Integrating metabolomic and transcriptomic to reveal the dynamics of ntramuscular fat in chicken meat
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ABSTRACT:
ORGANISM(S): Gallus gallus
PROVIDER: GSE294245 | GEO | 2025/07/16
REPOSITORIES: GEO
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Project description:As an essential micronutrient for animals, vitamin E plays crucial physiological roles in reproduction, antioxidant and immune functions, and lipid metabolism. The objective of this study was to reveal molecular mechanism of vitamin E on intramuscular fat (IMF) deposition through transcriptome sequencing of pectoral muscle in broiler chickens. A total of 240 one-day-old health female chicks were randomly allocated into five dietary treatments with each treatment six replicates. The birds were fed basal diet supplemented with 0 and 100 IU/kg vitamin E in the form of DL-α-tocopheryl acetate, respectively. The body weight, carcass performance and IMF content were measured. Transcriptome profile of pectoral muscle in 35-day-old chickens were sequencing from the control and 100 IU/kg vitamin E treatment. Functional enrichment analyzes of differentially expressed genes (DEGs) based on Gene ontology (GO), KEGG pathway and bio function, and network were performed. Results shown that IMF content of broiler chickens were significantly increased at 12.89% (P < 0.05) between 100 IU/kg vitamin E treatment and control. Transcriptome sequencing results for pectoralis major muscle of 100 IU vitamin E-supplemented and the control groups identified 57 up-regulated and 102 down-regulated DEGs. These DEGs were significantly enriched (FDR corrected P-value < 0.05) in 13 of 236 GO terms involved in muscle development- and lipid metabolism. Pathway functional enrichment analysis revealed that the DEGs were significantly enriched in three signalling pathways (FDR corrected P-value < 0.05). Two of them, MAPK signaling pathway and FoxO signaling pathway, play key roles in muscular and lipid metabolism. It is worth mentioning that 46 DEGs were significantly enriched in 28 skeletal and muscular system development and function categories and 31 DEGs were significantly enriched in 17 lipid metabolism function categories. Moreover, three lipid metabolism and muscular development-related networks of DEGs were also identified. These DEGEs, pathways, function categories and networks identified in this study provide us new insights for the vitamin E regulation of the IMF deposition in broiler chickens.
2021-07-08 | GSE179569 | GEO
Project description:Intramuscular fat (IMF) content is one of the key factors affecting meat quality. Carbohydrate response element binding protein (ChREBP) can promote glucose metabolism and fat synthesis by activating the expression of glycolysis and lipogenesis-related genes, but its function and regulatory mechanism in IMF are still unclear. This study evaluated the correlation between TG content and ChREBP expression level in muscles of different species to reveal the relationship between ChREBP and IMF. RNA-seq analysis showed that overexpressing ChREBP in C2C12 cells can significantly up-regulate fatty acid synthesis pathways, while significantly down-regulate the expression levels of muscle development pathways and related genes. In vivo, we found that overexpression of ChREBP or activation by fructose significantly increased the triglyceride content of the tibialis anterior muscle (TA) and the IMF content of yellow feather chicken leg and breast muscle in mice. And lipidomics data also found that feeding fructose can change the lipid composition of yellow feather broiler breast muscle and improve the flavor substances. This study demonstrated that ChREBP is a key gene regulating IMF deposition, providing a new target for genetic selection and nutritional regulation of IMF content.
