Transcriptional insights into key genes and pathways controlling muscle lipid metabolism in broiler chickens

Insights into flavor formation of braised chicken: Based on E-nose, GC-MS, GC-IMS, and UPLC-Q-Exactive-MS/MS

Effects of braising duration on volatile organic compounds (VOCs) and lipids in chicken were investigated. Aroma profiles identified by an electronic nose were effective in differentiating braising stages. During braising process, a total of 25 key VOCs were detected in braised chicken, and sample braised for 210 min exhibited the highest level of key VOCs. Additionally, a gas chromatography mass spectrometry fingerprint was established to evaluate the distribution of VOCs throughout the braising process. Partial least square discriminant analysis indicated that 2-heptanone, 3-methyl-2-butanone, octanal, nonanal, butanal, (E)-2-pentenal, 1-octen-3-ol, 1-hexanol, pentanal, hexanal, and 1-pentanol significantly affected flavor characteristics of braised chicken. Furthermore, 88 differential lipids were screened, and glycerolipids metabolic was found to be main metabolic pathway during braising process. Triglycerides (TG) and phosphatidyl ethanolamine (PE), such as TG (16:0/18:1/18:2), TG (18:0/18:1/18:2), TG (18:1/18:2/18:3), TG (18:1/18:1/18:2), PE (O-18:2/18:2), PE(O-18:2/18:1), and TG (16:0/16:1/18:2), played a vital role in the generation of VOCs.

Histology, fatty acid composition, antioxidant and glycolipid metabolism, and transcriptome analyses of the acute cold stress response in Phoxinus lagowskii

Water temperature is a crucial environmental factor that significantly affects the physiological and biochemical processes of fish. Due to the occurrence of cold events in aquaculture, it is imperative to investigate how fish respond to cold stress. This study aims to uncover the mechanisms responds to acute cold stress by conducting a comprehensive analysis of the histomorphology, glycolipid metabolic and antioxidant enzymes, fatty acid composition and transcriptome at three temperatures (16 °C, 10 °C and 4 °C) in Phoxinus lagowskii. Our results showed that cold stress not damaged muscle microstructure but caused autophagy (at 10 °C). In addition, serum glucose (Glu) and triglycerides (TG) increased during cold stress. The activities of reactive oxygen species (ROS), superoxide dismutase (SOD), catalase (CAT), fructose phosphokinase (PFK), hexokinase (HK), pyruvate kinase (PK), and malondialdehyde (MDA) content in muscle were measured and analyzed. During cold stress, superoxide dismutase and catalase activities increased, reactive oxygen species content decreased. No significant difference in Glutathione peroxidase (GPx) activity, malondialdehyde and total cholesterol (T-CHO) contents among groups. Phosphokinase and pyruvate kinase activities decreased, and HK activity increased during cold stress. Our study resulted in the identification of a total of 25,400 genes, with 2524 genes showing differential expression across different temperature treatments. Furthermore, KEGG pathway indicated that some pathways upregulated during light cold stress (at 10 °C, including autophagy, and AMP-activated protein kinase (AMPK) signaling pathway. Additionally, circadian rhythm is among the most enriched pathways in genes up-regulated during severe cold stress (at 4 °C). Our findings offer valuable insights into how cold-water fish respond to cold stress.

Integrated transcriptome and microbiome analyses of residual feed intake in ducks during high production period

Residual feed intake (RFI) is a crucial parameter for assessing the feeding efficiency of poultry. Minimizing RFI can enhance feed utilization and reduce costs. In this study, 315 healthy female ducks were individually housed in cages. Growth performance was monitored during the high laying period, from 290 to 325 d of age. The cecal transcriptome and microbiome of 12 ducks with high RFI and 12 with low residual feed intake (LRFI) were analyzed. Regarding growth performance, the LRFI group exhibited significantly lower RFI, feed conversion ratio (FCR), and feed intake (Fi) compared to the HRFI group (p < 0.01). However, there were no significant differences observed in body weight (BW), body weight gain (BWG), and egg mass (EML) between the groups (p > 0.05). Microbiome analysis demonstrated that RFI impacted gut microbial abundance, particularly affecting metabolism and disease-related microorganisms such as Romboutsia, Enterococcus, and Megamonas funiformis. Transcriptome analysis revealed that varying RFI changed the expression of genes related to glucose metabolism and lipid metabolism, including APOA1, G6PC1, PCK1, and PLIN1. The integrated analysis indicated that host genes were closely linked to the microbiota and primarily function in lipid metabolism, which may enhance feeding efficiency by influencing metabolism and maintaining gut homeostasis.

Comprehensive analysis of changes in expression of lncRNA, microRNA and mRNA in liver tissues of chickens with high or low abdominal fat deposition

1. The liver of chickens is a dominant lipid biosynthetic tissue and plays a vital role in fat deposition, particularly in the abdomen. To determine the molecular mechanisms involved in its lipid metabolism, the livers of chickens with high (H) or low (L) abdominal fat content were sampled and sequencing on long non-coding RNA (lncRNA), messenger RNA (mRNA) and small RNA (microRNA) was performed.2. In total, 351 expressed protein-coding genes for long non-coding RNA (DEL; 201 upregulated and 150 downregulated), 400 differentially expressed genes (DEG; 223 upregulated and 177 downregulated) and 10 differentially expressed miRNA (DEM; four upregulated and six downregulated) were identified between the two groups. Multiple potential signalling pathways related to lipogenesis and lipid metabolism were identified via pathway enrichment analysis. In addition, 173 lncRNA - miRNA - mRNA interaction regulatory networks were identified, including 30 lncRNA, 27 mRNA and seven miRNA.3. These networks may help regulate lipid metabolism and fat deposition. Five promising candidate genes and two lncRNA may play important roles in the regulation of adipogenesis and lipid metabolism in chickens.

Strand-Specific RNA Sequencing Reveals Gene Expression Patterns in F1 Chick Breast Muscle and Liver after Hatching

Heterosis refers to the phenomenon where hybrids exhibit superior performance compared to the parental phenotypes and has been widely utilized in crossbreeding programs for animals and crops, yet the molecular mechanisms underlying this phenomenon remain enigmatic. A better understanding of the gene expression patterns in post-hatch chickens is very important for exploring the genetic basis underlying economically important traits in the crossbreeding of chickens. In this study, breast muscle and liver tissues (n = 36) from full-sib F1 birds and their parental pure lines were selected to identify gene expression patterns and differentially expressed genes (DEGs) at 28 days of age by strand-specific RNA sequencing (ssRNA-seq). This study indicates that additivity is the predominant gene expression pattern in the F1 chicken post-hatch breast muscle (80.6% genes with additivity) and liver (94.2% genes with additivity). In breast muscle, Gene Ontology (GO) enrichment analysis revealed that a total of 11 biological process (BP) terms closely associated with growth and development were annotated in the identified DEG sets and non-additive gene sets, including STAT5A, TGFB2, FGF1, IGF2, DMA, FGF16, FGF12, STAC3, GSK3A, and GRB2. Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation presented that a total of six growth- and development-related pathways were identified, involving key genes such as SLC27A4, GLUL, TGFB2, COX17, and GSK3A, including the PPAR signaling pathway, TGF-beta signaling pathway, and mTOR signaling pathway. Our results may provide a theoretical basis for crossbreeding in domestic animals.

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.

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.

miR-19b-3p regulated by estrogen controls lipid synthesis through targeting MSMO1 and ELOVL5 in LMH cells

miR-19b-3p is reported to undertake various biological role, while its function and action mechanism in chicken hepatic lipid metabolism is unclear. Conservation analysis and tissue expression pattern of miR-19b-3p and its target gene were evaluated, respectively. Dual luciferase reporter system and Western blot technologies were adopted to validate miR-19b-3p target gene. Overexpression and knockdown assays were done to explore the biological functions of miR-19b-3p and target gene in Leghorn Male Hepatoma cell line (LMH). Regulatory approaches of estrogen on miR-19b-3p and target gene expressions are analyzed through site-directed mutation combined with estrogen receptors antagonist treatment assays. The results showed that chicken miR-19b-3p mature sequences are highly conserved among Capra hircus, Columba livia, Rattus norvegicus, Mus musculus, Cricetulus griseus, Danio rerio, Danio novaehollandiae, Orycodylus porosus, Crocodylus porosus, Gadus morhua, and widely expressed in lung, ovary, spleen, duodenum, kidney, heart, liver, leg muscle, and pectoral muscle tissues. miR-19b-3p could significantly increase intracellular triglyceride (TG) content and decrease intracellular cholesterol (TC) content via targeting methylsterol monooxygenase 1 (MSMO1) and elongase of very long chain fatty acids 5 (ELOVL5), which are highly conserved among species, in both mRNA and protein levels. Estrogen could inhibit miR-19b-3p expression, but directly promoted MSMO1 transcription via estrogen receptor α (ERα) and indirectly regulated ELOVL5 expression at the transcription level. Meanwhile, estrogen could also upregulate MSMO1 and ELOVL5 expression through inhibiting miR-19b-3p expression at the post-transcription level. Taken together, these results highlight the role and regulatory mechanism of miR-19b-3p in hepatic lipid metabolism in chicken, and might produce useful comparative information for human obesity studies and biomedical research.

