Expression data from subcutaneous adipose tissue of barrows and boars
Ontology highlight
ABSTRACT:
ORGANISM(S): Sus scrofa
SUBMITTER: Yuchang Yao
PROVIDER: E-GEOD-45710 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The male hypogonadism is closely associated with adipose tissue metabolism. Domestic pig has been a widely used experimental animal in biomedical research because of their similarity to humans in body size and other physiological/anatomical features. However, the transcriptional responses of pigs to male hypogonadism in subcutaneous adipose tissue remain unclear so far. We used microarrays to detail the transcriptional profiles of barrows and boars, and determined the gene networks regulated by castration-induced sex hormone deficiency. This study will help to provide a significant addition to knowledge about fat accumulation and lipid metabolism in hypogonadal man.
2013-04-08 | GSE45710 | GEO
Project description:In pigs, most of the lipogenic activity takes place in liver and the adipose tissue. Moreover, liver is responsible for the production and release of lipoproteins, which transports lipids from the liver to target tissues such as adipose and muscle. In the context of animal production, the amount and composition of lipoprotein have an implication in the accumulation of fat in adipose deposits but also in muscle in the form or intramuscular fat. These two events have consequences in the quality of the carcasses and meat. We have measured the level of liver gene expression in 104 commercial Duroc pigs belonging to two groups with extreme phenotypes for traits strongly related with lipid deposition and composition. This has allowed us to compare the physiological and metabolic implications of selecting for each of these extreme groups. This information has been complemented with genome-wide genotyping data in order to describe the implication of the liver transcriptome in the production traits which encompass the production and marketing of the products with consumer and industry-relevant added-value characteristics. 104 liver samples form pigs belonging to two groups of animals: HIGH group (n=53) had higher carcass, plasma and muscle fat content; LOW group (n=51) had lower carcass, plasma and muscle fat content
2014-01-01 | E-GEOD-48992 | biostudies-arrayexpress
Project description:Expression data from subcutaneous adipose tissue of barrows and boars
| PRJNA195911 | ENA
Project description:Feed efficiency (FE) is an indicator of efficiency in converting energy, attained from macronutrient ingestion, into tissue. Adipose tissue, besides being a master regulator of systemic lipid storage, is also an active endocrine organ that communicates with skeletal muscle, liver and brain to influence appetite, lipid & glucose metabolism and energy homeostasis. Adipose tissue is hypothesised to play a vital part in regulation of FE. The objective of the present study was to sequence the subcutaneous adipose tissue transcriptome in FE-divergent pigs (n=16) and identify relevant biological processes underpinning observed differences in FE.
2018-11-14 | E-MTAB-6255 | biostudies-arrayexpress
Project description:Background: Marketing products with added-value characteristics is a current trend in livestock production systems. Regarding meat, selection for intramuscular fat and muscular fatty acid composition is a way to improve the palatability and juiciness of meat while assuring a healthy fat content. This represents selecting animal with a different muscular metabolic profile with respect to the extended selection of lean animals. Results: The present study has analysed the muscular gene expression profiles of 68 commercial Duroc pigs belonging to two groups with extreme phenotypes for traits strongly related with lipid deposition and composition. This has allowed us to compare the physiological and metabolic implications of selecting for each of these extreme groups. Rather than upregulation of a single pathway, the main differences lied on the transcriptional levels of genes related with lipogenesis and lipolysis, revealing the existence of a cycle where triacylglycerols are continuously synthesized and degraded. Most strikingly, several genes which enhanced fatty acid β-oxidation and favoured insulin signalling and glucose uptake were upregulated in the fattest animals, indicating that the events leading to peripheral insulin resistance in humans with increased levels of intramuscular fat and obesity do not take place in these pigs. Moreover, neither was detected the well-characterised low-grade inflammatory state observed in overweighed humans. Conclusion: As a whole, our data suggest that selection for increasing intramuscular fat content in pigs would lead to a shift but not a disruption of the metabolic homeostasis of muscle cells. Future studies on the post-translational changes affecting protein activity or expression as well as information about protein location within the cell would be needed to fully understand how lipid deposition affects muscle physiology in pigs. 68 gluteus medius samples form 68 animals belonging to two groups of 34 animals each: HIGH group had higher carcass, plasma and muscle fat content; LOW group had lower carcass, plasma and muscle fat content