2024-08-08 | GSE228899 | GEO
Project description:Purpose: The goals of this study are to investigate the differentially expressed genes between High IMF chickens (WC) and Low IMF chickens (WRR) breast muscles by Illumina deep sequencing, to reveal the mechanism underlying chicken IMF deposition. Methods: Both WC chickens and WRR chickens were raised up to 120 d of age (D120) or 180 d of age (D180), two female birds of similar weight from each breed per age were subjected to RNA-sequencing by Illumina Hiseq 2000. So eight muscle samples in total were subjected to RNA-seq analysis, four WC chicken samples including WC.D120.B-1, WC.D120.B-3, WC.D180.B-2 and WC.D180.B-3, and four WRR chicken samples including WRR.D120.B-4, WRR.D120.B-6, WRR.D180.B-2 and WRR.D180.B-5. Results: The clean reads of each sample were over 20 million, the expressed genes ranged from 16202 to 17838, and a little higher in WRR samples than in WC samples. Differentially expresse analysis showed that there were 525, 161, 23, 87 DEGs detected in the comparisons of WRR.D120.B-VS-WC.D120.B, WRR.D180.B-VS-WC.D180.B, WC.D120.B-VS-WC.D180.B and WRR.D120.B-VS-WRR.D180.B, respectively. Many genes related to lipid catabolism were down-regulated in WC chickens. Conclusions: Our present study suggest that lower lipid catabolism exists in WC chickens but not in WRR chickens, and lower expression of SLC27A1 is through down-regulating fatty acid oxidation mediated by CPT1A to facilitate IMF deposition. Moreover, these findings indicate that reduced lipid catabolism, rather than increased lipid anabolism, contributes to chicken IMF deposition.
2016-09-15 | GSE86920 | GEO
Project description:Optimization of broiler chicken breast muscle protein accretion is key for the efficient production of poultry meat, whose demand is steadily increasing. In a context where antimicrobial growth promoters use is being restricted, it is important to find alternatives as well as to characterize the effect of immunological stress on broiler chicken growth. Despite of its importance, research on broiler chicken muscle protein dynamics has been mostly limited to the study of mixed protein turnover. The present study aims to characterize the effect of a bacterial challenge and the feed supplementation of a citrus and a cucumber extract on broiler chicken individual breast muscle proteins fractional synthesis rates (FSR) using a recently developed dynamic proteomics pipeline. 21 day-old broiler chickens were administered a single 2H2O dose before being culled at different timepoints. A total of 60 breast muscle protein extracts from five experimental groups (Unchallenged, Challenged, Control Diet, Diet 1 and Diet 2) were analyzed using a DDA proteomics approach. Proteomics data was filtered in order to reliably calculate multiple proteins FSR making use of a newly developed bioinformatics pipeline. Broiler breast muscle proteins FSR uniformly decreased following a bacterial challenge, this change was judged significant for 15 individual proteins, the two major functional clusters identified as well as for mixed breast muscle protein. Citrus or cucumber extract feed supplementation did not show any effect on the breast muscle protein FSR of immunologically challenged broilers. The present study has identified potential predictive markers of breast muscle growth and provided new information on broiler chicken breast muscle protein turnover which could be essential for improving the efficiency of broiler chicken meat production.
2024-04-04 | PXD044325 | Pride
Project description:Studies exploring the transcriptome of stress and its effects on meat quality are very limited, particularly in goats. Fifty-four male Spanish goats (8-mo old; BW = 29.7 ± 2.03 kg) were randomly subjected to one of three treatments (TRT; n = 18 goats / treatment): (i) transported for 180 min, (ii) transported for 30 min, or (iii) held in pens (control) to analyze the transcriptome of stress and meat quality in goats using RNA-seq technology. Blood samples were collected before and after treatment, and meat samples were collected after humane slaughter for stress hormone, meat quality (Longissimus dorsi), and transcriptomic analysis. Plasma epinephrine concentrations were higher (P < 0.01) in 180 min and 30 min groups compared to the control group; however, norepinephrine concentrations were not affected by the treatment. Muscle glycogen concentrations (15 min postmortem) were lower (P < 0.01) in both 30 min and 180 min groups compared to the control group. Calpastatin levels were higher (P < 0.01) in 180 min and 30 min groups than the control group. Warner-Bratzler shear force values of loin chops were the highest in the 180 min group (4 ± 0.15, kg), lowest in the control group (3.51 ± 0.10, kg), and intermediate in the 30 min group (3.78 ± 0.09, kg; P < 0.01) both at day 1 and day 6 aging time. Additionally, desmin levels of day 6 samples were lowest in the control group, highest in 180 min group, and intermediate in 30 min group (P < 0.05). RNA-seq results showed that a total of 10,633 genes were differentially expressed (5,194 up regulated; 5,439 down regulated) among all comparisons (blood and day 1 and day 6 muscle samples). Among these differentially expressed genes (DEGs), KLF9, AMPK, FOXO3, PTX3, GADD45, PTPN1, CASP7, MAPK4, HSPA12A, and JAK-STAT were probably associated with the effects of stress on skeletal muscle proteins and involved in biological process such as cellular response to corticosteroid stimulus, endoplasmic reticulum stress, insulin resistance, DNA repair, apoptosis, MAPK cascade and regulation of proteolysis. The KEGG analysis revealed that AMPK and JAK-SAT signaling pathways and autophagy were among the top 20 enriched pathways in our treatment comparisons. The results provide an understanding of the genes and pathways involved in stress responses and related changes in postmortem muscle metabolism and meat quality characteristics in goats.