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.

Characterization and comparative transcriptomic analysis of skeletal muscle in female Pekin duck and Hanzhong Ma duck during different growth stages using RNA-seq

Duck is an economically important poultry, and there is currently a major focus on improving its meat quality through breeding. There are wide variations in the growth regulation mechanisms of different duck breeds, that fundamental research on skeletal muscle growth is essential for understanding the regulation of unknown genes. The study aimed to broaden the understanding the duck skeletal muscle development and thereby to improve the performance of domestic ducks. In this study, RNA-seq data from skeletal muscles (breast muscle and leg muscle) of Pekin duck and Hanzhong Ma duck sampled at d 17, 21, and 27 of embryo (E17d, E21d, and E27d), as well as at 6-mo-old following birth (M6), to investigate and compare the mRNA temporal expression profiles and associated pathways that regulate skeletal myogenesis of different duck breeds. There were 331 to 1,440 annotated differentially expressed genes (DEGs) in breast muscle and 380 to 1,790 annotated DEGs in leg muscle from different databases between 2 duck breeds. Gene ontology (GO) enrichment in skeletal muscles indicated that these DEGs were mainly involved in biosynthetic process, developmental process, regulation of protein metabolic process and regulation of gene expression. KEGG analysis in skeletal muscles showed that a total of 41 DEGs were mapped to 7 KEGG pathways, including ECM-receptor interaction, focal adhesion, carbon metabolism, regulation of actin cytoskeleton, calcium signaling pathway, biosynthesis of amino acids and PPAR signaling pathway. The differential expression of 8 selected DEGs was verified by qRT-PCR, and the results were consistent with RNA-seq data. The identified DEGs, such as SDC, SPP1, PAK1, MYL9, PGK1, NOS1, PHGDH, TNNT2, FN1, and AQP4, were specially highlighted, indicating their associations with muscle development in the Pekin duck and Hanzhong Ma duck. This study provides a basis for revealing the differences in skeletal muscle development between Pekin duck and Hanzhong Ma duck.

Effect of dietary betaine supplementation on the liver transcriptome profile in broiler chickens under heat stress conditions

OBJECTIVE

The objective of the present study was to investigate the effect of dietary betaine (BT) supplementation on the hepatic transcriptome profiles in broiler chickens raised under heat stress (HS) conditions.

METHODS

A total of 180 (21-d-old) Ross 308 male broiler chicks were allotted to 1 of 3 treatment groups with 6 replicated cages in a completely randomized design. One group was kept under thermoneutral conditions at all times and was fed a basal diet (PC). Other 2 groups were exposed to a cyclic heat stress condition. One of the 2 groups under heat stress conditions was fed the basal diet as a negative control (NC), whereas the other group was fed the basal diet supplemented with 0.2% BT. All chickens were provided with diets and water ad libitum for 21 d. Following the experiment, the liver samples were collected for RNA sequencing analysis.

RESULTS

Broiler chickens in NC and BT group had decreased (p<0.05) growth performance. In the transcriptome analysis, the number of differentially expressed genes were identified in the liver by HS conditions and dietary BT supplementation. In the comparison between NC and PC treatments, genes related to energy and nucleic acid metabolism, amino acid metabolism, and immune system were altered by HS, which support the reason why heat-stressed poultry had decreased growth performance. In the comparison between NC and BT treatments, genes related to lipid metabolism, carbohydrate metabolism, and immune system were differently expressed under HS conditions.

CONCLUSION

HS negatively impacts various physiological processes, including DNA replication, metabolism of amino acids, lipids, and carbohydrates, and cell cycle progression in broiler chickens. Dietary BT supplementation, however, offers potential counteractive effects by modulating liver function, facilitating gluconeogenesis, and enhancing immune systems. These findings provide a basis for understanding molecular responses by HS and the possible benefits of dietary BT supplementation in broiler chickens exposed to HS.

Multi-Omics Analysis of Genes Encoding Proteins Involved in Alpha-Linolenic Acid Metabolism in Chicken

Alpha-linolenic acid (ALA, ω-3) is an antioxidant that reduces triglyceride (TG) levels in blood, a component of cell membranes and a precursor compound of eicosapentaenoic acid (EPA, ω-3) and eicosatrienoic acid (DHA, ω-3). Fatty acid content is a quantitative trait regulated by multiple genes, and the key genes regulating fatty acid metabolism have not been systematically identified. This study aims at investigating the protein-encoding genes regulating ω-3 polyunsaturated fatty acid (PUFA) content in chicken meat. We integrated genomics, transcriptomics and lipidomics data of Jingxing yellow chicken (JXY) to explore the interactions and associations among multiple genes involved in the regulation of fatty acid metabolism. Several key genes and pathways regulating ω-3 fatty acid metabolism in chickens were identified. The upregulation of GRB10 inhibited the mTOR signaling pathway, thereby improving the content of EPA and DHA. The downregulation of FGFR3 facilitated the conversion of ALA to EPA. Additionally, we analyzed the effects of ALA supplementation dose on glycerol esters (GLs), phospholipid (PL) and fatty acyl (FA) contents, as well as the regulatory mechanisms of nutritional responses in FFA metabolism. This study provides a basis for identifying genes and pathways that regulate the content of FFAs, and offers a reference for nutritional regulation systems in production.

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.

miR-128-3p inhibits intramuscular adipocytes differentiation in chickens by downregulating FDPS

BACKGROUND

Intramuscular fat (IMF) content is the major indicator for evaluating chicken meat quality due to its positive correlation with tenderness, juiciness, and flavor. An increasing number of studies are focusing on the functions of microRNAs (miRNAs) in intramuscular adipocyte differentiation. However, little is known about the association of miR-128-3p with intramuscular adipocyte differentiation. Our previous RNA-seq results indicated that miR-128-3p was differentially expressed at different periods in chicken intramuscular adipocytes, revealing a possible association with intramuscular adipogenesis. The purpose of this research was to investigate the biological functions and regulatory mechanism of miR-128-3p in chicken intramuscular adipogenesis.

RESULTS

The results of a series of assays confirmed that miR-128-3p could promote the proliferation and inhibit the differentiation of intramuscular adipocytes. A total of 223 and 1,050 differentially expressed genes (DEGs) were identified in the mimic treatment group and inhibitor treatment group, respectively, compared with the control group. Functional enrichment analysis revealed that the DEGs were involved in lipid metabolism-related pathways, such as the MAPK and TGF-β signaling pathways. Furthermore, target gene prediction analysis showed that miR-128-3p can target many of the DEGs, such as FDPS, GGT5, TMEM37, and ASL2. The luciferase assay results showed that miR-128-3p targeted the 3' UTR of FDPS. The results of subsequent functional assays demonstrated that miR-128-3p acted as an inhibitor of intramuscular adipocyte differentiation by targeting FDPS.

CONCLUSION

miR-128-3p inhibits chicken intramuscular adipocyte differentiation by downregulating FDPS. Our findings provide a theoretical basis for the study of lipid metabolism and reveal a potential target for molecular breeding to improve meat quality.

Transcriptome analysis reveals FABP5 as a key player in the development of chicken abdominal fat, regulated by miR-122-5p targeting

BACKGROUND

The development of abdominal fat and meat quality are closely related and can impact economic efficiency. In this study, we conducted transcriptome sequencing of the abdominal fat tissue of Gushi chickens at 6, 14, 22, and 30 weeks, and selected key miRNA-mRNA regulatory networks related to abdominal fat development through correlation analysis.

RESULTS

A total of 1893 differentially expressed genes were identified. Time series analysis indicated that at around 6 weeks, the development of chicken abdominal fat was extensively regulated by the TGF-β signaling pathway, Wnt signaling pathway, and PPAR signaling pathway. However, at 30 weeks of age, the apoptosis signaling pathway was the most significant, and correlation analysis revealed several genes highly correlated with abdominal fat development, including Fatty Acid Binding Protein 5 (FABP5). Based on miRNA transcriptome data, it was discovered that miR-122-5p is a potential target miRNA for FABP5. Cell experiments showed that miR-122-5p can directly target FABP5 to promote the differentiation of preadipocytes.

