and these DEGs were mainly enriched in catalytic activity and metabolic pathways. MeRIP sequencing results showed that among all 6,476 differentially modified m6A peaks, about 90% peaks (5,823) were differentially down regulated in XH chickens. The joint analysis of the mRNA and MeRIP sequencing data found 145 DEGs with differential m6A peak, ALKBH5 as a m6A demethylase, was also included. The highly expression of ALKBH5 in the muscle tissue of poultry and differential expression between XH and WRR chickens suggest that ALKBH5 may play a crucial role in regulating muscle development. Our results revealed that there were significant differences in growth rate, body weight, muscle fiber diameter, and fiber cross-section area between WRR and XH chicken, as well as significant differences in m6A methylation level and muscle metabolism level.

Assessment of selective breeding effects and selection signatures in Qingyuan partridge chicken and its strains

Qingyuan partridge chicken (QYM) is a highly regarded native breed in China, highly esteemed for its exceptional breeding characteristics. However, the investigation into the selection signatures and its strains remains largely unexplored. In this study, blood sampling, DNA extracting, and high-depth resequencing were performed in 27 QYMs. Integrating the genomic data of 14 chicken (70 individuals) breeds from other researches, to analyze the genetic structure, selection signatures, and effects of selective breeding within QYM and its 3 strains (QYMA, QYMB, and QYMC). Population structure analysis revealed an independent QYM cluster, which exhibited distinct from other breeds, with each of its 3 strains displaying distinct clustering patterns. Linkage disequilibrium analysis highlighted QYMB's notably slower decay rate, potentially influenced by selection pressure from various production indicators. Examination of selection signatures uncovered genes and genetic mechanisms associated with genomic changes resulting from extensive selective breeding within the QYM and its strains. Intriguingly, diacylglycerol kinase beta (DGKB) and catenin alpha 2 (CTNNA2) were identified as commonly selected genes across the 3 QYM strains, linked to energy metabolism, muscle development, and fat metabolism. Our research validates the substantial impact of selective breeding on QYM and its strains, concurrently identifying genomic regions and signaling pathways associated with their distinctive characters. This research also establishes a fundamental framework for advancing yellow-feathered broiler breeding strategies.

LncEDCH1 g.1703613 T>C regulates chicken carcass traits by targeting miR-196-2-3p

Single nucleotide polymorphisms (SNPs) are valuable genetic markers that can provide insights into the genetic diversity and variation within chicken populations. In poultry breeding, SNP analysis is widely utilized to accelerate the selection of desirable traits, improving the efficiency and effectiveness of chicken breeding programs. In our previous research, we identified an association between LncEDCH1 and muscle development. To further investigate its specific mechanism, we conducted SNP detection and performed genotyping, linkage disequilibrium, and haplotype analysis. Our research findings indicate that 16 SNPs in the LncEDCH1. Among these SNPs, g.1703497 C>T and g.1704262 C>T were significantly associated with breast muscle weight percentage, g.1703497 C>T and g.1703613 T>C were significantly associated with leg weight percentage, and g.1703497 C>T, g.1703589 T>C, g.1703613 T>C, g.1703636 C>A, g.1703768 T>C, g.1704079 C>T, g.1704250 T>C, g.1704253 G>A were significantly associated with skin yellowness. Two haplotype blocks composed of 6 SNPs that were significantly associated with wing skin yellowness, breast skin yellowness, full-bore weight, and carcass weight percentage. Furthermore, through dual-luciferase reporter assays, biotin-coupled miRNA pull-down assays, 5-ethynyl-2'-deoxyuridine (EDU) assays, immunofluorescence, and quantitative real-time polymerase chain reaction (qPCR), it has been confirmed that miR-196-2-3p inhibits the expression of LncEDCH1 directly by binding to LncEDCH1 g.1703613T>C, thereby achieving indirect regulation of muscle development. These findings provide valuable molecular markers for chicken molecular breeding and broaden our understanding of the regulatory mechanisms.

Weighted single-step GWAS identified candidate genes associated with carcass traits in a Chinese yellow-feathered chicken population

Carcass traits in broiler chickens are complex traits that are influenced by multiple genes. To gain deeper insights into the genetic mechanisms underlying carcass traits, here we conducted a weighted single-step genome-wide association study (wssGWAS) in a population of Chinese yellow-feathered chicken. The objective was to identify genomic regions and candidate genes associated with carcass weight (CW), eviscerated weight with giblets (EWG), eviscerated weight (EW), breast muscle weight (BMW), drumstick weight (DW), abdominal fat weight (AFW), abdominal fat percentage (AFP), gizzard weight (GW), and intestine length (IL). A total of 1,338 broiler chickens with phenotypic and pedigree information were included in this study. Of these, 435 chickens were genotyped using a 600K single nucleotide polymorphism chip for association analysis. The results indicate that the most significant regions for 9 traits explained 2.38% to 5.09% of the phenotypic variation, from which the region of 194.53 to 194.63Mb on chromosome 1 with the gene RELT and FAM168A identified on it was significantly associated with CW, EWG, EW, BMW, and DW. Meanwhile, the 5 traits have a strong genetic correlation, indicating that the region and the genes can be used for further research. In addition, some candidate genes associated with skeletal muscle development, fat deposition regulation, intestinal repair, and protection were identified. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses suggested that the genes are involved in processes such as vascular development (CD34, FGF7, FGFR3, ITGB1BP1, SEMA5A, LOXL2), bone formation (FGFR3, MATN1, MEF2D, DHRS3, SKI, STC1, HOXB1, HOXB3, TIPARP), and anatomical size regulation (ADD2, AKT1, CFTR, EDN3, FLII, HCLS1, ITGB1BP1, SEMA5A, SHC1, ULK1, DSTN, GSK3B, BORCS8, GRIP2). In conclusion, the integration of phenotype, genotype, and pedigree information without creating pseudo-phenotype will facilitate the genetic improvement of carcass traits in chickens, providing valuable insights into the genetic architecture and potential candidate genes underlying carcass traits, enriching our understanding and contributing to the breeding of high-quality broiler chickens.

Bulk and single-cell alternative splicing analyses reveal roles of TRA2B in myogenic differentiation

Alternative splicing (AS) disruption has been linked to disorders of muscle development, as well as muscular atrophy. However, the precise changes in AS patterns that occur during myogenesis are not well understood. Here, we employed isoform long-reads RNA-seq (Iso-seq) and single-cell RNA-seq (scRNA-seq) to investigate the AS landscape during myogenesis. Our Iso-seq data identified 61,146 full-length isoforms representing 11,682 expressed genes, of which over 52% were novel. We identified 38,022 AS events, with most of these events altering coding sequences and exhibiting stage-specific splicing patterns. We identified AS dynamics in different types of muscle cells through scRNA-seq analysis, revealing genes essential for the contractile muscle system and cytoskeleton that undergo differential splicing across cell types. Gene-splicing analysis demonstrated that AS acts as a regulator, independent of changes in overall gene expression. Two isoforms of splicing factor TRA2B play distinct roles in myogenic differentiation by triggering AS of TGFBR2 to regulate canonical TGF-β signalling cascades differently. Our study provides a valuable transcriptome resource for myogenesis and reveals the complexity of AS and its regulation during myogenesis.

The transmembrane protein TMEM182 promotes fat deposition and alters metabolomics and lipidomics

TMEM182, a transmembrane protein highly expressed in muscle and adipose tissues, plays a crucial role in muscle cell differentiation, metabolism, and signaling. However, its role in fat deposition and metabolism is still unknown. In this study, we used overexpression and knockout models to examine the impact of TMEM182 on fat synthesis and metabolism. Our results showed that TMEM182 overexpression increased the expression of fat synthesis-related genes and promoted the differentiation of preadipocytes into fat cells. In TMEM182 knockout mice, there was a significant decrease in abdominal fat deposition. RNA sequencing results showed that TMEM182 overexpression in preadipocytes enhanced the activity of pathways related to fat formation, ECM-receptor interaction, and cell adhesion. Furthermore, our analysis using UPLC-MS/MS showed that TMEM182 significantly altered the metabolite and lipid content and composition in chicken breast muscle. Specifically, TMEM182 increased the content of amino acids and their derivatives in chicken breast muscle, promoting amino acid metabolic pathways. Lipidomics also revealed a significant increase in the content of glycerophospholipids, sphingolipids, and phospholipids in the breast muscle after TMEM182 overexpression. These findings suggest that TMEM182 plays a crucial role in regulating fat deposition and metabolism, making it a potential target for treating obesity-related diseases and animal breeding.

