Differential regulation of intramuscular fat and abdominal fat deposition in chickens

Effects of emulsifiers on lipid metabolism and performance of yellow-feathered broilers

BACKGROUND

Reducing production costs while producing high-quality livestock and poultry products is an ongoing concern in the livestock industry. The addition of oil to livestock and poultry diets can enhance feed palatability and improve growth performance. Emulsifiers can be used as potential feed supplements to improve dietary energy utilization and maintain the efficient productivity of broilers. Therefore, further investigation is warranted to evaluate whether dietary emulsifier supplementation can improve the efficiency of fat utilization in the diet of yellow-feathered broilers. In the present study, the effects of adding emulsifier to the diet on lipid metabolism and the performance of yellow-feathered broilers were tested. A total of 240 yellow-feasted broilers (21-day-old) were randomly divided into 4 groups (6 replicates per group, 10 broilers per replicate, half male and half female within each replicate). The groups were as follows: the control group (fed with basal diet), the group fed with basal diet supplemented with 500 mg/kg emulsifier, the group fed with a reduced oil diet (reduced by 1%) supplemented with 500 mg/kg emulsifier, and the group fed with a reduced oil diet supplemented with 500 mg/kg emulsifier. The trial lasted for 42 days, during which the average daily feed intake, average daily gain, and feed-to-gain ratio were measured. Additionally, the expression levels of lipid metabolism-related genes in the liver, abdominal fat and each intestinal segment were assessed.

RESULTS

The results showed that compared with the basal diet group, (1) The average daily gain of the basal diet + 500 mg/kg emulsifier group significantly increased (P < 0.05), and the half-even-chamber rate was significantly increased (P < 0.05); (2) The mRNA expression levels of Cd36, Dgat2, Apob, Fatp4, Fabp2, and Mttp in the small intestine were significantly increased (P < 0.05). (3) Furthermore, liver TG content significantly decreased (P < 0.05), and the mRNA expression level of Fasn in liver was significantly decreased (P < 0.05), while the expression of Apob, Lpl, Cpt-1, and Pparα significantly increased (P < 0.05). (4) The mRNA expression levels of Lpl and Fatp4 in adipose tissue were significantly increased (P < 0.05), while the expression of Atgl was significantly decreased (P < 0.05). (5) Compared with the reduced oil diet group, the half-evading rate and abdominal fat rate of broilers in the reduced oil diet + 500 mg/kg emulsifier group were significantly increased (P < 0.05), and the serum level of LDL-C increased significantly (P < 0.05)0.6) The mRNA expression levels of Cd36, Fatp4, Dgat2, Apob, and Mttp in the small intestine were significantly increased (P < 0.05). 7) The mRNA expression levels of Fasn and Acc were significantly decreased in the liver (P < 0.05), while the mRNA expression levels of Lpin1, Dgat2, Apob, Lpl, Cpt-1, and Pparα were significantly increased (P < 0.05).

CONCLUSIONS

These results suggest that dietary emulsifier can enhance the fat utilization efficiency of broilers by increasing the small intestinal fatty acid uptake capacity, inhibiting hepatic fatty acid synthesis and promoting hepatic TG synthesis and transport capacity. This study provides valuable insights for the potential use of emulsifier supplementation to improve the performance of broiler chickens.

Genes involved in the cholecystokinin receptor signaling map were differentially expressed in the jejunum of steers with variation in residual feed intake

The jejunum is a critical site for nutrient digestion and absorption, and variation in its ability to take up nutrients within the jejunum is likely to affect feed efficiency. The purpose of this study was to determine differences in gene expression in the jejunum of beef steers divergent for residual feed intake (RFI) in one cohort of steers (Year 1), and to validate those genes in animals from a second study (Year 2). Steers from Year 1 (n = 16) were selected for high and low RFI. Jejunum mucosal tissue was obtained for RNA-seq. Thirty-two genes were differentially expressed (PFDR≤0.15), and five were over-represented in pathways including inflammatory mediator, cholecystokinin receptor (CCKR) signaling, and p38 MAPK pathways. Several differentially expressed genes (ALOX12, ALPI, FABP6, FABP7, FLT1, GSTA2, MEF2B, PDK4, SPP1, and TTF2) have been previously associated with RFI in other studies. Real-time qPCR was used to validate nine differentially expressed genes in the Year 1 steers used for RNA-seq, and in the Year 2 validation cohort. Six genes were validated as differentially expressed (P < 0.1) using RT-qPCR in the Year 1 population. In the Year 2 population, five genes displayed the same direction of expression as the Year 1 population and 3 were differentially expressed (P < 0.1). The CCKR pathway is involved in digestion, appetite control, and regulation of body weight making it a compelling candidate for feed efficiency in cattle, and the validation of these genes in a second population of cattle is suggestive of a role in feed efficiency.