CONCLUSION

The present study confirms that the key gene FABP5 and its target gene miR-122-5p are critical regulatory factors in the development of chicken abdominal fat. These results provide new insights into the molecular regulatory mechanisms associated with the development of abdomen-al fat in chickens.

Dietary Supplementation with Rutin Alters Meat Quality, Fatty Acid Profile, Antioxidant Capacity, and Expression Levels of Genes Associated with Lipid Metabolism in Breast Muscle of Qingyuan Partridge Chickens

Consumer demand for tasty and quality meat has been quickly increasing. This study investigated how dietary supplemented rutin affects meat quality, muscle fatty acid profile, and antioxidant capacity in the Chinese indigenous Qingyuan partridge chicken. A cohort of 180 healthy 119-day-old chickens was subjected to a randomized assignment into three groups, identified as the control, R200, and R400 groups, with respective supplementation of 0, 200, and 400 mg/kg of rutin. The results revealed insignificance in growth performance, namely, average daily gain, average daily feed intake, and feed-to-gain ratio, across the various treatment groups (p > 0.05). Nevertheless, dietary rutin supplementation increased (p < 0.05) breast muscle yield and intramuscular fat content in breast muscle and decreased (p < 0.05) drip loss in breast muscle. Rutin supplementation increased (p < 0.05) the content of high-density lipoprotein but decreased (p < 0.05) the contents of glucose, triglyceride, and total cholesterol in serum. Rutin supplementation increased (p < 0.05) the levels of DHA (C22:6n-3), total polyunsaturated fatty acids (PUFAs), n-3 PUFAs, decanoic acid (C10:0), the activity of Δ5 + Δ6 (22:6 (n - 3)/18:3 (n - 3)), and the ratio of PUFA/SFA in breast muscle but decreased (p < 0.05) the level of palmitoleic acid (C16:1n-7), the ratio of n-6/n-3 PUFAs, and the activity of Δ9 (16:1 (n - 7)/16:0). Rutin treatment also reduced (p < 0.05) the contents of malondialdehyde in serum and breast muscle, and increased (p < 0.05) the catalase activity and total antioxidant capacity in serum and breast muscle and the activity of total superoxide dismutase in serum. Additionally, rutin supplementation downregulated the expression of AMPKα and upregulated the expression of PPARG, FADS1, FAS, ELOVL7, NRF2, and CAT in breast muscle (p < 0.05). Convincingly, the results revealed that rutin supplementation improved meat quality, fatty acid profiles, especially n-3 PUFAs, and the antioxidant capacity of Qingyuan partridge chickens.

Dietary Cholesterol Supplementation Inhibits the Steroid Biosynthesis but Does Not Affect the Cholesterol Transport in Two Marine Teleosts: A Hepatic Transcriptome Study

Cholesterol has been used as additive in fish feeds due to the reduced use of fish meal and fish oil. In order to evaluate the effects of dietary cholesterol supplementation (D-CHO-S) on fish physiology, a liver transcriptome analysis was performed following a feeding experiment on turbot and tiger puffer with different levels of dietary cholesterol. The control diet contained 30% fish meal (0% fish oil) without cholesterol supplementation, while the treatment diet was supplemented with 1.0% cholesterol (CHO-1.0). A total of 722 and 581 differentially expressed genes (DEG) between the dietary groups were observed in turbot and tiger puffer, respectively. These DEG were primarily enriched in signaling pathways related to steroid synthesis and lipid metabolism. In general, D-CHO-S downregulated the steroid synthesis in both turbot and tiger puffer. Msmo1, lss, dhcr24, and nsdhl might play key roles in the steroid synthesis in these two fish species. Gene expressions related to cholesterol transport (npc1l1, abca1, abcg1, abcg2, abcg5, abcg8, abcb11a, and abcb11b) in the liver and intestine were also extensively investigated by qRT-PCR. However, the results suggest that D-CHO-S rarely affected the cholesterol transport in both species. The protein-protein interaction (PPI) network constructed on steroid biosynthesis-related DEG showed that in turbot, Msmo1, Lss, Nsdhl, Ebp, Hsd17b7, Fdft1, and Dhcr7 had high intermediary centrality in the dietary regulation of steroid synthesis. In conclusion, in both turbot and tiger puffer, the supplementation of dietary cholesterol inhibits the steroid metabolism but does not affect the cholesterol transport.

Integrative analysis of transcriptome and metabolome reveals probiotic effects on cecal metabolism in broilers

BACKGROUND

Probiotics play an important role in the host and have attracted widespread attention as an alternative to antibiotics. Arbor Acres broilers were used in the present experiment and fed different doses of compound probiotics at 1, 5, and 10 g kg^-1 . The effects of compound probiotics on broiler growth performance and cecal transcriptome and metabolome were investigated.

RESULTS

We discovered 425 differentially expressed genes (DEGs; upregulated: 256; downregulated: 169) in the cecal transcriptome study. These DEGs were assigned to fat metabolic pathways, such as the peroxisome proliferator-activated receptor (PPAR) signaling pathway, according to KEGG analysis. Probiotics downregulated LPL and upregulated PPARα expression in the cecum. In metabolome analysis of the cecum of cecum, we screened 86 differential metabolites and performed KEGG enrichment analysis of these metabolites. The KEGG analysis showed that these differentially expressed metabolites were annotated to nucleotide metabolism-related pathways, such as purine metabolism. In the cecum, probiotics upregulated the content of guanine, AMP, 3'-AMP, adenylosuccinate, deoxyguanosine, and ADP-ribose, whereas they downregulated the content of 5-hydroxyisourate. Comprehensive transcriptome and metabolome analysis revealed that glycolysis, gluconeogenesis, and glycerophospholipid metabolism pathways were jointly enriched in cecum of broilers fed a probiotic-containing diet.

CONCLUSION

This study provides valuable information for studying the regulation and gene metabolism network of probiotics on cecal metabolism in broilers. © 2022 Society of Chemical Industry.

Transcriptome, proteome and metabolome analysis provide insights on fat deposition and meat quality in pig

Intramuscular fat (IMF) content, which is an important determinant of meat quality characteristics such as tenderness, juiciness and flavor, has long been a research hotspot. Chinese local pig breeds are famous for their excellent meat quality which is mainly reflected in the high IMF content, strong hydraulic system and et al. However, there are few analysis of meat quality by omics methods. In our study, we identified 12 different fatty acids, 6 different amino acids, 1,262 differentially expression genes (DEGs), 140 differentially abundant proteins (DAPs) and 169 differentially accumulated metabolites (DAMs) (p < 0.05) with metabolome, transcriptome, and proteome. It has been found that DEGs, DAPs and DAMs were enriched in the Wnt signaling pathway, PI3K-Akt signaling pathway, Rap1 signaling pathway, and Ras signaling pathway which were related to meat quality. Moreover, our Weighted genes co-expression network construction (WGCNA) showed RapGEF1 was the key gene related to IMF content and the RT-qPCR analysis was used to perform validation of the significant genes. In summary, our study provided both fundamental data and new insights to further uncover the secret of pig IMF content.

Effects of Chinese Yam Polysaccharide on Intramuscular Fat and Fatty Acid Composition in Breast and Thigh Muscles of Broilers

The purpose of this study is to evaluate the influences of Chinese yam polysaccharide (CYP) dietary supplementation on the composition of intramuscular fat (IMF) and fatty acids (FA) in thigh and breast muscles of broilers. Three hundred and sixty healthy one-day-old broilers (the breed of Crossbred chicken is named 817) with gender-balanced and similar body weight (39 ± 1 g) were randomly allocated into four groups (control, CYP1, CYP2, and CYP3 groups). Broilers in the control group were only fed a basal diet, and broilers in CYP1 group were fed the same diets further supplemented with 250 mg/kg CYP, the CYP2 group was fed the same diets further supplemented with 500 mg/kg CYP, and the CYP3 group was fed the same diets further supplemented with 1000 mg/kg CYP, respectively. Each group consisted of three replicates and each replicate consisted of 30 birds. The feeding days were 48 days. The results observed that the CYP2 group (500 mg/kg) can up-regulate the mRNA expression levels of β-catenin in thigh muscle compared to the control group. At the same time, all CYP groups (CYP1, CYP2, and CYP3 groups) can up-regulate mRNA expression of Wnt1 and β-catenin in breast muscle, while mRNA expression of PPARγ and C/EBPα in breast and thigh muscles could be down-regulated (p < 0.05). In summary, 500 mg/kg of CYP dietary supplementation can reduce IMF content and improve the FAs composition, enhancing the nutritional value of chicken meat.

