Gene expression profile analysis of Fat and Lean chickens
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ABSTRACT:
ORGANISM(S): Gallus gallus
PROVIDER: GSE17445 | GEO | 2009/08/04
SECONDARY ACCESSION(S): PRJNA118869
REPOSITORIES: GEO
Similar Datasets
Project description:The aim of this study was to identify genes involved in the variation of the muscle glycogen content at death (estimated through the glycolytic potential, GP), a determining factor of meat quality in chicken. Gene expression profiles of Pectoralis major muscle were established using microarrays. We compared Fat and Lean chickens issued from two lines divergently selected for abdominal fatness and also differed for muscle GP. A total of 197 genes were differentially expressed between Fat and Lean pure chickens. Several of these genes were validated by qRT-PCR. For the genes with human orthologs, annotation analyses were performed and mainly revealed pathways involved carbohydrate, fatty-acid, and protein metabolism. The relationship between gene expression and meat quality has to now be validated by further e-QTL studies on the F2 population. 8 samples from Fat chickens were compared to 8 samples from Lean chickens, 4 of these were dye-swapped.
2010-06-24 | E-GEOD-17445 | biostudies-arrayexpress
Project description:The aim of this study was to identify genes involved in the variation of the muscle glycogen content at death (estimated through the glycolytic potential, GP), a determining factor in the meat quality of chicken. The gene expression profiles of the Pectoralis major muscle were established using microarrays. We compared animals showing extreme GP values, issued from a F2 cross between Fat and Lean lines. A total of 254 genes were differentially expressed between F2 birds with low or high GP. Several of these genes were validated by qRT-PCR. For the genes with human orthologs, annotation analyses were performed and mainly revealed pathways involved in carbohydrate, fatty-acid and protein metabolism. The relationship between gene expression and meat quality has to now be validated by further e-QTL studies on the F2 population. 8 high GP samples compared to 8 low GP samples, 4 of these were dye-swapped.
2010-06-24 | E-GEOD-17428 | biostudies-arrayexpress
Project description:The aim of this study was to identify genes involved in the variation of the muscle glycogen content at death (estimated through the glycolytic potential, GP), a determining factor in the meat quality of chicken. The gene expression profiles of the Pectoralis major muscle were established using microarrays. We compared animals showing extreme GP values, issued from a F2 cross between Fat and Lean lines. A total of 254 genes were differentially expressed between F2 birds with low or high GP. Several of these genes were validated by qRT-PCR. For the genes with human orthologs, annotation analyses were performed and mainly revealed pathways involved in carbohydrate, fatty-acid and protein metabolism. The relationship between gene expression and meat quality has to now be validated by further e-QTL studies on the F2 population.
2009-08-04 | GSE17428 | GEO
Project description:Chickens divergently selected for either high abdominal fat content (fat genotype) or low abdominal fat content (lean genotype) at Station Recherches Avicoles, Institut National de la Recherche Agronomique Nouzilly, France were used to profile abdominal fat gene expression at 7 weeks of age. The fat line (FL) and lean line (LL) chickens differ in various phenotypic and metabolic measurements, including abdominal fatness, plasma glycemia and triiodothyronine (T3). The FL and LL chickens represent unique models for characterizing biomedical and agricultural traits. Massively parallel RNA sequencing (RNA-Seq) was completed on an Illumina HiSeq 2000 System for transcription analysis of FL and LL abdominal fat. Statistical analysis was completed using CLC Genomics Workbench software. A total of 1,703 genes were differentially expressed in the FL versus LL adipose tissue [FDR<0.05 and fold change (FL/LL) > 1.2]. The differentially expressed genes include metabolic enzymes, acute phase proteins, growth factors, coagulation factors, immune factors, vasoregulators and transcription factors involved in various pathways. Several of the functional genes identified are also positional candidate genes within quantitative trait loci (QTL) in an F2 population created from an intercross of the FL and LL lines. Keywords: Divergently selected chickens, fatness, transcriptional profiling, differentially expressed genes Abdominal fat mRNA profiles of fat line (FL) and lean line (LL) chickens at 7 weeks of age were generated by deep sequencing (on an Illumina HiSeq 2000 system) employing several sequencing schemes to determine depth of coverage from 1, 4, and 8 multiplexed libraries per sequencing lane. Transcriptional analysis was completed by averaging short paired-end sequence reads (101 bp) for each bird across three sequencing depths.