Novel putative causal mutations associated with fat traits in Nellore cattle uncovered by eQTLs located in open chromatin regions

Intramuscular fat (IMF) and backfat thickness (BFT) are critical economic traits impacting meat quality. However, the genetic variants controlling these traits need to be better understood. To advance knowledge in this area, we integrated RNA-seq and single nucleotide polymorphisms (SNPs) identified in genomic and transcriptomic data to generate a linkage disequilibrium filtered panel of 553,581 variants. Expression quantitative trait loci (eQTL) analysis revealed 36,916 cis-eQTLs and 14,408 trans-eQTLs. Association analysis resulted in three eQTLs associated with BFT and 24 with IMF. Functional enrichment analysis of genes regulated by these 27 eQTLs revealed noteworthy pathways that can play a fundamental role in lipid metabolism and fat deposition, such as immune response, cytoskeleton remodeling, iron transport, and phospholipid metabolism. We next used ATAC-Seq assay to identify and overlap eQTL and open chromatin regions. Six eQTLs were in regulatory regions, four in predicted insulators and possible CCCTC-binding factor DNA binding sites, one in an active enhancer region, and the last in a low signal region. Our results provided novel insights into the transcriptional regulation of IMF and BFT, unraveling putative regulatory variants.

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.

Different fat-to-fiber ratios by changing wheat inclusion level impact energy metabolism and microbial structure of broilers

Introduction

Dietary nutrient content is crucial for energy metabolism and development of gut microbiota. Herein, this study aimed to explore the effects of fat-to-fiber ratios on nutrient transporter, energy metabolism and gut microbiota when ingredients composition was altered.

Methods

A total of 240 as-hatched broiler chickens were randomly assigned into three groups including low fat-high dietary fiber (LF-HD), medium fat-medium dietary fiber (MF-MD) and high fat-low dietary fiber (HF-LD), with diets being iso-protein, and broilers were offered the same commercial diets from 21 to 42 d. The data were analyzed using one-way ANOVA of SPSS.

Results and Discussion

Results showed that HF-LD diet significantly increased glucose content and decreased triglyceride in serum of broilers (p < 0.05). The mRNA abundance of jejunal gene involved in glucose transporter and tricarboxylic acid (TCA) cycle was significantly increased in broilers fed with HF-LD diets. Compared with LF-HD, HF-LD had a lower abundance of Anaerofilum and CHKCI001, and an increased proportion of beneficial bacteria such as Alistipes, Catenibacillus, Intestinimonas, Lactobacillus, and Peptococcus (p < 0.05). Functional prediction of these microbial changes indicated that HF-LD diet drove caecal microbiota to participate in carbohydrate metabolism and TCA cycle (p < 0.05). Dietary HF-LD-induced microbiota changes were positively correlated with growth performance of broilers (p < 0.05). Therefore, HF-LD diet increased glucose transporters and energy metabolism in intestine and shaped microbial structure and metabolic pathways, which may benefit the growth performance of broilers.

Verification of Key Target Molecules for Intramuscular Fat Deposition and Screening of SNP Sites in Sheep from Small-Tail Han Sheep Breed and Its Cross with Suffolk

Intramuscular fat (IMF) is vital for meat tenderness and juiciness. This study aims to explore the IMF deposition mechanism and the related molecular markers in sheep. Two populations, Small-tail Han Sheep (STH) and STH × Suffolk (SFK) F1 (SFK × STH), were used as the research object. Histological staining techniques compared the differences in the longissimus dorsi muscle among populations. A combination of transcriptome sequencing and biological information analysis screened and identified IMF-related target genes. Further, sequencing technology was employed to detect SNP loci of target genes to evaluate their potential as genetic markers. Histological staining revealed that the muscle fiber gap in the SFK × STH F1 was larger and the IMF content was higher. Transcriptome analysis revealed that PIK3R1 and PPARA were candidate genes. Histological experiments revealed that the expressions of PIK3R1 mRNA and PPARA mRNA were lower in SFK × STH F1 compared with the STH. Meanwhile, PIK3R1 and PPARA proteins were located in intramuscular adipocytes and co-located with the lipid metabolism marker molecule (FASN). SNP locus analysis revealed a mutation site in exon 7 of the PIK3R1 gene, which served as a potential genetic marker for IMF deposition. This study's findings will provide a new direction for meat quality breeding in sheep.

Identification of central regulators related to abdominal fat deposition in chickens based on weighted gene co-expression network analysis

Abdominal fat (AF) is one of the most important economic traits in chickens. Excessive AF in chickens will reduce feed utilization efficiency and negatively affect reproductive performance and disease resistance. However, the regulatory network of AF deposition needs to be further elucidated. In the present study, 300 one-day-old female Wannan chickens were reared to 17 wk of age, and 200 Wannan hens were selected to determine the abdominal fat percentage (AFP). Twenty AF tissue samples with the lowest AFP were selected as the low abdominal fat group (L-AFG), and 20 AF tissue samples with the highest AFP were selected as the high abdominal fat group (H-AFG). Eleven samples from L-AFG and 14 samples from H-AFG were selected for RNA-seq and used for weighted gene co-expression network analysis (WGCNA). Among the 25 RNA-seq samples, 5 samples with the lowest and highest AFP values were selected for differential expression gene analysis. Compared with the L-AFG, 225 and 101 genes were upregulated and downregulated in the H-AFG, respectively. A total of 20,503 genes were used to construct the WGCNA, and 44 co-expression gene modules were identified. Among these modules, 3 modules including turquoise, darkorange2, and floralwhite were identified as significantly associated with AFP traits. Furthermore, several genes including acyl-CoA oxidase 1 (ACOX1), stearoyl-CoA desaturase (SCD), aldehyde dehydrogenase 6 family member A1 (ALDH6A1), jun proto-oncogene, AP-1 transcription factor subunit (JUN), and fos proto-oncogene, AP-1 transcription factor subunit (FOS) involved in the "PPAR signaling pathway," "fatty acid metabolism," and "MAPK signaling pathway" were identified as central regulators that contribute to AF deposition. These results provide valuable information for further understanding of the gene expression and regulation of AF traits and contribute to future molecular breeding for AF in chickens.