MicroRNA expression profile of chicken jejunum in different time points Eimeria maxima infection

Coccidiosis stands as a protozoan disease of notable economic impact, characterized by an intracellular parasite that exerts substantial influence over poultry production. This invasion disrupts the integrity of the enteric mucosa, leading to the emergence of severe lesions and diminishing the efficiency of feed utilization in chickens. MicroRNA (miRNA) are short, non-coding RNA molecules with approximately 21-24 nucleotides long in size that play essential roles in various infectious diseases and inflammatory responses. However, the miRNA's expression patterns and roles in the context of Eimeria maxima infection of chicken intestines remain unclear. miRNA sequencing was employed to assess the miRNA expression profile in chicken jejunum during E. maxima infection. In this study, we analyzed miRNA expression profiles related to the host's immune response in the chicken jejunum during E. maxima infection. At 4 days infection and control (J4I versus J4C), 21 differentially expressed miRNAs in the jejunum were identified, comprising 9 upregulated and 12 downregulated miRNAs. Furthermore, in the jejunum, at 7 days infection and control (J7I versus J7C) groups, a total of 35 significantly differentially expressed miRNAs were observed, with 13 upregulated and 22 downregulated miRNAs. The regulatory networks were constructed between differentially expressed miRNA and mRNAs to offer insight into the interaction mechanisms between chickens and E. maxima coccidian infection. Furthermore, within the comparison group, we obtained 946, 897, and 281 GO terms that exhibited significant enrichment associated with host immunity in the following scenarios, J4I vs. J4C, J7I vs. J7C, and J4I vs. J7I, respectively. The KEGG pathway analysis indicated notable enrichment of differentially expressed miRNAs in the jejunum, particularly in J4I vs. J4C; enriched pathways included metabolic pathways, endocytosis, MAPK signaling pathway, regulation of actin cytoskeleton, and cytokine-cytokine receptor interaction. Moreover, in J7I vs. J7C, the KEGG pathway was significantly enriched, including metabolic pathways, protein processing in the endoplasmic reticulum, ubiquitin-mediated proteolysis, and FoxO signaling pathway. A comprehensive understanding of the host genetic basis of resistance with a combination of time-dependent infection to the Eimeria parasite is crucial for pinpointing resistance biomarkers for poultry production.

MYH1G-AS is a chromatin-associated lncRNA that regulates skeletal muscle development in chicken

BACKGROUND

Skeletal muscle development is pivotal for animal growth and health. Recently, long noncoding RNAs (lncRNAs) were found to interact with chromatin through diverse roles. However, little is known about how lncRNAs act as chromatin-associated RNAs to regulate skeletal muscle development. Here, we aim to investigate the regulation of chromatin-associated RNA (MYH1G-AS) during skeletal muscle development.

METHODS

We provided comprehensive insight into the RNA profile and chromatin accessibility of different myofibers, combining RNA sequencing (RNA-seq) with an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). The dual-luciferase reporter assay and chromatin immunoprecipitation (ChIP) assay were used to analyze the transcriptional regulation mechanism of MYH1G-AS. ALKBH5-mediated MYH1G-AS N6-methyladenosine (m6A) demethylation was assessed by a single-base elongation and ligation-based qPCR amplification method (SELECT) assay. Functions of MYH1G-AS were investigated through a primary myoblast and lentivirus/cholesterol-modified antisense oligonucleotide (ASO)-mediated animal model. To validate the interaction of MYH1G-AS with fibroblast growth factor 18 (FGF18) protein, RNA pull down and an RNA immunoprecipitation (RIP) assay were performed. Specifically, the interaction between FGF18 and SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 (SMARCA5) protein was analyzed by coimmunoprecipitation (Co-IP) and a yeast two-hybrid assay.

RESULTS

A total of 45 differentially expressed (DE) lncRNAs, with DE ATAC-seq peaks in their promoter region, were classified as open chromatin-associated lncRNAs. A skeletal muscle-specific lncRNA (MSTRG.15576.9; MYH1G-AS), which is one of the open chromatin-associated lncRNA, was identified. MYH1G-AS transcription is coordinately regulated by transcription factors (TF) SMAD3 and SP2. Moreover, SP2 represses ALKBH5 transcription to weaken ALKBH5-mediated m6A demethylation of MYH1G-AS, thus destroying MYH1G-AS RNA stability. MYH1G-AS accelerates myoblast proliferation but restrains myoblast differentiation. Moreover, MYH1G-AS drives a switch from slow-twitch to fast-twitch fibers and causes muscle atrophy. Mechanistically, MYH1G-AS inhibits FGF18 protein stabilization to reduce the interaction of FGF18 to SMARCA5, thus repressing chromatin accessibility of the SMAD4 promoter to activate the SMAD4-dependent pathway.

CONCLUSIONS

Our results reveal a new pattern of the regulation of lncRNA expression at diverse levels and help expound the regulation of m6A methylation on chromatin status.

Chicken muscle antibody array reveals the regulations of LDHA on myoblast differentiation through energy metabolism

Myoblast proliferation and differentiation are highly dynamic and regulated processes in skeletal muscle development. Given that proteins serve as the executors for the majority of biological processes, exploring key regulatory factors and mechanisms at the protein level offers substantial opportunities for understanding the skeletal muscle development. In this study, a total of 607 differentially expressed proteins between proliferation and differentiation in myoblasts were screened out using our chicken muscle antibody array. Biological function analysis revealed the importance of energy production processes and compound metabolic processes in myogenesis. Our antibody array specifically identified an upregulation of LDHA during differentiation, which was associated with the energy metabolism. Subsequent investigation demonstrated that LDHA promoted the glycolysis and TCA cycle, thereby enhancing myoblasts differentiation. Mechanistically, LDHA promotes the glycolysis and TCA cycle but inhibits the ETC oxidative phosphorylation through enhancing the NADH cycle, providing the intermediate metabolites that improve the myoblasts differentiation. Additionally, increased glycolytic ATP by LDHA induces Akt phosphorylation and activate the PI3K-Akt pathway, which might also contribute to the promotion of myoblasts differentiation. Our studies not only present a powerful tool for exploring myogenic regulatory factors in chicken muscle, but also identify a novel role for LDHA in modulating myoblast differentiation through its regulation of cellular NAD+ levels and subsequent downstream effects on mitochondrial function.

DNA methylation in poultry: a review

As an important epigenetic modification, DNA methylation is involved in many biological processes such as animal cell differentiation, embryonic development, genomic imprinting and sex chromosome inactivation. As DNA methylation sequencing becomes more sophisticated, it becomes possible to use it to solve more zoological problems. This paper reviews the characteristics of DNA methylation, with emphasis on the research and application of DNA methylation in poultry.