2022-08-14 | GSE210823 | GEO
Project description:Abstract: Ammonia is one of the most prominent air pollutants in poultry houses. High levels of ammonia have adverse effects on respiratory health, growth performance, meat production of broilers, and breast meat growth and yield are critical important in the broiler industry. To date, studies focus on the negative relationship of ammonia exposure and breast muscle tissue are still very limited, and the underlying molecular mechanisms remain poorly understood. In this study, high concentrations of atmospheric ammonia were found to lower slaughter rate and broiler breast meat yield significantly (P < 0.05). To explore the candidate genes that ammonia regulates breast meat yield of broilers, high throughout RNA-Seq was used to compare the transcriptome of breast muscle with different ammonia exposure (50 ppm vs 3 ppm). In total, 129 differentially expressed genes (DEGs) were identified (P-value < 0.05; fold-change ≥ 2), among which 87 genes were significantly down-regulated and 42 were up-regulated. Bioinformatics analysis suggested that DEGs (such as PDK4, ACSL1, GLUL, FBXO32) were involved in fatty acid degradation/metabolism, nitrogen metabolism, PPAR signaling and adipocytokine signaling pathways. Functional annotation showed that DEGs were mainly enriched in reactive oxygen species metabolic process and muscle contraction. It can be concluded that decreased meat yield was due to the DEGs participating in above biological processes and pathways. This study provides novel insights into transcriptional differences in breast meat between high- and low-ammonia exposed broiler chickens.
2017-10-14 | GSE104941 | GEO
Project description:Chronological age is one of the important factors influencing muscle development and meat quality in chickens. To evaluate the protein expression profiles during skeletal muscle development, we performed a tandem mass tag (TMT)-based quantitative proteomic strategy in pectoralis major (breast muscle) of Beijing-You chicken (BYC) at the age of 90, 120 and 150 days. A total of 1,413 proteins in chicken breast muscle and 197 of them were differentially expressed (fold change ≥ 1.2 or ≤ 0.8333 and p < 0.05). There were 110 up- and 71 down-regulated proteins in 120 d vs. 90 d group, 13 up- and 10 down-regulated proteins in 150 d vs. 120 d group. The proteomic profiles of BYC at 120 d were very similar to those at 150 d and highly different from those at 90 d, suggesting that 120 d might be an important chronological age for BYC. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that these differentially expressed proteins were mainly involved in the pathway of glycolysis/gluconeogenesis, adrenergic signaling in cardiomyocytes, focal adhesion, oocyte meiosis and phagosome. Protein expression analysis indicated that the differences in muscle growth rate between ages were regulated by proteins such as LDHA and ENO3, whereas ATP2A1 and HSP70 were associated with water-holding capacity (WHC), and PPP1CB and COL1A2 were suggested to lie in the role of intramuscular fat (IMF) deposition. In addition, RACK1 was thought to be crucial for the sexual maturation during chicken development. Furthermore, some DEPs were quantified using parallel reaction monitoring (PRM) to validate the results from TMT analysis. Overall, the present work could strengthen our view of the temporal expression profile during development and identify novel biomarkers for genetic breeding of chickens.