Isolation methods, proliferation, and adipogenic differentiation of adipose-derived stem cells from different fat depots in bovines

The adipose-derived stem cells (ASCs) are a valuable resource for regenerative medicine and essential materials for research in fat deposition. However, the isolation procedure of ASCs has not been standardized and needs to be harmonized; differences in proliferation and adipogenic differentiation of ASCs obtained from different fat depots have not been well characterized. In the present study, we compared the efficiency of ASCs isolation by enzymatic treatment and explant culture methods and the proliferation ability and adipogenic differentiation potential of ASCs isolated from subcutaneous and visceral fat depots. The explant culture method was simple and with no need for expensive enzymes while the enzymatic treatment method was complex, time consuming and costly. By the explant culture method, a larger number of ASCs were isolated from subcutaneous and visceral fat depots. By contrast, fewer ASCs were obtained by the enzymatic treatment method, especially from visceral adipose. ASCs isolated by the explant culture method performed well in cell proliferation and adipogenic differentiation, though they were slightly lower than those by the enzymatic treatment method. ASCs isolated from visceral depot demonstrated higher proliferation ability and adipogenic differentiation potential. In total, the explant culture method is simpler, more efficient, and lower cost than the enzymatic treatment method for ASCs isolation; compared with visceral adipose, subcutaneous adipose is easier to isolate ASCs; however, the visceral ASCs are superior to subcutaneous ASCs in proliferation and adipogenic differentiation.

RNA sequencing identifies key genes involved in intramuscular fat deposition in chickens at different developmental stages

BACKGROUND

Intramuscular fat (IMF) is an important factor in meat quality, and triglyceride (TG) and Phospholipids (PLIP), as the main components of IMF, are of great significance to the improvement of meat quality.

RESULTS

In this study, we used 30 RNA sequences generated from the transcriptome of chicken breast muscle tissues at different developmental stages to construct a gene expression matrix to map RNA sequence reads to the chicken genome and identify the transcript of origin. We used weighted gene co-expression network analysis (WGCNA) and identified 27 co-expression modules, 10 of which were related to TG and PLIP. We identified 150 highly-connected hub genes related to TG and PLIP, respectively, which were found to be mainly enriched in the adipocytokine signaling pathway, MAPK signaling pathway, mTOR signaling pathway, FoxO signaling pathway, and TGF-beta signaling pathway. Additionally, using the BioMart database, we identified 134 and 145 candidate genes related to fat development in the TG-related module and PLIP-related module, respectively. Among them, RPS6KB1, BRCA1, CDK1, RPS3, PPARGC1A, ACSL1, NDUFAB1, NDUFA9, ATP5B and PRKAG2 were identified as candidate genes related to fat development and highly-connected hub genes in the module, suggesting that these ten genes may be important candidate genes affecting IMF deposition.

CONCLUSIONS

RPS6KB1, BRCA1, CDK1, RPS3, PPARGC1A, ACSL1, NDUFAB1, NDUFA9, ATP5B and PRKAG2 may be important candidate genes affecting IMF deposition. The purpose of this study was to identify the co-expressed gene modules related to chicken IMF deposition using WGCNA and determine key genes related to IMF deposition, so as to lay a foundation for further research on the molecular regulation mechanism underlying chicken fat deposition.

Dietary macroalgae Chaetomorpha linum supplementation improves morphology of small intestine and pectoral muscle, growth performance, and meat quality of broilers

Background and Aim

Over the last decades, the poultry industry has experienced steady growth. Although the industry is gradually expanding in Indonesia, poultry feed production has always been expensive. There is a need to study alternative ingredients to obtain affordable feed from natural resources. Chaetomorpha linum (CL) is an abundant macroalgae available throughout the year in Indonesia. This study aimed to determine the effect of CL on the histological structure of the small intestine, pectoralis muscle, growth performance, and meat quality of broilers.

Materials and Methods

This study used 300-day-old chick (DOC) male broilers that were reared until they were 21 days old. This study used a completely randomized design with four treatment groups and five replications, and each replication group contained 15 DOC individuals. The treatment groups consisted of Control (CON), CON basal feed (BF), CL1 (0.75%/kg BF), CL2 (1.5%/kg BF), and CL3 (3%/kg BF) groups. The histological structure of the small intestine, pectoralis muscle, growth performance, and meat quality of the broiler was examined.