Investigation of potential genetic factors for growth traits in yellow-feather broilers using weighted single-step genome-wide association study

Yellow-feather broilers take a large portion of poultry industry in China due to its meat characteristics. Improving the growth traits of yellow-feathered broilers will have great significance for the Chinese poultry market. The current study was designed to investigate the potential genetic factors using the weighted single-step genome-wide association study (wssGWAS) method, which takes consideration of more factors including pedigree, sex, environment and has more accuracy than traditional GWAS. The yellow-feather dwarf chickens from Wens Nanfang Poultry Breeding Co. Ltd. were revolved to recode 9 growth traits: Average daily gain (ADG), body weight (BW) at 45 d, 49 d, 56 d, 63 d, 70 d, 77 d, 84 d, 91 d for analysis. For the results, the region 4.63 to 5.03 Mb on chromosome 15, which was the QTL overlapped in BW45, BW49, BW56, BW63, BW84, might be the crucial genetic region for growth traits. Seven GO terms and 3 KEGG pathways, GO:0005200, GO:0005882, GO:0045111, GO:0099513, GO:0099081, GO:0099512, GO:0099080, KEGG:gga04020, KEGG:gga04540, KEGG:gga04210, were detected to relevant with growth traits. The genes enriched in these biological processes (NRAS, TUBB1, ADORA2B, NTRK3, NGF, TNNC2, F-KER, LOC429492, LOC431325, LOC431324, LOC396480) might have the function in growth of yellow-feather broilers.

Evaluation of the selection of key individuals for genotype imputation in Chinese yellow-feathered chicken

Genotype imputation is a powerful technique employed by next-generation sequencing (NGS) and genotyping arrays, which can significantly enhance the cost-effectiveness and efficiency of genomic selection. The accuracy of imputation is largely determined by the choice of reference panel, with previous studies generally demonstrating that a closely related population as a reference panel leads to greater accuracy than a more distantly related population. Various strategies have been proposed for selecting desirable individuals via targeted resequencing, but their efficiencies need further improvement. In this study, we present a practical broiler selection methodology for a local Chinese chicken line that integrates established methods based on pedigree, genomics, and random sampling, and leverages genotype and pedigree information from the yellow-plumage dwarf chicken line. The efficacy of these selection strategies was assessed by evaluating their ability to accurately impute masked genotypes from data obtained using a 600K chip. Our findings reveal that the pedigree-based method yields superior accuracy in genotype imputation, whereas the haplotype-based method exhibits greater stability. Nonetheless, the impact of these targeted methods for selecting key individuals is slightly different when initiating a new sequencing project in a production context. Overall, this study highlights the advantages of using the pedigree-based approach as the preferred method for optimizing genotype imputation in broiler chickens.

Local GHR roles in regulation of mitochondrial function through mitochondrial biogenesis during myoblast differentiation

BACKGROUND

Myoblast differentiation requires metabolic reprogramming driven by increased mitochondrial biogenesis and oxidative phosphorylation. The canonical GH-GHR-IGFs axis in liver exhibits a great complexity in response to somatic growth. However, the underlying mechanism of whether local GHR acts as a control valve to regulate mitochondrial function through mitochondrial biogenesis during myoblast differentiation remains unknown.

METHODS

We manipulated the GHR expression in chicken primary myoblast to investigate its roles in mitochondrial biogenesis and function during myoblast differentiation.

RESULTS

We reported that GHR is induced during myoblast differentiation. Local GHR promoted mitochondrial biogenesis during myoblast differentiation, as determined by the fluorescence intensity of Mito-Tracker Green staining and MitoTimer reporter system, the expression of mitochondrial biogenesis markers (PGC1α, NRF1, TFAM) and mtDNA encoded gene (ND1, CYTB, COX1, ATP6), as well as mtDNA content. Consistently, local GHR enhanced mitochondrial function during myoblast differentiation, as determined by the oxygen consumption rate, mitochondrial membrane potential, ATP level and ROS production. We next revealed that the regulation of mitochondrial biogenesis and function by GHR depends on IGF1. In terms of the underlying mechanism, we demonstrated that IGF1 regulates mitochondrial biogenesis via PI3K/AKT/CREB pathway. Additionally, GHR knockdown repressed myoblast differentiation.

CONCLUSIONS

In conclusion, our data corroborate that local GHR acts as a control valve to enhance mitochondrial function by promoting mitochondrial biogenesis via IGF1-PI3K/AKT/CREB pathway during myoblast differentiation. Video Abstract.

Identifying driver pathways based on a parameter-free model and a partheno-genetic algorithm

BACKGROUND

Tremendous amounts of omics data accumulated have made it possible to identify cancer driver pathways through computational methods, which is believed to be able to offer critical information in such downstream research as ascertaining cancer pathogenesis, developing anti-cancer drugs, and so on. It is a challenging problem to identify cancer driver pathways by integrating multiple omics data.

RESULTS

In this study, a parameter-free identification model SMCMN, incorporating both pathway features and gene associations in Protein-Protein Interaction (PPI) network, is proposed. A novel measurement of mutual exclusivity is devised to exclude some gene sets with "inclusion" relationship. By introducing gene clustering based operators, a partheno-genetic algorithm CPGA is put forward for solving the SMCMN model. Experiments were implemented on three real cancer datasets to compare the identification performance of models and methods. The comparisons of models demonstrate that the SMCMN model does eliminate the "inclusion" relationship, and produces gene sets with better enrichment performance compared with the classical model MWSM in most cases.

CONCLUSIONS

The gene sets recognized by the proposed CPGA-SMCMN method possess more genes engaging in known cancer related pathways, as well as stronger connectivity in PPI network. All of which have been demonstrated through extensive contrast experiments among the CPGA-SMCMN method and six state-of-the-art ones.

Microplastic exposure induces muscle growth but reduces meat quality and muscle physiological function in chickens

Microplastic (MP) pollution has become one of the global environmental concerns, but the contamination and effect of MP on chicken skeletal muscle are scarcely researched. Here, we found MP contamination in the chicken skeletal muscles, which were directly collected from a large-scale chicken farm. Using Pyrolysis-Gas Chromatography-Mass Spectrometry and Agilent 8700 laser direct infrared imaging spectrometer, we found that polystyrene (PS) and polyamide are the significant type of MPs detected in chicken skeletal muscle. Constant PS-MP oral feeding for >21 days increases the content of MP deposited in chicken breast muscle, but the MP content in the leg muscle was gradually decreased. Surprisingly, the chicken's body and skeletal muscle weight was increased after constant PS-MP feeding. Physiological results showed that PS-MP exposure inhibited energy and lipid metabolism, induced oxidative stress, and potential for neurotoxicity in the skeletal muscle. Metabolomic analysis of the liquid chromatography-tandem mass spectrometry and gas chromatography coupled with the mass spectrometer results showed that PS-MP exposure changed the metabolomic profile and reduced meat quality. In vitro, experimental results showed that PS-MP exposure induced chicken primary myoblasts proliferation and apoptosis but decreased myoblasts differentiation. Transcriptome analysis of the skeletal muscle indicates that PS-MP exposure affects skeletal muscle function by regulating genes involved in neural function and muscle development. Considering that chicken is one of the most important meat foods in the world, this study will provide an essential reference for protecting meat food safety.

CD36 AFFECTS CHICKEN CARCASS, SKIN YELLOWNESS Detection of CD36 gene polymorphism associated with chicken carcass traits and skin yellowness

Investigations into the association between chicken traits and genetic variations provide helpful breeding information to improve production performance and economic benefits in chickens. The single nucleotide polymorphism technique is an important method in agricultural molecular breeding. In this study, we detected 11 SNPs in the CD36 gene, 2 SNPs (g.-1974 A>G, g.-1888 T>C) located in the 5' flanking regions, 8 SNPs (g.23496 G>A, g.23643 C>T, g.23931 T>C, g.23937 G>A, g.31256 C>A, g.31258 C>T, g.31335 C>T, g.31534 A>C) located in the intron region, 1 SNPs (g.23743 G>T) located in the exon region and it belongs to synonymous mutation. In SNPs g.23743 G>T, the abdominal fat weight and abdominal fat weight rate of the GG genotype were lower than that of the TT genotype. In SNPs g.23931 T>C, the full-bore weight rate and half-bore weight rate of the TT genotype were higher compared with the CC genotype. And the SNPs g.-1888 T>C, g.23496 G>A, g.23643 C>T, g.31335 C>T and g.31534 A>C were significantly associated with skin yellowness traits, the cloacal skin yellowness before slaughter of the TT genotype was higher than that of the TC and CC genotype in SNPs g.-1888 T>C. Furthermore, 3 haplotypes of the above eleven SNPs were calculated and they correlated with heart weight, stomach weight, wing weight, leg skin yellowness and shin skin yellowness before slaughter. Finally, the CD36 expression profile displayed the expression pattern of CD36 mRNA variation in different tissues.