2013-04-16 | E-GEOD-42980 | biostudies-arrayexpress
Project description:Chickens divergently selected for either high abdominal fat content (fat genotype) or low abdominal fat content (lean genotype) at Station Recherches Avicoles, Institut National de la Recherche Agronomique Nouzilly, France were used to profile abdominal fat gene expression at 7 weeks of age. The fat line (FL) and lean line (LL) chickens differ in various phenotypic and metabolic measurements, including abdominal fatness, plasma glycemia and triiodothyronine (T3). The FL and LL chickens represent unique models for characterizing biomedical and agricultural traits. Massively parallel RNA sequencing (RNA-Seq) was completed on an Illumina HiSeq 2000 System for transcription analysis of FL and LL abdominal fat. Statistical analysis was completed using CLC Genomics Workbench software. A total of 1,703 genes were differentially expressed in the FL versus LL adipose tissue [FDR<0.05 and fold change (FL/LL) > 1.2]. The differentially expressed genes include metabolic enzymes, acute phase proteins, growth factors, coagulation factors, immune factors, vasoregulators and transcription factors involved in various pathways. Several of the functional genes identified are also positional candidate genes within quantitative trait loci (QTL) in an F2 population created from an intercross of the FL and LL lines. Keywords: Divergently selected chickens, fatness, transcriptional profiling, differentially expressed genes
2013-04-16 | GSE42980 | GEO
Project description:Chickens divergently selected for either high abdominal fat content (fat genotype) or low abdominal fat content (lean genotype) at SRA-INRA, France were used to profile hepatic gene expression during juvenile development (1 to 11 weeks of age) and to identify differentially expressed genes associated with genotype and age. The fat line (FL) and lean line (LL) chickens are different in various phenotypic and metabolic measurements, including abdominal fatness, plasma glycemia and T3. The FL and LL chickens represent unique models for characterizing biomedical and agricultural traits. The Del-Mar 14K Chicken Integrated Systems microarrays were used for a transcriptional scan in liver during juvenile development using a balanced block hybridization design. Log2-transformed fluorescence intensities were analyzed with a two-stage mixed model. A total of 905 differentially expressed "functional" genes were identified (FDR<0.10). The greatest number of differentially expressed genes (400) was detected at 7 weeks of age. The differentially expressed genes include metabolic enzymes, acute phase proteins, growth factors, immune factors and transcription factors involved in various pathways. Several of the functional genes are also identified as positional candidate genes within QTLs in an F2 population established from an intercross between the FL and LL lines. Keywords: Divergently selected chickens, fatness, transcriptional profiling, differentially expressed genes
2007-09-01 | GSE8812 | GEO
Project description:Western commercial pig breeds have been intensively selected, resulting in a sizeable, rapid, and efficient accretion of muscle but a reduction in meat quality. When compared with Western commercial pig breeds, Chinese indigenous pig breeds exhibited slower growth rates and reduced lean meat content but superior perceived meat quality. To study the factors that determine meat quality, we examined piglets of one Western commercial breed (Yorkshire) and one Chinese indigenous breed (Wannanhua) and sequenced the longissimus dorsi muscle using RNA-sequencing (RNA-seq). We analyzed their transcriptomes, focusing on identifying candidate genes that may influence porcine muscle growth, meat quality and adipose deposition. Gene ontology functional enrichment and pathway enrichment analyses identified differentially expressed genes primarily associated with glycolytic metabolism, biological processes of muscle development and signaling pathways related to fatty acid metabolism, growth and carcass traits. This finding suggests that the differentially expressed genes may play important roles in determining meat quality traits. Quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) confirmed the differential expression of twelve selected differentially expressed genes. This study identified a number of novel candidate genes for porcine meat quality and carcass traits that merit further investigation to elucidate the molecular mechanisms responsible for muscle growth and fat deposition.
2015-11-30 | GSE75045 | 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:Wooden Breast (WB) is a novel myopathy affecting the pectoralis major muscle of modern broiler chickens. We selected pectoralis fillet samples, a normal(healthy) fillet and a WB fillet.
2022-04-13 | GSE200516 | GEO
Project description:Chickens divergently selected for either high abdominal fat content (fat genotype) or low abdominal fat content (lean genotype) at SRA-INRA, France were used to profile abdominal adipose gene expression during juvenile development (1 to 11 weeks of age) and to identify differentially expressed genes associated with genotype and age. The fat line (FL) and lean line (LL) chickens are different in various phenotypic and metabolic measurements, including abdominal fatness, plasma glycemia and T3. The FL and LL chickens represent unique models for characterizing biomedical and agricultural traits. The Del-Mar 14K Chicken Integrated Systems microarrays were used for a transcriptional scan in abdominal adipose during juvenile development using a balanced block hybridization design. Fluorescence intensities were normalized within array (without background subtraction), and between array (aquantile method) in LIMMA package R [Smyth, G. K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3] producing M-values (log-2 expression ratios) and A-values (average log-2 expression values). Normalized values were analyzed using a two factor ANOVA model. A total of 1,020 differentially expressed functional genes were identified (FDR<0.05). Genes were determined to have a significant effect of age (422), genotype (344), or an age by genotype interaction (254). The differentially expressed genes include metabolic enzymes, acute phase proteins, growth factors, coagulation factors, immune factors and transcription factors involved in various pathways. Several of the functional genes are also identified as positional candidate genes within QTLs in an F2 population established from an intercross between the FL and LL lines. Keywords: Divergently selected chickens, fatness, transcriptional profiling, differentially expressed genes A balanced block design was used for microarray hybridizations, where half of the birds of each genotype and age were labeled with Alexa Flour 647 (red) and the other half with Alexa Flour 555 (green). Four biological replicates were used for each genotype (FL or LL) at six different ages (1, 3, 5, 7, 9 and 11 wk).
2012-04-26 | E-GEOD-37585 | biostudies-arrayexpress