Results

Small intestine and pectoral muscle histomorphology, growth performance, and meat quality were significantly improved in the CL2 (1.5%) and CL3 (3%) groups compared with the CL1 (0.75%) and CON groups.

Conclusion

Dietary CL supplementation ameliorates small intestine and pectoral muscle histomorphology, growth performance, and meat quality of broilers.

Evaluation of coffee husks in pellet bedding, performance characteristics, footpad dermatitis scoring, and meat quality of broiler ducks

The study aimed to analyze the chemical composition of pellet bedding made of straw or coffee husks (10, 25, 50%) and the performance characteristics of broiler ducks and footpad dermatitis. During rearing, the properties of the bedding and utility features of ducks were analyzed, and the frequency of footpad dermatitis (FPD) in ducks was verified. There was a decrease in dry matter from the 28th day of rearing. The crude fiber, NDF, ADF, and nitrogen content decreased compared to fresh bedding, while phosphorus and potassium increased. The highest pH was found in the CH25 and CH50 groups in fresh bedding on day 42 and in CH50 on day 14. High adj. R2 was found due to rearing time and bedding material (0.817-0.985). The ducks' growth rate in the CH25 group was higher at week 6 than in the other groups. In CH10 and CH25 groups, higher carcass weight was found than in group C. In group CH10, a higher weight of pectoral muscles and lower wing proportion was found than in C. In CH25, a higher remains weight was shown than in C and CH50. In CH50, lower water-holding capacity in the pectoral muscles was found than in the other groups. Considering the bedding (the content of nitrogen, phosphorus, and potassium), carcass features, and meat quality (water-holding capacity, intramuscular fat, and water content), it is possible to use 10, 25 or 50% of coffee husks in straw pellets in the rearing of broiler ducks. Due to the FPD, the moisture should be lowered.

Screening of Genes Related to Fat Deposition of Pekin Ducks Based on Transcriptome Analysis

Subcutaneous fat deposition is an important index with which to evaluate meat-producing ducks, and affects their meat quality and feed conversion rate. Studying the differentially expressed genes in subcutaneous fat will help to comprehensively understand the potential mechanisms regulating fat deposition in ducks. In this study, 72 Nankou 1 Pekin Ducks and 72 Jingdian Pekin Ducks (half male and half female) at 42 days of age were selected for slaughter performance and transcriptome analysis. The results showed that the breast-muscle yield of Nankou 1 ducks was significantly higher than that of Jingdian ducks, but that the abdominal fat yield and subcutaneous fat yield were higher than that of Jingdian ducks. Thousands of DEGs, including many important genes involved in fat metabolism regulation, were detected by transcriptome. KEGG enrichment analysis showed that the DEGs were significantly enriched on pathways such as regulation of lipolysis in adipocytes, primary bile acid biosynthesis, and biosynthesis of unsaturated fatty acids. SCD, FGF7, LTBP1, PNPLA3, ADCY2, and ACOT8 were selected as candidate genes for regulating subcutaneous fat deposition. The results indicated that Nankou 1 had superior fat deposition ability compared to Jingdian ducks, and that the candidate genes regulated fat deposition by regulating fat synthesis and decomposition.

Transcriptome and Weighted Gene Co-Expression Network Analysis for Feather Follicle Density in a Chinese Indigenous Breed

Feather follicle density plays an important role in appealing to consumers' first impressions when making purchasing decisions. However, the molecular network that contributes to this trait remains largely unknown. The aim of this study was to perform transcriptome and weighted gene co-expression network analyses to determine the candidate genes relating to feather follicle density in Wannan male chickens. In total, five hundred one-day-old Wannan male chickens were kept in a conventional cage system. Feather follicle density was recorded for each bird at 12 weeks of age. At 12 weeks, fifteen skin tissue samples were selected for weighted gene co-expression network analysis, of which six skin tissue samples (three birds in the H group and three birds in the L group) were selected for transcriptome analysis. The results showed that, in total, 95 DEGs were identified, and 56 genes were upregulated and 39 genes were downregulated in the high-feather-follicle-density group when compared with the low-feather-follicle-density group. Thirteen co-expression gene modules were identified. The red module was highly significantly negatively correlated with feather follicle density (p < 0.01), with a significant negative correlation coefficient of -0.72. In total, 103 hub genes from the red module were screened. Upon comparing the 103 hub genes with differentially expressed genes (DEGs), it was observed that 13 genes were common to both sets, including MELK, GTSE1, CDK1, HMMR, and CENPE. From the red module, FOXM1, GTSE1, MELK, CDK1, ECT2, and NEK2 were selected as the most important genes. These genes were enriched in the DNA binding pathway, the heterocyclic compound binding pathway, the cell cycle pathway, and the oocyte meiosis pathway. This study suggests that FOXM1, GTSE1, MELK, CDK1, ECT2, and NEK2 may be involved in regulating the development of feather follicle density in Wannan male chickens. The results of this study reveal the genetic structure and molecular regulatory network of feather follicle density in Wannan male chickens, and provide a basis for further elucidating the genetic regulatory mechanism and identifying molecular markers with breeding value.