CircPLXNA2 Affects the Proliferation and Apoptosis of Myoblast through circPLXNA2/gga-miR-12207-5P/MDM4 Axis

CircRNAs are newly identified special endogenous RNA molecules that covalently close a loop by back-splicing with pre-mRNA. In the cytoplasm, circRNAs would act as molecular sponges to bind with specific miRNA to promote the expression of target genes. However, knowledge of circRNA functional alternation in skeletal myogenesis is still in its infancy. In this study, we identified a circRNA–miRNA–mRNA interaction network in which the axis may be implicated in the progression of chicken primary myoblasts’ (CPMs) myogenesis by multi-omics (i.e., circRNA-seq and ribo-seq). In total, 314 circRNA–miRNA–mRNA regulatory axes containing 66 circRNAs, 70 miRNAs, and 24 mRNAs that may be relevant to myogenesis were collected. With these, the circPLXNA2-gga-miR-12207-5P-MDM4 axis aroused our research interest. The circPLXNA2 is highly differentially expressed during differentiation versus proliferation. It was demonstrated that circPLXNA2 inhibited the process of apoptosis while at the same time stimulating cell proliferation. Furthermore, we demonstrated that circPLXNA2 could inhibit the repression of gga-miR-12207-5p to MDM4 by directing binding to gga-miR-12207-5p, thereby restoring MDM4 expression. In conclusion, circPLXNA2 could function as a competing endogenous RNA (ceRNA) to recover the function of MDM4 by directing binding to gga-miR-12207-5p, thereby regulating the myogenesis.

Haplotype analysis of genomic prediction by incorporating genomic pathway information based on high-density SNP marker in Chinese yellow-feathered chicken

Genomic selection using single nucleotide polymorphism (SNP) markers is now intensively investigated in breeding and has been widely utilized for genetic improvement. Currently, several studies have used haplotype (consisting of multiallelic SNPs) for genomic prediction and revealed its performance advantage. In this study, we comprehensively evaluated the performance of haplotype models for genomic prediction in 15 traits, including 6 growth, 5 carcass, and 4 feeding traits in a Chinese yellow-feathered chicken population. We adopted 3 methods to define haplotypes from high-density SNP panels, and our strategy included combining Kyoto Encyclopedia of Genes and Genomes pathway information and considering linkage disequilibrium (LD) information. Our results showed an increase in prediction accuracy due to haplotypes ranging from -0.04∼27.16% in all traits, where the significant improvements were found in 12 traits. The estimates of haplotype epistasis heritability were strongly correlated with the accuracy increase by haplotype models. In addition, incorporating genomic annotation information could further increase the accuracy of the haplotype model, where the further increase in accuracy is significantly relative to the increase of relative haplotype epistasis heritability. The genomic prediction using LD information for constructing haplotypes has the best prediction performance among the 4 traits. These results uncovered that haplotype methods were beneficial for genomic prediction, and the accuracy could be further increased by incorporating genomic annotation information. Moreover, using LD information would potentially improve the performance of genomic prediction.

Integration of transcriptome sequencing and whole genome resequencing reveal candidate genes in egg production of upright and pendulous-comb chickens

Egg production performance plays an important role in the poultry industry across the world. Previous studies have shown a great difference in egg production performance between pendulous-comb (PC) and upright-comb (UC) chickens. However, there are no reports to identify potential candidate genes for egg production in PC and UC chickens. In the present study, 1,606 laying chickens were raised, and the egg laid by individual chicken was collected for 100 d. Moreover, the expression level of estrogen and progesterone hormones was measured at the start-laying and peak-laying periods of hens. Besides, 4 PC and 4 UC chickens were selected at 217 d of age to perform transcriptome sequencing (RNA-seq) and whole genome resequencing (WGS) to screen the potential candidate genes of egg production. The results showed that PC chicken demonstrated better egg production performance (P < 0.05) and higher estrogen and progesterone hormone expression levels than UC chicken (P < 0.05). RNA-seq analysis showed that 341 upregulated and 1,036 downregulated differentially expressed genes (DEGs) were identified in the ovary tissues of PC and UC chickens. These DEGs were mainly enriched in protein-related, lipid-related, and nucleic acids-related biological processes including ribosome, peptide biosynthetic process, lipid transport terms, and catalytic activity acting on RNA which can significantly affect egg production in chicken. The enrichment results of WGS analysis were consistent with RNA-seq. Further, joint analysis of WGS and RNA-seq data was utilized to screen 30 genes and CAMK1D, CLSTN2, MAST2, PIK3C2G, TBC1D1, STK3, ADGRB3, and PPARGC1A were identified as potential candidate genes for egg production in PC and UC chickens. In summary, our study provides a wealth of information for a better understanding of the genetic and molecular mechanism for the future breeding of PC and UC chickens for egg production.

LncRNA-TBP mediates TATA-binding protein recruitment to regulate myogenesis and induce slow-twitch myofibers

BACKGROUND

Skeletal muscle is comprised of heterogeneous myofibers that differ in their physiological and metabolic parameters. Of these, slow-twitch (type I; oxidative) myofibers have more myoglobin, more mitochondria, and higher activity of oxidative metabolic enzymes compared to fast-twitch (type II; glycolytic) myofibers.

METHODS

In our previous study, we found a novel LncRNA-TBP (for "LncRNA directly binds TBP transcription factor") is specifically enriched in the soleus (which has a higher proportion of slow myofibers). The primary myoblast cells and animal model were used to assess the biological function of the LncRNA-TBP in vitro or in vivo. Meanwhile, we performed a RNA immunoprecipitation (RIP) and pull-down analysis to validate this interaction between LncRNA-TBP and TBP.

RESULTS

Functional studies demonstrated that LncRNA-TBP inhibits myoblast proliferation but promotes myogenic differentiation in vitro. In vivo, LncRNA-TBP reduces fat deposition, activating slow-twitch muscle phenotype and inducing muscle hypertrophy. Mechanistically, LncRNA-TBP acts as a regulatory RNA that directly interacts with TBP protein to regulate the transcriptional activity of TBP-target genes (such as KLF4, GPI, TNNI2, and CDKN1A).

CONCLUSION

Our findings present a novel model about the regulation of LncRNA-TBP, which can regulate the transcriptional activity of TBP-target genes by recruiting TBP protein, thus modulating myogenesis progression and inducing slow-twitch fibers. Video Abstract.

Identification of candidate genes associated with skin yellowness in yellow chickens

The yellow color of the skin is an important economic trait for yellow chickens. Low and non-uniform skin yellowness would reduce economic efficiency. However, the regulatory mechanism of chicken skin yellowness has not been fully elucidated. In this study, we evaluated the skin yellowness of 819 chickens by colorimeter and digital camera, which are from the same batch and the same age of 2 pure lines with significant differences in skin yellowness. A total of 982 candidate differential expressed genes (DEGs) were detected in duodenal tissue by RNA-seq analysis for high and low yellowness chickens. Among the DEGs, we chose fatty acid translocase (CD36) gene and identified a single nucleotide polymorphism (SNP) upstream of the CD36 gene that was significantly associated with skin yellowness at multiple parts of the chicken, and its different genotypes had significant effects on the promoter activity of the CD36 gene. These findings will help to further elucidate the molecular mechanism of chicken skin yellowness and is helpful for improving chicken skin yellowness.