Study on fatty acid binding protein in lipid metabolism of livestock and poultry

Fatty acid binding proteins (FABPs) are key proteins in lipid transport, and 12 family members have been documented in the literature. In recent years, new insights have been gained into the structure and function of FABPs, which are important regulators of lipid metabolic processes in the body and play a central role in coordinating lipid transport and metabolism in various tissues and organs across species. This paper provides a brief overview of the structure and biological functions of FABPs and reviews related studies on lipid metabolism in livestock and poultry to lay the foundation for research on the mechanism underlying the regulatory effect of FABPs on lipid metabolism in livestock and poultry and for the genetic improvement of livestock and poultry.

Effects of Dietary Vitamin E on Intramuscular Fat Deposition and Transcriptome Profile of the Pectoral Muscle of Broilers

Vitamin E is an essential micronutrient for animals. The aim of this study was to determine the effect of vitamin E on intramuscular fat (IMF) deposition and the transcriptome profile of the pectoral muscle in broiler chickens. Arbor Acres chickens were divided into five treatment groups fed a basal diet supplemented with 0, 20, 50, 75, and 100 IU/kg dietary DL-α-tocopheryl acetate (vitamin E), respectively. Body weight, carcass performance, and IMF content were recorded. Transcriptome profiles of the pectoral muscles of 35-day-old chickens in the control and treatment groups (100 IU/kg of vitamin E) were obtained by RNA sequencing. The results showed that diets supplemented with 100 IU/kg of vitamin E significantly increased IMF deposition in chickens on day 35. In total, 159 differentially expressed genes (DEGs), including 57 up-regulated and 102 down-regulated genes, were identified in the treatment (100 IU/kg vitamin E) group compared to the control group. These DEGs were significantly enriched in 13 Gene Ontology terms involved in muscle development and lipid metabolism; three signaling pathways, including the mitogen-activated protein kinase and FoxO signaling pathways, which play key roles in muscular and lipid metabolism; 28 biofunctional categories associated with skeletal and muscular system development; 17 lipid metabolism functional categories; and three lipid metabolism and muscle development-related networks. The DEGs, pathways, functional categories, and networks identified in this study provide new insights into the regulatory roles of vitamin E on IMF deposition in broilers. Therefore, diets supplemented with 100 IU/kg of vitamin E will be more beneficial to broiler production.

Evaluation of dietary metabolizable energy concentrations on meat quality and lipid metabolism-related gene expression in yellow-feathered chickens

This study evaluated the effects of different dietary metabolizable energy (ME) concentrations on the meat quality, carcass traits, volatile flavour and lipid metabolism-related gene expression levels in yellow-feathered chickens. In total, 600 Huxu female chickens aged 90 days were randomly assigned to six dietary treatments, each with 10 replicates of 10 birds. During the finisher phase, the birds were fed diets containing 2880 (low), 2940, 3000, 3060, 3120 and 3180 (high) kcal ME/kg. The results showed that the average daily gain of chickens increased as the dietary ME concentration increased, while the feed to gain improved (p < 0.05), and the intramuscular fat content of breast muscle increased (p < 0.05). The energy concentration had no effect on the breast muscle pH (45 min and 24 h), colour parameter (L*) or percentage of drip loss (p > 0.05), but the shear force values decreased significantly (p < 0.05). The diameter and area of the breast muscle fiber decreased and the muscle fibre density increased as the dietary ME concentration increased (p < 0.05). The highest ME concentration (3180 kcal) increased the percentages of aldehydes (hexanal, heptanal, 2,4-nonadienal, octanal, nonanal and 2-decenal), alcohols (2-nonen-1-ol, trans-2-undecen-1-ol, 7-hexadecenal, 2-hexyl-1-decanoal and n-nonadecanol-1,3,7,11-trimethyl-1-dodecanol), alkanes (2,6-dimethyl-heptadecane) and carboxylic acids (9-hexadecenoic acid), but reduced the percentages of octadecanal, octadecane, heneicosane and tetradecanal (p < 0.05). In addition, the mRNA gene expression levels of fatty acid-binding protein 3 and apolipoprotein B were significantly upregulated in the liver, whereas that of cholesteryl ester transfer protein was significantly downregulated. In conclusion, increasing the ME diet to 3180 kcal/kg significantly improved the quality and flavour of the meat from yellow-feathered broilers. our finding may help poultry producers to improve the taste of meat by regulating genes related to lipid metabolism, thereby achieving the flavour and taste characteristics preferred by consumers.

Integrated Transcriptome and 16S rDNA Analyses Reveal That Transport Stress Induces Oxidative Stress and Immune and Metabolic Disorders in the Intestine of Hybrid Yellow Catfish (Tachysurus fulvidraco♀ × Pseudobagrus vachellii♂)

Live fish are often transported in aquaculture. To explore the effects of transport stress, hybrid yellow catfish (Tachysurus fulvidraco♀ × Pseudobagrus vachellii♂) were subjected to simulated transport treatments (0–16 h) with 96 h of recovery after the 16-h transport treatment, and intestinal biochemical parameters, the transcriptome, and gut microbiota were analyzed. Transportation affected the number of mucus cells and led to oxidative stress in the intestine, which activated immune responses. Changes in lipid metabolism reflected metabolic adaptation to oxidative stress. Toll-like receptor signaling, peroxisome proliferator-activated receptor signaling, and steroid biosynthesis pathways were involved in the transport stress response. Gene expression analyses indicated that transport-induced local immune damage was reversible, whereas disordered metabolism recovered more slowly. A 16S rDNA analysis revealed that transport stress decreased the alpha diversity of the gut microbiota and disrupted its homeostasis. The dominant phyla (Fusobacteria, Bacteroidetes) and genera (Cetobacterium, Barnesiellaceae) were involved in the antioxidant, immune, and metabolic responses of the host to transportation stress. Correlation analyses suggested that gut microbes participate in the transport stress response and the host–microbiota interaction may trigger multiple events in antioxidant, immune, and metabolic pathways. Our results will be useful for optimizing transport processes.

Fatty acid metabolism-related genes are associated with flavor-presenting aldehydes in Chinese local chicken

Aldehydes are primary volatile organic compounds (VOCs) in local Chinese chicken meat and contribute green grass, fatty, citrus, and bitter almond aromas to chicken meat. To understand the genetic basis of these aldehyde VOC aromas, we used approximately 500 Chinese Jingxing Yellow (JXY) chickens to conduct genome-wide association studies (GWAS) on the flavor traits with the data of single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs). In total, 501 association variants (253 SNPs and 248 INDELs) were found to be suggestively (SNPs: p-value < 2.77e-06 and INDELs: p-value < 3.78e-05) associated with total aldehydes (the sum of nine aldehydes), hexanal, heptanal, benzaldehyde, (E,E)-2,4-nonadienal, octanal, (E)-2-decenal, nonanal, decanal, and octadecanal. Of them, six SNPs and 23 INDELs reached a genome-wide significance level (SNPs: p-value < 1.38e-07 and INDELs: p-value < 1.89e-06). Potential candidate aldehyde genes were functionally annotated for lipid metabolism, especially fatty acid-related pathways and phospholipid-related gene ontology (GO) terms. Moreover, the GWAS analysis of total aldehydes, hexanal, and nonanal generated the most significant signals, and phenotypic content differed between different genotypes at candidate gene-related loci. For total aldehydes and hexanal traits, candidate genes were annotated based on the significant and suggestive variants on chromosomes 3 and 8 with highly polymorphic linkage blocks. The following candidate genes were also identified: GALM, MAP4K3, GPCPD1, RPS6KA2, CRLS1, ASAP1, TRMT6, SDC1, PUM2, ALDH9A1, MGST3, GMEB1, MECR, LDLRAP1, GPAM and ACSL5. We also found that polyunsaturated fatty acids (PUFAs) (C18:2n6c linoleic acid and C18:3n3 linolenic acid) were significantly correlated with total aldehydes and hexanal contents. PUFAs are important aldehyde precursors, and consistently, our results suggested that candidate genes involved in fatty acid pathways and phospholipid GO terms were identified in association loci. This work provides an understanding of the genetic basis of aldehyde formation, which is a key flavor-forming compound.