Lipidomics reveals lipid changes in the intramuscular fat of geese at different growth stages

The quality (color, tenderness, juiciness, protein content, and fat content) of poultry meat is closely linked to age, with older birds typically exhibiting increased intramuscular fat (IMF) deposition. However, specific lipid metabolic pathways involved in IMF deposition remain unknown. To elucidate the mechanisms underlying lipid changes, we conducted a study using meat geese at 2 distinct growth stages (70 and 300 d). Our findings regarding the approximate composition of the meat revealed that as the geese aged 300 d, their meat acquired a chewier texture and displayed higher levels of IMF. Liquid chromatography-mass spectrometry (LC-MS) was employed for lipid profiling of the IMF. Using a lipid database, we identified 849 lipids in the pectoralis muscle of geese. Principal component analysis and orthogonal partial least squares discriminant analysis were used to distinguish between the 2 age groups and identify differential lipid metabolites. As expected, we observed significant changes in 107 lipids, including triglycerides, diglycerides, phosphatidylethanolamine, alkyl-glycerophosphoethanolamine, alkenyl-glycerophosphoethanolamine, phosphatidylcholine, phosphatidylinositol, lysophosphatidylserine, ceramide-AP, ceramide-AS, free fatty acids, cholesterol lipids, and N-acyl-lysophosphatidylethanolamine. Among these, the glyceride molecules exhibited the most pronounced changes and played a pivotal role in IMF deposition. Additionally, increased concentration of phospholipid molecules was observed in breast muscle at 70 d. Unsaturated fatty acids attached to lipid side chain sites enrich the nutritional value of goose meat. Notably, C16:0 and C18:0 were particularly abundant in the 70-day-old goose meat. Pathway analysis demonstrated that glycerophospholipid and glyceride metabolism were the pathways most significantly associated with lipid changes during goose growth, underscoring their crucial role in lipid metabolism in goose meat. In conclusion, this work provides an up-to-date study on the lipid composition and metabolic pathways of goose meat and may provide a theoretical basis for elucidating the nutritional value of goose meat at different growth stages.

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.

Revelation of genes associated with energy generating metabolic pathways in the fighter type Aseel chicken of India through skeletal muscle transcriptome sequencing

In this study, comparative analysis of skeletal muscle transcriptome was carried out for four biological replicates of Aseel, a fighter type breed and Punjab Brown, a meat type breed of India. The profusely expressed genes in both breeds were related to muscle contraction and motor activity. Differential expression analysis identified 961 up-regulated and 979 down-regulated genes in Aseel at a threshold of log2 fold change ≥ ±2.0 (padj<0.05). Significantly enriched KEGG pathways in Aseel included metabolic pathways and oxidative phosphorylation, with higher expression of genes associated with fatty acid beta-oxidation, formation of ATP by chemiosmotic coupling, response to oxidative stress, and muscle contraction. The highly connected hub genes identified through gene network analysis in the Aseel gamecocks were HNF4A, APOA2, APOB, APOC3, AMBP, and ACOT13, which are primarily associated with energy generating metabolic pathways. The up-regulated genes in Punjab Brown chicken were found to be related to muscle growth and differentiation. There was enrichment of pathways such as focal adhesion, insulin signaling pathway and ECM receptor interaction in these birds. The results presented in this study help to improve our understanding of the molecular mechanisms associated with fighting ability and muscle growth in Aseel and Punjab Brown chicken, respectively.

Cloning and functional characterization of porcine AACS revealing the regulative roles for fat deposition in pigs

Fat deposition is a quantitative trait controlled by multiple genes in pigs. Using transcriptome sequencing, we previously reported that AACS is differentially expressed in the subcutaneous fat tissue of Dingyuan pigs with divergent backfat thickness. Therefore, with the aim of further characterizing this gene and its protein, we cloned the entire 3286-bp mRNA sequence of the porcine AACS, and the encoded AACS protein is a hydrophilic protein without a signal peptide or transmembrane sequence. Our findings suggested that among various tissues and pig breeds, AACS was highly expressed in subcutaneous fat. We have identified three completely linked SNP loci in the AACS gene: A-1759C, C-1683T, and A-1664G. The double luciferase activity test in the 5' flanking region indicated that the flanking region of AACS contained several active regulatory elements. The three linked SNPs that were identified in one of the critical active elements, and might serve as important molecular markers regulating backfat thickness. Finally, we observed that AACS overexpression inhibited the proliferation and differentiation of subcutaneous preadipocytes. Collectively, our results suggest that AACS inhibits subcutaneous fat deposition in pigs. This study provides a new molecular marker for understanding the mechanism of porcine fat deposition.