TAT gene polymorphism and its relationship with production traits in Muscovy ducks (Cairina Moschata)

In a previous study, the laying pattern of Muscovy duck was explored by macro-fitting the laying curve of Muscovy duck, and transcriptome sequencing technique of the ovarian tissues was used to screen the egg-related gene "TAT." Moreover, recent results have shown that TAT is expressed in organs such as oviduct, ovary, and testis. The objective of this study is to examine the effect of TAT gene on egg production traits of Muscovy ducks. First, the expression levels of TAT gene in highest producing (HP) and lowest producing (LP) in 3 tissues related to reproduction were examined, and the results indicated that the expression of TAT gene in hypothalamus was significantly different between HP and LP groups. Then, 6 SNP loci (g. 120G>T, g, 122G>A, g, 254G> A, g. 270C >T, g, 312G>A, and g. 341C>A) were detected in TAT gene. Further, association analysis between the six SNP loci of TAT gene and egg production traits of 652 individual Muscovy ducks was done. The results showed that g. 254G>A and g. 270C>T were significantly correlated (P < 0.05 or 0.001) with the egg production traits of Muscovy ducks. This study elucidated the molecular mechanism that TAT gene might be regulating the egg production traits of Muscovy ducks.

m6A demethylase FTO regulate CTNNB1 to promote adipogenesis of chicken preadipocyte

BACKGROUND

N6-methyladenosine (m⁶A) is an abundant post-transcriptional RNA modification that affects various biological processes. The fat mass and obesity-associated (FTO) protein, a demethylase encoded by the FTO gene, has been found to regulate adipocyte development in an m⁶A-dependent manner in multiple species. However, the effects of the m⁶A methylation and FTO demethylation functions on chicken adipogenesis remain unclear. This study aims to explore the association between m⁶A modification and chicken adipogenesis and the underlying mechanism by which FTO affects chicken preadipocyte development.

RESULTS

The association between m⁶A modification and chicken lipogenesis was assessed by treating chicken preadipocytes with different doses of methyl donor betaine and methylation inhibitor cycloleucine. The results showed that betaine significantly increased methylation levels and inhibited lipogenesis, and the inverse effect was found in preadipocytes after cycloleucine treatment. Overexpression of FTO significantly inhibited m⁶A levels and promoted proliferation and differentiation of chicken preadipocytes. Silencing FTO showed opposite results. Mechanistically, FTO overexpression increased the expression of catenin beta 1 (CTNNB1) by improving RNA stability in an m⁶A-dependent manner, and we proved that FTO could directly target CTNNB1. Furthermore, CTNNB1 may be a positive regulator of adipogenesis in chicken preadipocytes.

CONCLUSIONS

m⁶A methylation of RNA was negatively associated with adipogenesis of chicken preadipocytes. FTO could regulate CTNNB1 expression in a demethylation manner to promote lipogenesis.

Transcriptome analysis of differentially expressed circRNAs miRNAs and mRNAs during the challenge of coccidiosis

Avian coccidiosis is a common enzootic disease caused by infection of Eimeria species parasites. It causes huge economic losses in the global poultry industry. Current control using anticoccidial drugs or vaccination is limited due to drug resistance and the relatively high cost of vaccines. Improving host genetic resistance to Eimeria species is considered an effective strategy for improved control of coccidiosis. Circular RNAs (circRNAs) have been found to function as biomarkers or diagnoses of various kinds of diseases. The molecular biological functions of circRNAs, miRNAs, and mRNAs related to Sasso chicken have not yet been described during Eimeria species challenge. In this study, RNA-seq was used to profile the expression pattern of circRNAs, miRNAs, and mRNAs in spleens from Eimeria tenella-infected and non-infected commercial dual-purpose Sasso T445 breed chickens. Results showed a total of 40 differentially expressed circRNAs (DEcircRNAs), 31 differentially expressed miRNAs (DEmiRNAs), and 820 differentially expressed genes (DEmRNAs) between infected and non-infected chickens. Regulatory networks were constructed between differentially expressed circRNAs, miRNAs, and mRNAs to offer insights into the interaction mechanisms between chickens and Eimeria spp. Functional validation of a significantly differentially expressed circRNA, circMGAT5, revealed that circMGAT5 could sponge miR-132c-5p to promote the expression of the miR-132c-5p target gene monocyte to macrophage differentiation-associated (MMD) during the infection of E. tenella sporozoites or LPS stimulation. Pathologically, knockdown of circMGAT5 significantly upregulated the expression of macrophage surface markers and the macrophage activation marker, F4/80 and MHC-II, which indicated that circMGAT5 might inhibit the activation of macrophage. miR-132c-5p markedly facilitated the expression of F4/80 and MHC-II while circMGAT5 could attenuate the increase of F4/80 and MHC-II induced by miR-132c-5p, indicating that circMGAT5 exhibited function through the circMGAT5-miR-132c-5p-MMD axis. Together, our results indicate that circRNAs exhibit their resistance or susceptive roles during E. tenella infection. Among these, circMGAT5 may inhibit the activation of macrophages through the circMGAT5-miR-132c-5p-MMD axis to participate in the immune response induced by Eimeria infection.

Polymorphisms of CRELD1 and DNAJC30 and their relationship with chicken carcass traits

Carcass traits play important roles in the broiler industry and single nucleotide polymorphism (SNP) can be efficient molecular markers for marker-assisted breeding of chicken carcass traits. Based on our previous RNA-seq data (accession number GSE58755), cysteine rich with epidermal growth factor like domains 1 (CRELD1) and DnaJ heat shock protein family member C30 (DNAJC30) are differentially expressed in breast muscle between white recessive rock chicken (WRR) and Xinghua chicken (XH). In this study, we further characterize the potential function and SNP mutation of CRELD1 and DNAJC30 in chicken for the first time. According to protein interaction network and enrichment analysis, CRELD1 and DNAJC30 may play some roles in chicken muscle development and fat deposition. In WRR and XH, the results of the relative tissue expression pattern demonstrated that CRELD1 and DNAJC30 are not only differentially expressed in breast muscle but also leg muscle and abdominal fat. Therefore, we identified 5 SNP sites of CRELD1 and 7 SNP sites of DNAJC30 and genotyped them in an F₂ chicken population. There are 4 sites of CRELD1 and 3 sites of DNAJC30 are associated with chicken carcass traits like breast muscle weight, body weight, dressed weight, leg weight percentage, eviscerated weight with giblet percentage, intermuscular adipose width, shank length, and girth. These results suggest that the SNP sites of CRELD1 and DNAJC30 can be potential molecular markers to improve the chicken carcass traits and lay the foundation for marker-assisted selection.

Advances on genetic and genomic studies of ALV resistance

Avian leukosis (AL) is a general term for a variety of neoplastic diseases in avian caused by avian leukosis virus (ALV). No vaccine or drug is currently available for the disease. Therefore, the disease can result in severe economic losses in poultry flocks. Increasing the resistance of poultry to ALV may be one effective strategy. In this review, we provide an overview of the roles of genes associated with ALV infection in the poultry genome, including endogenous retroviruses, virus receptors, interferon-stimulated genes, and other immune-related genes. Furthermore, some methods and techniques that can improve ALV resistance in poultry are discussed. The objectives are willing to provide some valuable references for disease resistance breeding in poultry.

Transcriptome analysis of the inhibitory effect of cycloleucine on myogenesis

N6-Methyladenosine (m⁶A) has been reported to involve and play an important role in various biological activities but seldom in poultry myogenesis. Cycloleucine usually functions as a nucleic acid methylation inhibitor, the inhibition efficiency of cycloleucine at the m⁶A level and corresponding dynamic changes of poultry muscle cells remain unknown. In this study, we aim to find out the effect of cycloleucine on the total N6-Methyladenosine level and its molecular mechanism for regulating myogenesis. A total of 745 differentially expressed genes (DEGs) were obtained by 10 mM, 20 mM, and 30 mM of cycloleucine treatment compared with 0 mM treatment. DEGs in 10 mM cycloleucine were significantly enriched in the biological process of skeletal muscle and satellite cell proliferation and differentiation, DEGs in 20 and 30 mM cycloleucine were enriched in some metabolic and biosynthetic processes. The trend analysis showed that 85% of all DEGs were significantly clustered into 4 files, among them 59% DEGs were dose-dependent and 26% were dose-independent, 52% DEGs were in downtrend and 33% DEGs were in uptrend. Also, the cycloleucine treatment could trigger cell cycle arrest in the G1 phase and depress myoblast cell proliferation and inhibit myotube formation. In conclusion, cycloleucine could continuously reduce the m⁶A level of myoblast cells, depress myoblast cell proliferation and inhibit myotube formation.