Whole transcriptome RNA Sequencing Reveals the Global Molecular Responses and circRNA/lncRNA-miRNA-mRNA ceRNA Regulatory Network in Chicken Fat Deposition

Fat deposition is a vital factor affecting the economics of poultry production. Numerous studies on fat deposition have been done. However, the molecular regulatory mechanism is still unclear. In the present study, the whole-transcriptome RNA sequencing in abdominal fat, back skin, and liver both high- and low-abdominal fat groups was used to uncover the competitive endogenous RNA (ceRNA) regulation network related to chicken fat deposition. The results showed that differentially expressed (DE) genes in abdominal fat, back skin, liver were 1207(784 mRNAs, 330 lncRNAs, 41 circRNAs, 52 miRNAs), 860 (607 mRNAs, 166 lncRNAs, 26 circRNAs, 61 miRNAs), and 923 (501 mRNAs, 262 lncRNAs, 15 circRNAs, 145 miRNAs), respectively. The ceRNA regulatory network analysis indicated that the fatty acid metabolic process, monocarboxylic acid metabolic process, carboxylic acid metabolic process, glycerolipid metabolism, fatty acid metabolism, and peroxisome proliferator-activated receptor (PPAR) signaling pathway took part in chicken fat deposition. Meanwhile, we scan the important genes, FADS2, HSD17B12, ELOVL5, AKR1E2, DGKQ, GPAM, PLIN2, which were regulated by gga-miR-460b-5p, gga-miR-199-5p, gga-miR-7470-3p, gga-miR-6595-5p, gga-miR-101-2-5p. While these miRNAs were competitive combined by lncRNAs including MSTRG.18043, MSTRG.7738, MSTRG.21310, MSTRG.19577, and circRNAs including novel_circ_PTPN2, novel_circ_CTNNA1, novel_circ_PTPRD. This finding provides new insights into the regulatory mechanism of mRNA, miRNA, lncRNA, and circRNA in chicken fat deposition.

Non-Targeted Metabolomic Analysis of Chicken Kidneys in Response to Coronavirus IBV Infection Under Stress Induced by Dexamethasone

Stress in poultry can lead to changes in body metabolism and immunity, which can increase susceptibility to infectious diseases. However, knowledge regarding chicken responses to viral infection under stress is limited. Dexamethasone (Dex) is a synthetic glucocorticoid similar to that secreted by animals under stress conditions, and has been widely used to induce stress in chickens. Herein, we established a stress model in 7-day-old chickens injected with Dex to elucidate the effects of stress on IBV replication in the kidneys. The metabolic changes, immune status and growth of the chickens under stress conditions were comprehensively evaluated. Furthermore, the metabolic profile, weight gain, viral load, serum cholesterol levels, cytokines and peripheral blood lymphocyte ratio were compared in chickens treated with Dex and infected with IBV. An LC-MS/MS-based metabolomics method was used to examine differentially enriched metabolites in the kidneys. A total of 113 metabolites whose abundance was altered after Dex treatment were identified, most of which were lipids and lipid-like molecules. The principal metabolic alterations in chicken kidneys caused by IBV infection included fatty acid, valine, leucine and isoleucine metabolism. Dex treatment before and after IBV infection mainly affected the host’s tryptophan, phenylalanine, amino sugar and nucleotide sugar metabolism. In addition, Dex led to up-regulation of serum cholesterol levels and renal viral load in chickens, and to the inhibition of weight gain, peripheral blood lymphocytes and IL-6 production. We also confirmed that the exogenous cholesterol in DF-1 cells promoted the replication of IBV. However, whether the increase in viral load in kidney tissue is associated with the up-regulation of cholesterol levels induced by Dex must be demonstrated in future experiments. In conclusion, chick growth and immune function were significantly inhibited by Dex. Host cholesterol metabolism and the response to IBV infection are regulated by Dex. This study provides valuable insights into the molecular regulatory mechanisms in poultry stress, and should support further research on the intrinsic link between cholesterol metabolism and IBV replication under stress conditions.

Integrating genomics and transcriptomics to identify candidate genes for subcutaneous fat deposition in beef cattle

Fat deposition is a complex economic trait regulated by polygenic genetic basis and environmental factors. Therefore, integrating multi-omics data to uncover its internal regulatory mechanism has attracted extensive attention. Here, we performed genomics and transcriptomics analysis to detect candidates affecting subcutaneous fat (SCF) deposition in beef cattle. The association of 770K SNPs with the backfat thickness captured nine significant SNPs within or near 11 genes. Additionally, 13 overlapping genes regarding fat deposition were determined via the analysis of differentially expressed genes and weighted gene co-expression network analysis (WGCNA). We then calculated the correlations of these genes with BFT and constructed their interaction network. Finally, seven biomarkers including ACACA, SCD, FASN, ACOX1, ELOVL5, HACD2, and HSD17B12 were screened. Notably, ACACA, identified by the integration of genomics and transcriptomics, was more likely to exert profound effects on SCF deposition. These findings provided novel insights into the regulation mechanism underlying bovine fat accumulation.

Effect of season on slaughter performance, meat quality, muscle amino acid and fatty acid composition, and metabolism of pheasants (Phasianus colchicus)

This study aimed to investigate the effect of summer and winter on slaughter performance, muscle quality, flavor-related substance content, and gene expression levels related to the fat metabolism of pheasants. One-hundred 1-day-old pheasants were fed for 5 months starting in March and July and then, respectively, slaughtered in summer (August) and winter (December). The results revealed that compared with summer, winter not only increased pheasant live weight, dressed percentage, full-eviscerated yield, and muscle yield (p < 0.05) but also enhanced the activities of SOD and CAT in serum (p < 0.05). Winter significantly increased meat color, the contents of inosinic acid, and flavor amino acid in muscle. Amino acid contents in leg muscles of pheasants in winter were significantly higher than in summer except for histidine (p < 0.05). Winter increased the contents of muscle mono-unsaturated fatty acid, reducing saturated fatty acid. Summer improved fat synthesis in liver, promoted the deposition of triglycerides and cholesterol, and reduced the expression levels of fat metabolism-related genes in muscle, while winter increased the expression levels of genes related to muscle fat metabolism to provide energy for body and affect muscle fatty acid profile. Overall, pheasants fed in winter had better sensory quality and flavor than summer.

A selected population study reveals the biochemical mechanism of intramuscular fat deposition in chicken meat

BACKGROUND

Increasing intramuscular fat (IMF) is an important strategy to improve meat quality, but the regulation mechanism of IMF deposition needs to be systematically clarified.

RESULTS

A total of 520 chickens from a selected line with improved IMF content and a control line were used to investigate the biochemical mechanism of IMF deposition in chickens. The results showed that the increased IMF would improve the flavor and tenderness quality of chicken meat. IMF content was mainly determined both by measuring triglyceride (TG) and phospholipid (PLIP) in muscle tissue, but only TG content was found to be decisive for IMF deposition. Furthermore, the increase in major fatty acid (FA) components in IMF is mainly derived from TGs (including C16:0, C16:1, C18:1n9c, and C18:2n6c, etc.), and the inhibition of certain very-long-chain FAs would help to IMF/TG deposition.

CONCLUSIONS

Our study elucidated the underlying biochemical mechanism of IMF deposition in chicken: Prevalent accumulation of long-chain FAs and inhibitions of medium-chain FAs and very long chain FA would jointly result in the increase of TGs with the FA biosynthesis and cellular uptake ways. Our findings will guide the production of high-quality chicken meat.

Effect of high-concentrate diets on mRNA expression of genes related to muscle fiber type and metabolism of psoas major muscle in goats

In the process of modern breeding, high-concentrate diets are widely used to meet the high energy nutritional requirements of animals but change the form of access to energy and nutrients and the way the organism metabolizes them. Goat psoas major (PM) muscle is a hybrid skeletal muscle whose characteristics are important for the motility and meat quality of goats. However, there are few studies on the effects of high-concentrate diets on the muscle type and metabolic characteristics of PM in goats. In this study, two treatment groups were set up: high concentrate group (HC) and control group (C). The expression of genes related to muscle type and metabolism of the PM was examined by quantitative PCR. The results showed that high concentrate promoted the conversion of PM fibers from intermediate to slow type at the mRNA level, improved the absorption, transport, and oxidation of fat by PM, and upregulated the expression of calpain system. These changes may be regulated by the involvement of differential expression of MSTN, Myf-5, and IGF-2. These results suggest that high concentrate may exert a positive effect on skeletal muscle function, metabolism, and meat quality in goats by affecting the expression of muscle type and metabolism-related genes.