The Identification of Functional Genes Affecting Fat-Related Meat Traits in Meat-Type Pigeons Using Double-Digest Restriction-Associated DNA Sequencing and Molecular Docking Analysis

The Chinese indigenous Shiqi (SQ) pigeon and the imported White King (WK) pigeon are two meat-type pigeon breeds of economical and nutritional importance in China. They displayed significant differences in such meat quality traits as intramuscular fat (IMF) content and fatty acid (FA) compositions in the breast muscles. In this study, we aimed to screen candidate genes that could affect fat-related meat quality traits in meat-type pigeons. We investigated the polymorphic variations at the genomic level using double-digest restriction-associated DNA (ddRAD) sequencing in 12 squabs of SQ and WK pigeons that exhibited significant inter-breed differences in IMF content as well as FA and amino acid compositions in the breast muscles, and screened candidate genes influencing fat-related traits in squabs through gene ontology analysis and pathway analysis. By focusing on 6019 SNPs, which were located in genes with correct annotations and had the potential to induce changes in the encoded proteins, we identified 19 genes (ACAA1, ACAA2, ACACB, ACADS, ACAT1, ACOX3, ACSBG1, ACSBG2, ACSL1, ACSL4, ELOVL6, FADS1, FADS2, HACD4, HADH, HADHA, HADHB, MECR, OXSM) as candidate genes that could affect fat-related traits in squabs. They were significantly enriched in the pathways of FA metabolism, degradation, and biosynthesis (p < 0.05). Results from molecular docking analysis further revealed that three non-synonymous amino acid alterations, ACAA1(S357N), ACAA2(T234I), and ACACB(H1418N), could alter the non-bonding interactions between the enzymatic proteins and their substrates. Since ACAA1, ACAA2, and ACACB encode rate-limiting enzymes in FA synthesis and degradation, alterations in the enzyme-substrate binding affinity may subsequently affect the catalytic efficiency of enzymes. We suggested that SNPs in these three genes were worthy of further investigation into their roles in explaining the disparities in fat-related traits in squabs.

Integrated LC/MS-based lipidomics and transcriptomics analyses revealed lipid composition heterogeneity between pectoralis intramuscular fat and abdominal fat and its regulatory mechanism in chicken

Intramuscular fat (IMF) content is conducive to multiple meat quality properties, while abdominal fat (AF) is treated as waste product in chicken industry. However, the heterogeneity and distinct regulatory mechanisms of lipid composition between the IMF and AF are still unclear. In this study, we carried out non-targeted lipidomics analyses of pectoralis IMF and AF, and detected a total of 423 differential lipid molecules (DLMs) between chicken IMF and AF, including 307 up-regulated and 116 down-regulated DLMs in pectoral IMF. These DLMs exhibited the definite alteration of lipid composition. The up-reglated DLMs in IMF were mainly glycerophospholipids (GPs), including the bulk of phosphatidylcholines (PC, PC (P) and PC (O)), phosphatidylethanolamines (PE, PE (P) and PE (O)), phosphatidylglycerols (PG) and phosphatidylinositol (PI), while the up-reglated DLMs in AF were mainly glycerolipids (GLs), including most of triacylglycerols (TG) and diacylglycerols (DG). We further identified 28 main DLMs contributing to the heterogeneous deposition of IMF and AF, including 11 TGs common to IMF and AF, 12 PCs/PC (P)s specific to IMF and 5 DGs specific to AF. Further integration of transcriptome with the main DLMs by weighted gene co-expression network analysis (WGCNA), we found five key gene sets that included 386 unique genes promoting IMF deposition in pectoralis, 213 unique genes promoting AF deposition, 6 unique genes detrimental to AF deposition, 7 common genes that promote IMF deposition in pectoralis while adversely affect AF deposition, and 28 genes that only promoted IMF deposition in pectoralis but had no effect on AF deposition. In addition, we also observed the expression characteristics of key genes in vivo and in vitro, and found that transmembrane protein family gene TMEM164 might be mainly involved in the positive regulation of intramuscular fat deposition in pectoralis and zinc finger protein family gene ZNF488 had a potential unique positive regulatory function on abdominal fat deposition. These findings provide new perspectives for understanding IMF and AF heterodeposition and will serve as a valuable information resource for improving meat quality via breeding selection in chicken.

Effect of crossbreeding and sex on slaughter performance and meat quality in Xingguo gray goose based on multiomics data analysis

Here, we examined the effects of crossbreeding and sex on growth performance, slaughter performance, and meat quality in Xingguo gray (XG) goose, using transcriptomic and metabolomic techniques. The experiment was conducted using 400 goslings (1-day old) of 2 genotypes: the XG breed and its ternary hybrids [F₂ geese; (XG Goose♂ × Yangzhou Goose♀)♀ × Shitou Goose♂]. The goslings were divided into 4 groups: female XG, male XG, female F₂ geese, and male F₂ geese, and growth parameters were examined at 70 d of age, using 30 birds from each group. Following slaughter, samples of breast and thigh muscles were collected from each group for chemical, metabolome, and transcriptome analyses. Growth rate, live body and slaughter weights, meat chemical composition, and muscle fiber diameter were affected by crossbreeding and sex. Crossbreeding significantly improved the dressing percentage, semieviscerated rate, eviscerated yield, and abdominal fat yield of XG geese. To clarify the potential regulatory network affected by crossbreeding and sex, we used RNA-seq and nontargeted metabolomics to detect changes in male and female goose breast muscle. The transcriptome results showed that there were 534, 323, 297, and 492 differently expressed genes (DEGs) among the 4 comparison groups (XG-Female vs. F₂-Female, XG-Male vs. F₂-Male, F₂-Male vs. F₂-Female, and XG-Male vs. XG-Female, respectively) that were mainly related to muscle growth and development and fatty acid metabolism pathways. A total of 141 significantly differentially accumulated metabolites (DAMs) were enriched in serine and threonine, propionate, and pyruvate metabolism. Finally, we comprehensively analyzed the metabolome and transcriptome data and found that many DEGs and DAMs played crucial roles in lipid metabolism and muscle growth and development. In summary, crossbreeding can improve XG goose production performance and affect breast muscle gene expression and metabolites in both female and male geese.