RNA Sequencing Reveals the Regulation of Betaine on Chicken Myogenesis

Betaine is trimethylglycine and a universal methyl donor which could provide methyl and glycine for cells and animals. As a new star in epigenetics, N6-Methyladenosine has been reported to regulate multiple biological activities, but the regulatory mechanism of betaine on N6-Methyladenosine as well as myogenesis was little studied. In this study, we treated chicken primary myoblast cells with different concentrations of betaine (0, 10, 25, and 50 mmol/L) and found that myoblast cell proliferation was inhibited, although the cell cycle was promoted in the S phase by betaine, where the myotube area was increased as well as the differentiation marker genes MyoD, MyoG, MyHC, Myomarker, and Ckm. RNA sequencing obtained a total of 61 differentially expressed genes (DEGs); DEGs caused by 50 mmol/L betaine were mainly enriched in the regulation of skeletal muscle tissue regeneration and some amino acid metabolic processes. The gene expression pattern trends of all DEGs were mainly clustered into 2 profiles, with the increase in betaine concentration, the gene expression pattern either increased or decreased continuously. Overall, a low concentration betaine can increase the N6-Methyladenosine modification level and myotube area but depresses myoblast cell proliferation in vitro.

Metagenomic analysis reveals the microbiome and antibiotic resistance genes in indigenous Chinese yellow-feathered chickens

Yellow-feathered chickens have great nutritional value and are widely and traditionally used in China, on an industrial scale as broilers. The presence of intestinal microbes has been shown to correlate with poultry performance and serves as an essential reservoir of antibiotic resistance genes (ARGs). Antibiotic resistance is a major public health concern. Here, we investigated functional characteristics of the gut microbiome of indigenous Chinese yellow-feathered chickens (the Huiyang Bearded, Xinghua, Huaixiang, Zhongshan Shanlan, Qingyuan Partridge, and Yangshan chickens) through metagenomic sequencing and reconstructed 409 draft genomes, including 60 novel species and 6 novel genera. Furthermore, we assessed the functions of the intestinal microbial communities and examined the ARGs within them. The results showed that the microbial populations of yellow-feathered broilers were primarily dominated by Bacteroidetes and Firmicutes at the phylum level and Bacteroides at the genus level. Furthermore, the Qingyuan Partridge chicken showed a significantly higher abundance of Prevotella than the other five breeds of chicken. Principal coordinates analysis indicated significant differences in the structures of microbial communities and ARGs, based on the binary Jaccard distance, among the six chicken breeds. Moreover, 989 ARGs conferring tetracycline, multidrug, and aminoglycoside resistance were identified, which represented more than 80% of the faecal resistomes; the most abundant gene in the yellow-feathered chickens was tet(Q). In addition, we found the greatest abundance of resistance genes in Xinghua chickens, indicating that Xinghua chickens are highly resistant to antibiotics. Overall, our findings revealed differences in the gut microbial community structure of indigenous Chinese yellow-feathered broiler breeds and the composition and characteristics of ARGs and antibiotic resistance that enabled us to reconstruct the yellow-feathered chicken gut microbial community genomes. The current data significantly improves our knowledge of the gut microbiome and antibiotic resistance of popular broiler breeds in China.

Influence of Eimeria maxima coccidia infection on gut microbiome diversity and composition of the jejunum and cecum of indigenous chicken

Coccidiosis is an economically significant protozoan disease and an intracellular parasite that significantly impacts poultry production. The gastrointestinal tract microbiota plays a central role in host health and metabolism, and these microbes enhance chickens’ immune systems and nutrient absorption. In this study, we analyzed the abundance and diversity of microbiota of the jejunum and cecum of a dual-purpose indigenous Horro chicken following Eimeria maxima infection. We compared microbial abundance, composition, and diversity at the 4- and 7- days post-infection using 16S rRNA gene sequencing. We obtained, on average, 147,742 and 132,986 high-quality sequences per sample for jejunum and cecum content, respectively. Firmicutes, Proteobacteria, Campilobacterota and Bacteroidota were the major microbial phylum detected in the jejunum content. Firmicutes were the dominant phylum for 4- and 7-days jejunum control groups accounting for (>60% of the sequences). In the infected group Campilobacterota was the dominant phylum in the jejunum (> 24% of sequences) at 4-and 7-days post-infection groups, while Proteobacteria was predominant at 4- and 7-days post-infection of the cecum (> 40% of the sequences). The microbial genus Lactobacillus and Helicobacter were found in the jejunum, while Alistipes, Barnesiella and Faecalibacterium were detected in the cecum. In the jejunum, Helicobacter was dominant at 4 -and-7 days post-infection (≥24%), and Lactobacillus was dominant at 4 -and 7- days in the control group (> 50%). In 4- and 7-days post-infection, Alistipes genus was the more prevalent (> 38%) in the cecum. Thus, clear differences were observed in the bacterial microbiota distribution and abundance between the jejunum and cecum, as well as between infected and control groups for both tissues. The results indicate that chicken intestinal microbial imbalance (dysbiosis) is associated with Eimeria parasite infection and will likely affect the host-microbial non-pathogenic and pathogenic molecular interactions.

Research Note: Association of Single Nucleotide Polymorphism of AKT3 with Egg Production Traits in White Muscovy Ducks (Cairina moschata)

Prior studies on transcriptomes of hypothalamus and ovary revealed that AKT3 is one of the candidate genes that might affect egg production in White Muscovy ducks. The role of AKT3 in the uterus during reproductive processes cannot be overemphasized. However, functional role of this gene in the tissues and on egg production traits of Muscovy ducks remains unknown. To identify the relationship between AKT3 and egg production traits in ducks, relative expression profile was first examined prior to identifying the variants within AKT3 that may underscore egg production traits [age at first egg (AFE), number of eggs at 300 d (N300D), and number of eggs at 59 wk (N59W)] in 549 ducks. The mRNA expression of AKT3 gene in high producing (HP) ducks was significantly higher than low producing (LP) ducks in the ovary, oviduct, and hypothalamus (P < 0.05 or 0.001). Three variants in AKT3 (C-3631A, C-3766T, and C-3953T) and high linkage block between C-3766T and C-3953T which are significantly (P < 0.05) associated with N300D and N59W were discovered. This study elucidates novel knowledge on the molecular mechanism of AKT3 that might be regulating egg production traits in Muscovy ducks.

PPARGC1A Is a Moderator of Skeletal Muscle Development Regulated by miR-193b-3p

Meat production performance is one of the most important factors in determining the economic value of poultry. Myofiber is the basic unit of skeletal muscle, and its physical and chemical properties determine the meat quality of livestock and poultry to a certain extent. Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PPARGC1A) as a transcriptional coactivator has been found to be widely involved in a series of biological processes. However, PPARGC1A is still poorly understood in chickens. In this manuscript, we reported that PPARGC1A was highly expressed in slow-twitch myofibers. PPARGC1A facilitated mitochondrial biogenesis and regulated skeletal muscle metabolism by mediating the flux of glycolysis and the TCA cycle. Gain- and loss-of-function analyses revealed that PPARGC1A promoted intramuscular fatty acid oxidation, drove the transformation of fast-twitch to slow-twitch myofibers, and increased chicken skeletal muscle mass. Mechanistically, the expression level of PPARGC1A is regulated by miR-193b-3p. Our findings help to understand the genetic regulation of skeletal muscle development and provide a molecular basis for further research on the antagonism of skeletal muscle development and fat deposition in chickens.