Metagenomic and Transcriptomic Analyses Reveal the Differences and Associations Between the Gut Microbiome and Muscular Genes in Angus and Chinese Simmental Cattle

Gut microbiome and heredity are two important factors affecting the intramuscular fat (IMF) of cattle, excluding age, sex, and nutrition. This study aimed at deciphering these two differences by analyzing the gut microbiome and intramuscular differentially expressed genes (DEGs) in the Angus and Chinese Simmental cattle. Feces and longissimus dorsi were collected from the two groups of animals (n = 20/group) for multiomics analysis. Angus holds a significantly higher diversity than Chinese Simmental, and the relative abundance of Roseburia, Prevotella, Coprococcus, etc., was obviously higher in Angus. Chinese Simmental had higher levels of isobutyrate, isovalerate, and valerate, although similar levels of acetate, propionate, and butyrate were observed for the two groups. The DEGs upregulated in Chinese Simmental were mainly involved in immune and inflammatory responses, while those in Angus were associated with the regulation of muscle system and myofibril. We finally identified 17 species, including Eubacterium rectale, etc., which were positively correlated to muscle and fat metabolism genes (MSTN, MYLPF, TNNT3, and FABP3/4) and illustrate the associations between them. Our study unveils the gut microbial differences and significant DEGs as well as their associations between the two breeds, providing valuable guidance for future mechanism research and development of intervention strategies to improve meat quality.

Differential regulation of intramuscular fat and abdominal fat deposition in chickens

Background

Chicken intramuscular fat (IMF) content is closely related to meat quality and performance, such as tenderness and flavor. Abdominal fat (AF) in chickens is one of the main waste products at slaughter. Excessive AF reduces feed efficiency and carcass quality.

Results

To analyze the differential deposition of IMF and AF in chickens, gene expression profiles in the breast muscle (BM) and AF tissues of 18 animals were analyzed by differential expression analysis and weighted co-expression network analysis. The results showed that IMF deposition in BM was associated with pyruvate and citric acid metabolism through GAPDH, LDHA, GPX1, GBE1, and other genes. In contrast, AF deposition was related to acetyl CoA and glycerol metabolism through FABP1, ELOVL6, SCD, ADIPOQ, and other genes. Carbohydrate metabolism plays an essential role in IMF deposition, and fatty acid and glycerol metabolism regulate AF deposition.

Conclusion

This study elucidated the molecular mechanism governing IMF and AF deposition through crucial genes and signaling pathways and provided a theoretical basis for producing high-quality broilers.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08538-0.

Influences of Thermal Stress During Three Weeks Before Market Age on Histology and Expression of Genes Associated With Adipose Infiltration and Inflammation in Commercial Broilers, Native Chickens, and Crossbreeds

The objectives of this study were to examine the effects of cyclic thermal stress on histological characteristics of breast muscle and gene expression regarding adipose infiltration and inflammation in breast muscles collected from different breeds of chickens. The birds, from commercial broilers (CB, Ross 308, 3 weeks), native (NT, 100% Thai native Chee, 9 weeks), H75 (crossbred; 75% broiler and 25% NT, 5 weeks), and H50 (crossbred; 50% broiler and 50% NT, 7 weeks), were equally assigned into control or treatment groups. The control samples were reared under a constant temperature of 26 ± 1°C, while the treatment groups were exposed to 35 ± 1°C (6 h per day). After a 20-day thermal challenge, 12 male birds per treatment group were randomly collected for determination of live body weight, breast weight, numbers of growth-related myopathies, and breast meat chemical composition. Histological lesions were evaluated in the pectoralis major muscle immediately collected within 20 min postmortem based on hematoxylin and eosin staining. The results indicated that despite interaction between thermal stress and breed effects, thermal challenge significantly reduced feed intake, live body weight, and breast weight of the birds and increased moisture content in breast meat (p < 0.05). An interaction between the two main factors was found for protein content (p < 0.05) for which control CB showed less protein than the other groups. Heat stress decreased histological scores for adipose infiltration in CB (p < 0.05), but it did not significantly influence such scores in the other groups. CB received histological scores for adipose tissue at greater extent than those for the other groups. Differential absolute abundance of CD36, FABP4, LITAF, PDGFRA, PLIN1, PPARG, POSTN, SCD1, and TGFB1 in the muscle samples well-agreed with the trend of histological scores, suggesting potential involvement of dysregulated fibro-adipogenic progenitors together with imbalanced lipid storage and utilization in the breast muscle. The findings demonstrated that the cyclic thermal challenge restricted growth performance and breast mass of the birds, but such effects attenuated infiltration of adipose tissue and inflammatory cells in the CB breast muscle.

Identification of Candidate Genes for Meat Color of Chicken by Combing Selection Signature Analyses and Differentially Expressed Genes

Meat color, an important index of chicken quality, is highly related to heme pigment, glycolysis, and intramuscular fat metabolisms. The objective of this study is to obtain candidate genes associated with meat color in chickens based on the comparison of fast-growing, white-feathered chickens (Line B) and slow-growing, yellow-feathered chickens (Jingxing Yellow), which have significant differences in meat color. The differentially expressed genes (DEGs) between Line B and Jingxing Yellow were identified in beast muscle. The fixation index (F_ST) method was used to detect signatures of positive selection between the two breeds. Screening of 1109 genes by the F_ST and 1317 candidate DEGs identified by RNA-seq. After gene ontology analysis along with the Kyoto Encyclopedia of Genes and Genomes, 16 genes associated with glycolysis, fatty acid metabolism, protein metabolism, and heme content were identified as candidate genes that regulate the color of chicken breast meat, especially TBXAS1 (redness), GDPD5 (yellowness), SLC2A6 (lightness), and MMP27 (lightness). These findings should be helpful for further elucidating the molecular mechanisms and developing molecular markers to facilitate the selection of chicken meat color.

Identification of Diagnostic Biomarkers Associated with Stromal and Immune Cell Infiltration in Fatty Infiltration After Rotator Cuff Tear by Integrating Bioinformatic Analysis and Machine-Learning

Purpose

The present study aimed to explore potential diagnostic biomarkers for fatty infiltration (FI) of the rotator cuff muscles after rotator cuff tear (RCT) and investigate the influence of stromal and immune cell infiltration on this pathology.

Methods

The GSE130447 and GSE103266 datasets were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified, and gene set enrichment analyses were performed by R software. Two machine learning algorithms, random forest and multiple support vector machine recursive feature elimination (mSVM-RFE), were used to screen candidate biomarkers. The diagnostic value of the screened biomarkers was further validated by the area under the ROC curve (AUC) in the GSE103266 dataset. Murine microenvironment cell population counter (mMCP-counter) method was employed to estimate stromal and immune cell infiltration of FI. The correlation between biomarkers and infiltrated immune and stromal cell subsets was further analyzed.

Results

A total of 2123 DEGs were identified. The identified DEGs were predominantly linked to immune system process, extracellular matrix organization and PPAR signalling pathway. FABP5 (AUC = 0.958) and MGP (AUC = 1) were screened as diagnostic biomarkers of FI. Stromal and immune cell infiltration analysis showed that monocytes, mast cells, vessels, endothelial cells and fibroblasts may be related to the process of FI. FABP5 and MGP were positively correlated with vessels whereas negatively correlated with monocytes and mast cells.

Conclusion

FABP5 and MGP can serve as diagnostic biomarkers of FI after RCT, and stromal and immune cell infiltration may play a crucial role in this pathology.

The SLC27A1 Gene and Its Enriched PPAR Pathway Are Involved in the Regulation of Flavor Compound Hexanal Content in Chinese Native Chickens

The role of hexanal in flavor as an indicator of the degree of oxidation of meat products is undeniable. However, the genes and pathways of hexanal formation have not been characterized in detail. In this study, we performed differential gene expression analysis and weighted gene co-expression network analysis (WGCNA) on groups of Tiannong partridge chickens with different relative hexanal content in order to find the genes involved in the formation of hexanal and the specific pathways of hexanal formation. Then we confirmed the relationship of these candidate genes with hexanal using Jingxing Yellow chicken and Wenchang chicken. In this study, WGCNA revealed a module of co-expressed genes that were highly associated with the volatile organic compound hexanal. We also compared transcriptome gene expression data of samples from chicken groups with high and low relative contents of hexanal and identified a total of 651 differentially expressed genes (DEGs). Among them, 356 genes were up regulated, and 295 genes were downregulated. The different biological functions associated with the DEGs, hub genes and hexanal were identified by functional analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations. Among all the hub genes in the significant module identified by WGCNA, more were enriched in the PPAR signaling pathway, the proteasome pathway, etc. Additionally, we found that DEGs and hub genes, including SLC27A1, ACOX3, NR4A1, VEGFA, JUN, EGR1, CACNB1, GADD45A and DUSP1, were co-enriched in the peroxisome proliferator-activated receptor (PPAR) signaling pathway, p53 signaling pathway and mitogen-activated protein kinases (MAPK) signaling pathway, etc. Transcriptome results of the Jingxing Yellow chicken population showed that the SLC27A1 gene was significantly associated with hexanal and enriched in the PPAR pathway. Our study provides a comprehensive insight into the key genes related to hexanal content, and can be further explored by functional and molecular studies.