Genome-wide mapping of signatures of selection using a high-density array identified candidate genes for growth traits and local adaptation in chickens

BACKGROUND

Availability of single nucleotide polymorphism (SNP) genotyping arrays and progress in statistical analyses have allowed the identification of genomic regions and genes under selection in chicken. In this study, SNP data from the 600 K Affymetrix chicken array were used to detect signatures of selection in 23 local Italian chicken populations. The populations were categorized into four groups for comparative analysis based on live weight (heavy vs light) and geographical area (Northern vs Southern Italy). Putative signatures of selection were investigated by combining three extended haplotype homozygosity (EHH) statistical approaches to quantify excess of haplotype homozygosity within (iHS) and between (Rsb and XP-EHH) groups. Presence of runs of homozygosity (ROH) islands was also analysed for each group.

RESULTS

After editing, 541 animals and 313,508 SNPs were available for statistical analyses. In total, 15 candidate genomic regions that are potentially under selection were detected among the four groups: eight within a group by iHS and seven by combining the results of Rsb and XP-EHH, which revealed divergent selection between the groups. The largest overlap between genomic regions identified to be under selection by the three approaches was on chicken chromosome 8. Twenty-one genomic regions were identified with the ROH approach but none of these overlapped with regions identified with the three EHH-derived statistics. Some of the identified regions under selection contained candidate genes with biological functions related to environmental stress, immune responses, and disease resistance, which indicate local adaptation of these chicken populations.

CONCLUSIONS

Compared to commercial lines, local populations are predominantly reared as backyard chickens, and thus, may have developed stronger resistance to environmental challenges. Our results indicate that selection can play an important role in shaping signatures of selection in local chicken populations and can be a starting point to identify gene mutations that could have a useful role with respect to climate change.

The cecal ecosystem is a great contributor to intramuscular fat deposition in broilers

Intramuscular fat (IMF) content is a meat quality trait of major economic importance in animal production. Emerging evidence has demonstrated that meat quality can be improved by regulating the gut microbiota. However, the organization and ecological properties of the gut microbiota and its relationship with the IMF content remain unclear in chickens. Here, we investigated the microbial communities of 206 cecal samples from broilers with excellent meat quality. We noted that the cecal microbial ecosystem obtained from hosts reared under the same management and dietary conditions showed clear compositional stratification. Two enterotypes, in which the ecological properties, including diversity and interaction strengths, were significantly different, described the microbial composition pattern. Compared with enterotype 2, enterotype 1, distinguished by the Clostridia_vadinBB60_group, had a higher fat deposition, although no discrepancy was found in growth performance and meat yield. A moderate correlation was observed in the IMF content between 2 muscle tissues, despite the IMF content of thigh muscle was 42.76% greater than that of breast muscle. Additionally, the lower abundance of cecal vadinBE97 was related to higher IMF levels in both muscle tissues. Although vadinBE97 accounted for 0.40% of the total abundance of genera in the cecum, it exhibited significant and positive correlations with other genera (accounting for 25.3% of the tested genera). Our results highlight important insights into the cecal microbial ecosystem and its association with meat quality. Microbial interactions should be carefully considered when developing approaches to improve the IMF content by regulating the gut microbiota in broilers.

Genome-Wide Association Study Revealed the Effect of rs312715211 in ZNF652 Gene on Abdominal Fat Percentage of Chickens

Abdominal fat percentage (AFP) is an important economic trait in chickens. Intensive growth selection has led to the over-deposition of abdominal fat in chickens, but the genetic basis of AFP is not yet clear. Using 520 female individuals from selection and control lines of Jingxing yellow chicken, we investigated the genetic basis of AFP using a genome-wide association study (GWAS) and fixation indices (F_ST). A 0.15 MB region associated with AFP was located on chromosome 27 and included nine significant single nucleotide polymorphisms (SNPs), which could account for 3.34-5.58% of the phenotypic variation. In addition, the π value, genotype frequency, and dual-luciferase results identified SNP rs312715211 in the intron region of ZNF652 as the key variant. The wild genotype was associated with lower AFP and abdominal fat weight (AFW), but higher body weight (BW). Finally, annotated genes based on the top 1% SNPs were used to investigate the physiological function of ZNF652. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis suggested that ZNF652 may reduce AFW and BW in broilers through the TGF-β1/SMad2/3 and MAPK/FoxO pathways via EGFR and TGFB1. Our findings elucidated the genetic basis of chicken AFP, rs312715211 on the ZNF652 gene, which can affect BW and AFW and was the key variant associated with AFP. These data provide new insight into the genetic mechanism underlying AF deposition in chickens and could be beneficial in breeding chickens for AF.