A missense mutation in ISPD contributes to maintain muscle fiber stability

Background

Results

Conclusion

The study of candidate genes in the improvement of egg production in ducks – a review

Duck is the second-largest poultry species aside from chicken. The rate of egg production is a major determinant of the economic income of poultry farmers. Among the reproductive organs, the ovary is a major part of the female reproductive system which is highly important for egg production. Based on the importance of this organ, several studies have been carried out to identify candidate genes at the transcriptome level, and also the expression level of these genes at different tissues or egg-laying conditions, and single nucleotide polymorphism (SNPs) of genes associated with egg production in duck. In this review, expression profile and association study analyses at SNPs level of different candidate genes with egg production traits of duck were highlighted. Furthermore, different studies on transcriptome analysis, Quantitative Trait Loci (QTL) mapping, and Genome Wide Association Study (GWAS) approach used to identify potential candidate genes for egg production in ducks were reported. This review would widen our knowledge on molecular markers that are associated or have a positive correlation to improving egg production in ducks, for the increasing world populace.

Integrative Analysis of Metabolomic and Transcriptomic Data Reveals the Antioxidant Potential of Dietary Lutein in Chickens

Lutein can increase the body's skin color and has antioxidant potential. However, how it affects lipid metabolism and oxidative stress in chickens remains unknown. In this study, 74-day-old male chickens raised on feed supplemented with lutein had higher hip, back, breast, leg, shin and abdominal fat yellowness than the control group, and the livers of chickens in the lutein group had higher superoxide dismutase and glutathione peroxidase and lower malondialdehyde activities. To clarify the potential regulatory network regulated by lutein, we used RNA-seq and nontargeted metabolomics to detect changes in the male chicken liver and plasma, respectively. A total of 243 differentially expressed genes were significantly enriched in cytokine–cytokine receptor interaction signaling pathways, among others. A total of 237 significantly different metabolites were enriched in lysine biosynthesis and degradation and glycerophospholipid metabolism signaling pathways, among others. Finally, we comprehensively analyzed metabolome and transcriptome data and found that many differentially expressed genes and significantly different metabolites play crucial roles in lipid metabolism and oxidative stress. In summary, dietary lutein can improve male chicken skin yellowness and antioxidant indices and affect liver gene expression and plasma metabolites and may help improve the health of chickens.

Construction and Analysis of Disuse Atrophy Model of the Gastrocnemius Muscle in Chicken

Disuse muscle atrophy is identified as the physiological, biochemical, morphological, and functional changes during restricted movement, immobilization, or weightlessness. Although its internal mechanism has been extensively studied in mammals and was thought to be mainly related to oxidative stress, it was unclear whether it behaved consistently in non-mammals such as chickens. In this study, we tried to construct a disuse atrophy model of the gastrocnemius muscle in chickens by limb immobilization, and collected the gastrocnemius muscles of the fixed group and the control group for RNA sequencing. Through analysis of muscle loss, HE staining, immunohistochemistry, and oxidative stress level, we found that limb immobilization could lead to loss of muscle mass, decrease in muscle fiber diameter, decrease in the proportion of slow muscle fibers, and increase in the proportion of fast muscle fibers, and also cause elevated levels of oxidative stress. In addition, a total of 565 different expression genes (DEGs) were obtained by RNA sequencing, which was significantly enriched in the biological processes such as cell proliferation and apoptosis, reactive oxygen species metabolism, and fast and slow muscle fiber transformation, and it showed that the FOXO signaling pathway, closely related to muscle atrophy, was activated. In brief, we initially confirmed that limb immobilization could induce disuse atrophy of skeletal muscle, and oxidative stress was involved in the process of disuse muscle atrophy.

Galbase: a comprehensive repository for integrating chicken multi-omics data

Background

Multi-omics data can provide a stereoscopic view to explore potential causal variations and genes, as well as underlying genetic mechanisms of complex traits. However, for many non-mammalian species, including chickens, these resources are poorly integrated and reused, greatly limiting genetic research and breeding processes of the species.

Results

Here, we constructed Galbase, an easily accessible repository that integrates public chicken multi-omics data from 928 re-sequenced genomes, 429 transcriptomes, 379 epigenomes, 15,275 QTL entries, and 7,526 associations. A total of 21.67 million SNPs, 2.71 million InDels, and 488,583 cis-regulatory elements were included. Galbase allows users to retrieve genomic variations in geographical maps, gene expression profiling in heatmaps, and epigenomic signals in peak patterns. It also provides modules for batch annotation of genes, regions, and loci based on multi-layered omics data. Additionally, a series of convenient tools, including the UCSC Genome Browser, WashU Epigenome Browser, BLAT, BLAST, and LiftOver, were also integrated to facilitate search, visualization, and analysis of sequence features.

Conclusion

Galbase grants new opportunities to research communities to undertake in-depth functional genomic studies on chicken. All features of Galbase make it a useful resource to identify genetic variations responsible for chicken complex traits. Galbase is publicly available at http://animal.nwsuaf.edu.cn/ChickenVar.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08598-2.

Long noncoding RNA ZFP36L2-AS functions as a metabolic modulator to regulate muscle development

Skeletal muscle is the largest metabolic organ in the body, and its metabolic flexibility is essential for maintaining systemic energy homeostasis. Metabolic inflexibility in muscles is a dominant cause of various metabolic disorders, impeding muscle development. In our previous study, we found lncRNA ZFP36L2-AS (for “ZFP36L2-antisense transcript”) is specifically enriched in skeletal muscle. Here, we report that ZFP36L2-AS is upregulated during myogenic differentiation, and highly expressed in breast and leg muscle. In vitro, ZFP36L2-AS inhibits myoblast proliferation but promotes myoblast differentiation. In vivo, ZFP36L2-AS facilitates intramuscular fat deposition, as well as activates fast-twitch muscle phenotype and induces muscle atrophy. Mechanistically, ZFP36L2-AS interacts with acetyl-CoA carboxylase alpha (ACACA) and pyruvate carboxylase (PC) to induce ACACA dephosphorylation and damaged PC protein stability, thus modulating muscle metabolism. Meanwhile, ZFP36L2-AS can activate ACACA to reduce acetyl-CoA content, which enhances the inhibition of PC activity. Our findings present a novel model about the regulation of lncRNA on muscle metabolism.

LncRNA SMARCD3-OT1 Promotes Muscle Hypertrophy and Fast-Twitch Fiber Transformation via Enhancing SMARCD3X4 Expression

Long noncoding RNA (lncRNA) plays a crucial part in all kinds of life activities, especially in myogenesis. SMARCD3 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily d, member 3) is a member of the SWI/SNF protein complex and was reported to be required for cell proliferation and myoblast differentiation. In this study, we identified a new lncRNA named SMARCD3-OT1 (SMARCD3overlappinglncRNA), which strongly regulated the development of myogenesis by improving the expression of SMARCD3X4 (SMARCD3transcripts4). We overexpressed and knockdown the expression of SMARCD3-OT1 and SMARCD3X4 to investigate their function on myoblast proliferation and differentiation. Cell experiments proved that SMARCD3-OT1 and SMARCD3X4 promoted myoblast proliferation through the CDKN1A pathway and improved differentiation of differentiated myoblasts through the MYOD pathway. Moreover, they upregulated the fast-twitch fiber-related genes and downregulated the slow-twitch fiber-related genes, which indicated that they facilitated the slow-twitch fiber to transform into the fast-twitch fiber. The animals’ experiments supported the results above, demonstrating that SMARCD3-OT1 could induce muscle hypertrophy and fast-twitch fiber transformation. In conclusion, SMARCD3-OT1 can improve the expression of SMARCD3X4, thus inducing muscle hypertrophy. In addition, SMARCD3-OT1 can facilitate slow-twitch fibers to transform into fast-twitch fibers.