RNA-Seq reveals the potential molecular mechanisms of bovine KLF6 gene in the regulation of adipogenesis

Marbling influences the taste and tenderness of meat and is the main determinant of carcass quality in many countries. This study aims to investigate the influence of KLF6 (Kruppel Like Factor 6) and associated molecular mechanisms on lipid metabolism in bovine adipocytes. In the current study, KLF6 gene expression was down regulated via siRNA (small interfering RNA) in bovine adipocytes in vitro. Subsequently, adipogenic cells were collected from the culture media after 9 days, and subjected to fluorescent imaging and RNA sequencing. After confirming that KLF6 was down regulated in bovine adipocytes by siRNA, differential gene expression analysis was used to characterize the infuence of KLF6 on gene expression profiles in bovine adipocytes. A total of 10,812 genes were characterized as differentially expressed genes (DEGs) of which, 109 were up-regulated and 62 were down-regulated genes. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis identified that the DEGs were associated with lipid metabolism, carbohydrate metabolism, cell growth and death, cancer, and the signaling pathways for calcium, AMPK (Adenosine Monophosphate-Activated Protein Kinase), PI3K-Akt (Phosphatidylinositol 3-kinase), PPAR (Peroxisome proliferator-activated receptors), MAPK (mitogen-activated protein kinase), cAMP (Cyclic adenosine monophosphate), and Wnt (Wingless-related integration site). Similarly, gene ontology analysis indicated that down-regulation of KLF6 gene significantly up regulated the genes that regulate adipogenesis, differentiation and regulation of adipocytes and homeostasis of bovine adipocytes, specifically regulating the cell-type specific apoptotic action, negative regulation of apoptotic pathways, programmed cell death, and growth. Results indicate that KLF6 has a role in regulating lipid metabolism in bovine adipocytes. These findings provide evidence that may inform further investigations into molecular mechanisms that underlie the role of bovine KLF6 gene in regulating adipogenesis.

Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis

Folliculogenesis is a complex biological process involving a central oocyte and its surrounding somatic cells. Three-dimensional chromatin architecture is an important transcription regulator; however, little is known about its dynamics and role in transcriptional regulation of granulosa cells during chicken folliculogenesis. We investigate the transcriptomic dynamics of chicken granulosa cells over ten follicular stages and assess the chromatin architecture dynamics and how it influences gene expression in granulosa cells at three key stages: the prehierarchical small white follicles, the first largest preovulatory follicles, and the postovulatory follicles. Our results demonstrate the consistency between the global reprogramming of chromatin architecture and the transcriptomic divergence during folliculogenesis, providing ample evidence for compartmentalization rearrangement, variable organization of topologically associating domains, and rewiring of the long-range interaction between promoter and enhancers. These results provide key insights into avian reproductive biology and provide a foundational dataset for the future in-depth functional characterization of granulosa cells.

The domestic chicken Gallus gallus domesticus is a classic model for the study of folliculogenesis. Here the authors integrate multi-omics analyses characterizing the dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis.

Single-Cell Transcriptome Profiling Reveals Multicellular Ecosystem of Nucleus Pulposus during Degeneration Progression

Although degeneration of the nucleus pulposus (NP) is a major contributor to intervertebral disc degeneration (IVDD) and low back pain, the underlying molecular complexity and cellular heterogeneity remain poorly understood. Here, a comprehensive single-cell resolution transcript landscape of human NP is reported. Six novel human NP cells (NPCs) populations are identified by their distinct molecular signatures. The potential functional differences among NPC subpopulations are analyzed. Predictive transcripts, transcriptional factors, and signal pathways with respect to degeneration grades are explored. It is reported that fibroNPCs is the subpopulation for end-stage degeneration. CD90+NPCs are observed to be progenitor cells in degenerative NP tissues. NP-infiltrating immune cells comprise a previously unrecognized diversity of cell types, including granulocytic myeloid-derived suppressor cells (G-MDSCs). Integrin αM (CD11b) and oxidized low density lipoprotein receptor 1 (OLR1) as surface markers of NP-derived G-MDSCs are uncovered. The G-MDSCs are found to be enriched in mildly degenerated (grade II and III) NP tissues compared to severely degenerated (grade IV and V) NP tissues. Their immunosuppressive function and alleviation effects on NPCs' matrix degradation are revealed in vitro. Collectively, this study reveals the NPC-type complexity and phenotypic characteristics in NP, thereby providing new insights and clues for IVDD treatment.

Large-Scale Whole Genome Sequencing Study Reveals Genetic Architecture and Key Variants for Breast Muscle Weight in Native Chickens

Breast muscle weight (BrW) is one of the most important economic traits in chicken, and directional breeding for that results in both phenotypic and genetic changes. The Jingxing yellow chicken, including an original (without human-driven selection) line and a selected line (based on selection for increased intramuscular fat content), were used to dissect the genetic architecture and key variants associated with BrW. We detected 1069 high-impact single nucleotide polymorphisms (SNPs) with high conserved score and significant frequency difference between two lines. Based on the annotation result, the ECM-receptor interaction and fatty acid biosynthesis were enriched, and muscle-related genes, including MYOD1, were detected. By performing genome-wide association study for the BrW trait, we defined a major haplotype and two conserved SNPs that affected BrW. By integrated genomic and transcriptomic analysis, IGF2BP1 was identified as the crucial gene associated with BrW. In conclusion, these results offer a new insight into chicken directional selection and provide target genetic markers by which to improve chicken BrW.

Transcriptomics analysis of Daheng broilers reveals that PLIN2 regulates chicken preadipocyte proliferation, differentiation and apoptosis

BACKGROUND

Intramuscular fat content, an important meat quality trait, strongly affects flavor, juiciness, and tenderness. Sex hormones regulate lipid metabolism, and female hormones stimulate fat deposition, thereby making the female chickens always fatter than males. In this study, the effect of sex on IMF deposition was screened following transcriptomics in chickens.

METHODS AND RESULTS

Results confirmed significantly higher IMF content of 150-day female chickens as compared to the male chickens. The female chickens manifested higher serum TG, LDL-C, and VLDL, and significantly lower HDL-C contents than male chickens. Moreover, differential expression of genes involved in lipid metabolism were obtained in the muscle and liver between female and male chicken, which could partly interpret the possible reasons for the sex-mediated differences of IMF content. Cellular results revealed that inhibition of PLIN2 significantly inhibited chicken preadipocyte proliferation and induces apoptosis of preadipocytes, as well as promoted adipocyte differentiation.

CONCLUSIONS

According to our results, PLIN2 may be considered as a molecular marker for poultry meat quality and applying this gene in early breed selection.

Changes of Metabolites and Gene Expression under Different Feeding Systems Associated with Lipid Metabolism in Lamb Meat

The effects of the different feeding systems, graze feeding (GSF), time-limited graze feeding (GF), and stall-feeding (SF)) on the fatty acid content, metabolites, and genes expression of the longissimus dorsi (LD) in Tan lambs were investigated in the present study. Thirty-nine 4-month-old male Tan lambs with similar body weight (24.91 ± 1.74 kg) were selected and divided into the three feeding systems (n = 13) randomly. Lambs were slaughtered after 83 days of the feeding trails, and LD muscle samples were collected for further analysis. The results indicated that different feeding systems have no significant effect on short-chain fatty acids in Tan lambs (p > 0.05). However, the total saturated fatty acids (∑SFA) and monounsaturated fatty acids (∑MUFA) in the GSF and GF groups were lower than those in the SF group (p < 0.001). The total polyunsaturated fatty acids (∑PUFA) in the GSF group were higher than those in the GF and SF groups (p < 0.001). Moreover, in the comparison of both GF vs GSF groups and SF vs GSF groups, metabolomic analysis showed that metabolites such as cis-(6,9,12)-linolenic acid, arachidic acid, acetylcarnitine, and L-carnitine with lower concentration were significantly enriched in the biosynthesis of unsaturated fatty acid pathway (p < 0.05), but metabolites such as phosphorylcholine, glycerophosphocholine, cytidine 5'-diphosphocholine, and glycerol-3-phosphate with higher concentrations were enriched in the glycerophospholipid metabolism pathway. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis of the results indicated that in the comparison of the GSF group with the SF group, differentially expressed genes (DEGs) such as LIPC, ERFE, FABP3, PLA2R1, LDLR, and SLC10A6, were enriched in the steroid biosynthesis and cholesterol metabolism pathways. In addition, differential metabolites and genes showed a significant correlation with the content of ∑SFA, ∑MUFA, and ∑PUFA in lamb meat (p < 0.05). These findings demonstrated that the feeding system was an important factor in regulating fatty acid content by affecting lipid-metabolism-related metabolites and gene expression in muscle, and graze-feeding system provided lamb meat with higher ∑PUFA content than time-limited-grazing and stall-feeding systems.

Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

Comparison of genomic footprints in chicken breeds with different selection history is a powerful tool in elucidating genomic regions that have been targeted by recent and more ancient selection. In the present work, we aimed at examining and comparing the trajectories of artificial selection in the genomes of the native egg-type Russian White (RW) and meat-type White Cornish (WC) breeds. Combining three different statistics (top 0.1% SNP by F_ST value at pairwise breed comparison, hapFLK analysis, and identification of ROH island shared by more than 50% of individuals), we detected 45 genomic regions under putative selection including 11 selective sweep regions, which were detected by at least two different methods. Four of such regions were breed-specific for each of RW breed (on GGA1, GGA5, GGA8, and GGA9) and WC breed (on GGA1, GGA5, GGA8, and GGA28), while three remaining regions on GGA2 (two sweeps) and GGA3 were common for both breeds. Most of identified genomic regions overlapped with known QTLs and/or candidate genes including those for body temperatures, egg productivity, and feed intake in RW chickens and those for growth, meat and carcass traits, and feed efficiency in WC chickens. These findings were concordant with the breed origin and history of their artificial selection. We determined a set of 188 prioritized candidate genes retrieved from the 11 overlapped regions of putative selection and reviewed their functions relative to phenotypic traits of interest in the two breeds. One of the RW-specific sweep regions harbored the known domestication gene, TSHR. Gene ontology and functional annotation analysis provided additional insight into a functional coherence of genes in the sweep regions. We also showed a greater candidate gene richness on microchromosomes relative to macrochromosomes in these genomic areas. Our results on the selection history of RW and WC chickens and their key candidate genes under selection serve as a profound information for further conservation of their genomic diversity and efficient breeding.

Detection of selection signatures in the genome of a farmed population of anadromous rainbow trout (Oncorhynchus mykiss)

Domestication processes and artificial selection are likely to leave signatures that can be detected at a molecular level in farmed rainbow trout (Oncorhynchus mykiss). These signatures of selection are genomic regions that contain functional genetic variants conferring a higher fitness to their bearers. We genotyped 749 rainbow trout from a commercial population using a rainbow trout Axiom 57 K SNP array panel and identified putative genomic regions under selection using the pcadapt, Composite Likelihood Ratio (CLR) and Integrated Haplotype Score (iHS) methods. After applying quality-control pipelines and statistical analyses, we detected 12, 96 and 16 SNPs putatively under selection, associated with 96, 781 and 115 candidate genes, respectively. Several of these candidate genes were associated with growth, early development, reproduction, behavior and immune system traits. In addition, some of the SNPs were found in interesting regions located in autosomal inversions on Omy05 and Omy20. These findings could represent a genome-wide map of selection signatures in farmed rainbow trout and could be important in explaining domestication and selection for genetic traits of commercial interest.

Large-scale transcriptome sequencing in broiler chickens to identify candidate genes for breast muscle weight and intramuscular fat content

BACKGROUND

In broiler production, breast muscle weight and intramuscular fat (IMF) content are important economic traits. Understanding the genetic mechanisms that underlie these traits is essential to implement effective genetic improvement programs. To date, genome-wide association studies (GWAS) and gene expression analyses have been performed to identify candidate genes for these traits. However, GWAS mainly detect associations at the DNA level, while differential expression analyses usually have low power because they are typically based on small sample sizes. To detect candidate genes for breast muscle weight and IMF contents (intramuscular fat percentage and relative content of triglycerides, cholesterol, and phospholipids), we performed association analyses based on breast muscle transcriptomic data on approximately 400 Tiannong partridge chickens at slaughter age.

RESULTS

First, by performing an extensive simulation study, we evaluated the statistical properties of association analyses of gene expression levels and traits based on the linear mixed model (LMM) and three regularized linear regression models, i.e., least absolute shrinkage and selection operator (LASSO), ridge regression (RR), and elastic net (EN). The results show that LMM, LASSO and EN with tuning parameters that are determined based on the one standard error rule exhibited the lowest type I error rates. Using results from all three models, we detected 43 candidate genes with expression levels that were associated with breast muscle weight. In addition, candidate genes were detected for intramuscular fat percentage (1), triglyceride content (2), cholesterol content (1), and phospholipid content (1). Many of the identified genes have been demonstrated to play roles in the development and metabolism of skeletal muscle or adipocyte. Moreover, weighted gene co-expression network analyses revealed that many candidate genes were harbored by gene co-expression modules, which were also significantly correlated with the traits of interest. The results of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that these modules are involved in muscle development and contraction, and in lipid metabolism.

CONCLUSIONS

Our study provides valuable insight into the transcriptomic bases of breast muscle weight and IMF contents in Chinese indigenous yellow broilers. Our findings could be useful for the genetic improvement of these traits in broiler chickens.

Differential Expression of Myogenic and Calcium Signaling-Related Genes in Broilers Affected With White Striping

White Striping (WS) has been one of the main issues in poultry production in the last years since it affects meat quality. Studies have been conducted to understand WS and other myopathies in chickens, and some biological pathways have been associated to the prevalence of these conditions, such as extracellular calcium level, oxidative stress, localized hypoxia, possible fiber-type switching, and cellular repairing. Therefore, to understand the genetic mechanisms involved in WS, 15 functional candidate genes were chosen to be analyzed by quantitative PCR (qPCR) in breast muscle of normal and WS-affected chickens. To this, the pectoral major muscle (PMM) of 16 normal and 16 WS-affected broilers were collected at 42 days of age and submitted to qRT-PCR analysis. Out of the 15 genes studied, six were differentially expressed between groups. The CA2, CSRP3, and PLIN1 were upregulated, while CALM2, DNASE1L3, and MYLK2 genes were downregulated in the WS-affected when compared to the normal broilers. These findings highlight that the disruption on muscle and calcium signaling pathways can possibly be triggering WS in chickens. Improving our understanding on the genetic basis involved with this myopathy might contribute for reducing WS in poultry production.

FOSL2 Is Involved in the Regulation of Glycogen Content in Chicken Breast Muscle Tissue

The glycogen content in muscle of livestock and poultry animals affects the homeostasis of their body, growth performance, and meat quality after slaughter. FOS-like 2, AP-1 transcription factor subunit (FOSL2) was identified as a candidate gene related to muscle glycogen (MG) content in chicken in our previous study, but the role of FOSL2 in the regulation of MG content remains to be elucidated. Differential gene expression analysis and weighted gene coexpression network analysis (WGCNA) were performed on differentially expressed genes (DEGs) in breast muscle tissues from the high-MG-content (HMG) group and low-MG-content (LMG) group of Jingxing yellow chickens. Analysis of the 1,171 DEGs (LMG vs. HMG) identified, besides FOSL2, some additional genes related to MG metabolism pathway, namely PRKAG3, CEBPB, FOXO1, AMPK, and PIK3CB. Additionally, WGCNA revealed that FOSL2, CEBPB, MAP3K14, SLC2A14, PPP2CA, SLC38A2, PPP2R5E, and other genes related to the classical glycogen metabolism in the same coexpressed module are associated with MG content. Also, besides finding that FOSL2 expression is negatively correlated with MG content, a possible interaction between FOSL2 and CEBPB was predicted using the STRING (Search Tool for the Retrieval of Interacting Genes) database. Furthermore, we investigated the effects of lentiviral overexpression of FOSL2 on the regulation of the glycogen content in vitro, and the result indicated that FOSL2 decreases the glycogen content in DF1 cells. Collectively, our results confirm that FOSL2 has a key role in the regulation of the MG content in chicken. This finding is helpful to understand the mechanism of MG metabolism regulation in chicken and provides a new perspective for the production of high-quality broiler and the development of a comprehensive nutritional control strategy.