Addition of a Blend Based on Zinc Chloride and Lignans of Magnolia in the Diet of Broilers to Substitute for a Conventional Antibiotic: Effects on Intestinal Health, Meat Quality, and Performance

This study aimed to determine whether adding a blend based on zinc chloride and lignans from magnolia to the diet of broilers could replace conventional performance enhancers. For this study, 360 chickens were divided into four groups, with six repetitions per group (n = 15), as follows: CN, without promoter; GPC, control, 50 mg/kg of enramycin growth promoter; T-50, additive blend at a dose of 50 g/ton; and T-100, additive blend at a dose of 100 g/ton. Chickens fed with the additive blend at 50 g/ton showed a production efficiency index equal to that in the GPC group (p < 0.05). At 42 days, the lowest total bacterial count (TBC) was found in the T-100 group, followed by that in the GPC group (p < 0.001). For E. coli, the lowest count was observed in the T-100 group, followed by that in the CP and T-50 groups (p < 0.001). Higher villus/crypt ratios were observed in birds belonging to the T-100 and T-50 groups than in the GPC and NC groups (p < 0.001). Greater water retention was found in the T-50 group than in NC and T-100 groups (p < 0.048). The lowest water loss during cooking was also noted in the T-50 group (p < 0.033). We concluded that adding the antimicrobial blend, primarily at 50 g/ton, maintains the efficiency of the index of production and improves the intestinal health and meat quality of the birds.

Integrated Analysis of Long Non-Coding RNA and mRNA to Reveal Putative Candidate Genes Associated with Backfat Quality in Beijing Black Pig

Pigs' backfat quality has an important impact on the quality of pork and pork products and has a strong relationship with nutrition and sensory characteristics. This study aimed to identify the related candidate genes of backfat quality and to preliminary clarify the molecular regulatory mechanism underlying pig backfat quality phenotypes. Expression assessments of long non-coding RNA (lncRNA) and mRNA profiling in backfat from high-quality (firm and white) and low-quality (soft and yellow) Beijing Black pigs were performed by RNA sequencing. Significantly different expressions were observed in 610 protein-coding genes and 290 lncRNAs between the two groups. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway annotation showed that some candidate differentially expressed genes that participate in lipid-related pathways and pigmentation terms may play a role in backfat quality in pigs. The cis-target and trans-target genes were predicted to explore the regulatory function of lncRNAs, and integrative analyses of different expression lncRNAs targets and different expression genes were performed. The results showed the regulatory networks of lncRNA-mRNA related to backfat quality, and our study obtained strong candidate genes for backfat quality: ELOVL5, SCD, DGAT2, SLC24A5, and TYRP1, which were involved in fat metabolism, adipogenesis regulation, and pigmentation. To our knowledge, this study is the first to demonstrate the molecular genetic mechanisms of backfat quality in pigs, and these findings improve the current understanding of backfat quality mechanisms and provide a foundation for further studies.

A genome-wide landscape of mRNAs, lncRNAs, circRNAs and miRNAs during intramuscular adipogenesis in cattle

Background

Intramuscular preadipocyte differentiation plays a critical role in bovine intramuscular fat (IMF) deposition. However, the roles of different RNAs, including mRNAs, circRNAs, lncRNAs and miRNAs, in regulating the adipogenic differentiation of intramuscular preadipocytes remain largely unclear.

Results

In the present study, a whole transcriptome sequencing and analysis, including the analysis of mRNAs, circRNAs, lncRNAs and miRNAs, during different differentiation stages (0, 3, 6, and 9 d) of intramuscular preadipocytes from Qinchuan cattle was performed. All samples were prepared with 3 biological replicates. Here, a total of 27,153 mRNAs, 14,070 circRNAs, 7035 lncRNAs, and 427 miRNAs were annotated. Among them, we identified 4848 differentially expressed mRNAs (DEMs), 181 DE circRNAs (DECs), 501 DE lncRNAs (DELs) and 77 DE miRNAs (DEmiRs) between 0 d and other differentiation days (3, 6, and 9 d). GO and KEGG functional enrichment analyses showed that these differentially expressed genes were mainly enriched in cell differentiation, fat metabolism and adipogenesis-related pathways. Furthermore, weighted gene coexpression network analysis (WGCNA) and co-expression network analysis screened out multiple important mRNAs, circRNAs and lncRNAs related to intramuscular adipogenesis. Based on the competing endogenous RNA (ceRNA) regulatory mechanism, we finally identified 24 potential ceRNA networks and 31 potential key genes, including FOXO1/miR-330/circRNA2018/MSTRG.20301, GPAM/miR-27b/ciRNA489 and SESN3/miR-433/circRNA2627MSTRG.20342.

Conclusions

This study provides new insights into the differential expression patterns of different transcript types (i.e., mRNAs, circRNAs, lncRNAs and miRNAs) in intramuscular preadipocyte differentiation. Our findings provide data support for studying the molecular mechanism of key mRNAs and noncoding RNAs in IMF deposition, and provide new candidate markers for the molecular breeding of beef cattle.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08911-z.