2021-09-10 | PXD023871 | Pride
Project description:The experiment aimed at studying gene expression differences in longissimus dorsi muscle from pigs from two groups: High versus low intramuscular fat (IMF). The animals were selected from a crossbred population of Landrace x Yorkshire/Landrace x Duroc animals, where we have previously found a highly significant QTL for IMF (Grindflek et al. 2001: "Detection of quantitative trait loci for meat quality in a commercial slaughter pig cross", Mammalian Genome 12(4): 299-304), and by microarray analysis we hoped to identify candidate genes for the QTL and/or pathways that are affected by the genes responsible for the QTL. Keywords: phenotype comparison Direct dye-swap design, with 14 animals in each group (high IMF and low IMF) on 14 separate arrays
2013-01-01 | E-GEOD-12927 | biostudies-arrayexpress
Project description:Intramuscular fat (IMF) storage is a biological process with strong impact on nutritional and technological properties of meat, and also with relevant consequences on human health. The genetic architecture of IMF content and composition phenotypes has been thoroughly studied in pigs through the identification of quantitative trait loci (QTL) and the estimation of genetic parameters. A question that has not been elucidated yet is if the genetic determinants of IMF-related phenotypes are muscle specific or, conversely, they have broad effects on the whole skeletal muscle compartment. We have addressed this question by generating lipid QTL maps for two muscles with a high commercial value, gluteus medius (GM) and longissimus thoracis et lumborum (LTL), in a Duroc commercial population (N=350). As a complementary approach, we have analysed the mRNA expression pattern of both muscles at a whole genome scale. The lack of concordance between the GM and LTL QTL maps evidenced that the effects of polymorphisms influencing IMF, cholesterol and fatty acids contents are modulated to some extent by complex spatial factors related with muscle location, metabolism and function. This interpretation was supported by our finding that genes influencing cell differentiation, muscle development and function and lipid metabolism are differentially expressed between muscles. These results have important implications on the implementation of genomic selection schemes aimed to improve the lipid profile of swine meat. Moreover, they confirm pigs as a valuable model to dissect the genetic basis of muscle lipid phenotypes of clinical interest in human. Longissimus thoracis et lumborum muscle tissue from 10 high and 9 low fattening Duroc pigs were compared in this study.
2010-12-01 | E-GEOD-25708 | biostudies-arrayexpress
Project description:Background: Intramuscular fat (IMF) content is highly valued as it improves meat product quality by enhancing taste, juiciness, and tenderness. IMF content can be significantly different between breeds. Thought many lipid metabolism-related genes are stated to be associated with IMF deposition, the molecular mechanism of IMF deposition is still poorly understood. To date, no gene or mutation loci responsible for the difference of IMF content among cattle breeds has been identified. To identify transcripts with potential regulatory role in lipid accumulated in muscle tissue, RNA sequencing was performed to compare the mRNAs, lncRNAs, and circRNAs expression patterns in the longissimus dorsi muscle and back fat between Chinese buffalo and cattle. Results: A total of 12 cDNA libraries were constructed. A total of 925,441,106 and 512,507,068 raw reads were obtained from buffalo and cattle, respectively. After filtering the adaptor and low quality reads, 909,040,352 and 491,967,820 clean reads were retained. In total, 19,917 mRNAs, 43,975 lncRNAs, and 10,701 circRNAs were identified in buffalo and 19,383 mRNAs, 8,265 lncRNAs, and 18,535 circRNAs were identified in cattle.
2020-10-20 | GSE139102 | GEO