Growth Hormone Receptor Controls Adipogenic Differentiation of Chicken Bone Marrow Mesenchymal Stem Cells by Affecting Mitochondrial Biogenesis and Mitochondrial Function

Growth hormone receptor (GHR) can activate several signaling pathways after binding to growth hormone (GH) to regulate cell growth and development. Sex-linked dwarf (SLD) chickens, normal protein functions are prevented because of exon mutations in the GHR gene, have more severe fat deposition. However, the specific molecular mechanisms responsible for this phenotype remains unclear. We therefore investigated the effect of the GHR gene on adipogenic differentiation of chicken bone marrow mesenchymal stem cells (BMSCs). We found that bone marrow fat deposition was more severe in SLD chickens compared to normal chickens, and the expression of genes related to adipogenic differentiation was enhanced in SLD chicken BMSCs. We also detected enhanced mitochondrial function of BMSCs in SLD chickens. In vitro, overexpression of GHR in chicken BMSCs increased mitochondrial membrane potential but decreased reactive oxygen and ATP contents, oxidative phosphorylation complex enzyme activity, and mitochondrial number. Expression of genes associated with mitochondrial biogenesis and function was repressed during adipogenic differentiation in chicken BMSCs, the adipogenic differentiation capacity of chicken BMSCs was also repressed. With knockdown of GHR, opposite results were observed. We concluded that GHR inhibited adipogenic differentiation of chicken BMSCs by suppressing mitochondrial biogenesis and mitochondrial function.

CircMGA Depresses Myoblast Proliferation and Promotes Myotube Formation through miR-144-5p/FAP Signal

Circular RNAs are endogenous and abundant in skeletal muscle, and may not only be involved in regulating gene expression in a variety of ways, but also function as important regulators in poultry muscle development. Our previous research found that circMGA was differentially expressed during chicken muscle embryo development; however, as a novel circular RNA, the regulating mechanism of circMGA in myogenesis has never been studied before. In this study, we aimed to investigate the functional roles and related molecular mechanisms of circMGA in chicken primary myoblast cells. CircMGA originated from the exon 13–14 of MGA gene, was differentially expressed during embryo development and myogenesis differentiation, and could inhibit myoblast cell proliferation by repressing cell cycle related genes and promote myotube formation through MyoD and MyHC. Biotin-labeled miRNA pulldown assay and luciferase reporter assay result showed that miR-144-5p could directly target circMGA and FAP, indicating that there could be a competing endogenous RNA mechanism between circMGA and FAP. In function, miR-144-5p showed opposite regulation in myoblast cell with circMGA and FAP, just as expected. circMGA co-transfected with miR-144-5p or si-FAP could effectively eliminate the inhibition of miR-144-5p on myoblast proliferation and differentiation. In conclusion, we found a novel circRNA, named circMGA, which generated from the 13–14 exon of the MGA gene, and could inhibit myoblast proliferation and promote myotube formation by acting as the sponge of miR-144-5p and through miR-144-5p/FAP signal. Moreover, circMGA could effectively eliminate the inhibition of miR-144-5p on myoblast differentiation, thus releasing FAP and promoting myotube formation.

De novo assembly of 20 chicken genomes reveals the undetectable phenomenon for thousands of core genes on micro-chromosomes and sub-telomeric regions

The gene numbers and evolutionary rates of birds were assumed to be much lower than those of mammals, which is in sharp contrast to the huge species number and morphological diversity of birds. It is, therefore, necessary to construct a complete avian genome and analyze its evolution. We constructed a chicken pan-genome from 20 de novo assembled genomes with high sequencing depth, and identified 1,335 protein-coding genes and 3,011 long noncoding RNAs not found in GRCg6a. The majority of these novel genes were detected across most individuals of the examined transcriptomes but were seldomly measured in each of the DNA sequencing data regardless of Illumina or PacBio technology. Furthermore, different from previous pan-genome models, most of these novel genes were overrepresented on chromosomal subtelomeric regions and microchromosomes, surrounded by extremely high proportions of tandem repeats, which strongly blocks DNA sequencing. These hidden genes were proved to be shared by all chicken genomes, included many housekeeping genes, and enriched in immune pathways. Comparative genomics revealed the novel genes had 3-fold elevated substitution rates than known ones, updating the knowledge about evolutionary rates in birds. Our study provides a framework for constructing a better chicken genome, which will contribute toward the understanding of avian evolution and the improvement of poultry breeding.

Growth hormone receptor gene influences mitochondrial function and chicken lipid metabolism by AMPK-PGC1α-PPAR signaling pathway

Background

Adipose tissue is an important endocrine and energy-storage organ in organisms, and it plays a crucial role in the energy-metabolism balance. Previous studies have found that sex-linked dwarf (SLD) chickens generally have excessively high abdominal fat deposition during the growing period, which increases feeding costs. However, the underlying mechanism of this fat deposition during the growth of SLD chickens remains unknown.

Results

The Oil Red O staining showed that the lipid-droplet area of SLD chickens was larger than that of normal chickens in E15 and 14d. Consistently, TG content in the livers of SLD chickens was higher than that of normal chickens in E15 and 14d. Further, lower ΔΨm and lower ATP levels and higher MDA levels were observed in SLD chickens than normal chickens in both E15 and 14d. We also found that overexpression of GHR reduced the expression of genes related to lipid metabolism (AMPK, PGC1α, PPARγ, FAS, C/EBP) and oxidative phosphorylation (CYTB, CYTC, COX1, ATP), as well as reducing ΔΨm and ATP levels and increasing MDA levels. In addition, overexpression of GHR inhibited fat deposition in CPPAs, as measured by Oil Red O staining. On the contrary, knockdown of GHR had the opposite effects in vitro.

Conclusions

In summary, we demonstrate that GHR promotes mitochondrial function and inhibits lipid peroxidation as well as fat deposition in vivo and in vitro. Therefore, GHR is essential for maintaining the stability of lipid metabolism and regulating mitochondrial function in chicken.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08268-9.

PGC-1α affects skeletal muscle and adipose tissue development by regulating mitochondrial biogenesis

The discovery and interpretation of peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) protein in mitochondrial biogenesis, skeletal muscle and adipose tissue development has broad research prospects, so it is important to review the related studies of PGC-1α in detail and comprehensively. PGC-1α is a protein composed of 798 amino acids (aa) with a molecular weight of about 91 kDa. PGC-1α is involved in the operation of the respiratory chain by combining with deacetylase and phosphorylase to bind some nuclear receptors. In addition, PGC-1α affects skeletal muscle and adipose metabolism by regulating mitochondrial oxidative phosphorylation. Recently, new data suggest that regulating mitochondrial metabolism in adipose tissue may be an effective adjunct to the treatment of obesity. In addition, dietary resveratrol, which has an effective anti-obesity effect, has been shown to promote mitochondrial biosynthesis by activating AMPK/PGC-1α axis, as well as to regenerate muscle damaged by obesity. In this review, we combined previous studies to explore the latest studies, showing that PGC-1α can regulate mitochondrial biogenesis and is regulated by AMPK and SIRT1. Furthermore, PGC-1α is a favored protein, which not only regulates muscle fiber type, inhibits muscle atrophy, but also participates in browning of white adipose tissue (WAT) and regulates body heat production. So, we concluded that PGC-1α is a key gene in mitochondrial biogenesis and plays an important role in the regulation and regulation of mitochondrial biogenesis along with other genes involved in the process. Meanwhile, PGC-1α acts as a core metabolic regulator in adipose tissue and skeletal muscle. This review comprehensively summarizes a large number of research findings. First, the role of PGC-1α in mitochondrial biogenesis was clarified, and then the key role of PGC-1α in the development of skeletal muscle and adipose tissue was reevaluated. Furthermore, the role of PGC-1α in some human diseases was discussed. Finally, the role of PGC-1α as a major gene in poultry was pointed out, and the future research direction was proposed.