2010-03-07 | E-GEOD-19275 | 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:In the last 20 years, there has been significant research towards defining the genetic basis of lipid metabolism and meat quality related traits in pigs. Nowadays, the study of the transcriptome and its regulatory mechanisms allows going far beyond in the genetic dissection of these complex traits. In present study, a genome-wide eQTL scan aiming to detect pig genome regions regulating levels of skeletal muscle mRNA expression has been performed. This study has been conducted on a commercial Duroc population where a number of QTL for muscle fat deposition and fatty acid composition had been detected. GeneChip Porcine Genome® arrays (Affymetrix) were used to determine the gene expression levels of gluteus medius samples from 105 Duroc pigs belonging to two groups with divergent phenotypes for fatness traits. This experimental design aimed to favour detection of eQTL affecting genes related to lipid metabolism and meat quality traits. The whole genome scan with a panel of 110 microsatellites allowed us detecting 613 genome-wide significant eQTL unequally distributed across the pig genome, SSC5 and SSC3 harbouring the highest number of eQTL. Moreover, 11 genome regions with eQTL affecting the expression levels of a high number of genes (eQTL hot spots) have been described. After mapping target probes and discarding low quality probes, a total of 59 cis- and 396 trans-acting eQTL were retained for further analyses. The functional classification showed that lipid-related GO terms were not the most enriched by the list of eQTL-regulated genes. However, a number of regulated genes functionally related to lipid metabolism and fat deposition traits were identified, and their functional relationship with these phenotypes were further investigated. With this purpose, eQTL results were integrated with 1) QTL linkage maps and 2) correlation data between phenotypes and gene expression levels. As a result, a comprehensive list of 29 positional and functional candidate genes was elaborated. These results represent a valuable contribution to the comprehension of genetic regulation of skeletal muscle individual gene expression in swine species, and a first step towards disentangling gene networks and molecular mechanisms involved in lipid metabolism and meat quality traits. 105 gluteus medius samples from 105 animals belonging to two groups of 53 and 52 animals each: HIGH group had higher carcass, plasma and muscle fat content; LOW group had lower carcass, plasma and muscle fat content
2010-12-16 | E-GEOD-26091 | biostudies-arrayexpress
Project description:We studied the influence of genetic type (pure Iberian pigs vs crossbred with Duroc) on l.dorsi transcriptome Background: The two main genetic types in Iberian pig production show important phenotypic differences in growth, fattening and tissue composition since early developmental stages. The objective of this work was the evaluation of muscle transcriptome profile in young animals of both genetic types, in order to identify genes, pathways and transcription factors responsible of their phenotypic differences. Contemporary families coming from pure Iberian pigs (IB) or from crossing with Duroc boars (DUxIB) were generated. Piglets (14 from each genetic type) were sacrificed at weaning (28 days) and longissimus dorsi muscle was sampled for composition and gene expression studies. RNA was obtained and hybridized to Affymetrix Porcine Genechip expression arrays. Results: Loin muscle composition showed significant differences between genetic types in intramuscular fat content (6% vs. 4.2% in IB and DUxIB animals, respectively, P=0.009) and in saturated and monounsaturated fatty acid contents (P=0.019 and P=0.044, respectively). Statistical analysis of gene expression data allowed the identification of 256 differentially expressed (DE) genes between genetic types (FDR<0.10), 102 upregulated in IB and 154 upregulated in DUxIB. The size of the effects ranged between 1.2x and 7.8x. Transcript differences were validated for a subset of DE genes by qPCR. Some candidate genes with known effects on muscle growth were found among the DE genes upregulated in DUxIB (IGF2, collagens, integrins). Genes related to lipid metabolism and proteolysis were found among the genes upregulated in IB (ME1, ELOVL6, caspases, catepsins, ubiquitination proteins). We observed alteration in biological functions related to extracellular matrix organization, cellular adhesion, muscle growth and lipid metabolism. Transcription factors (TF) potentially involved in the expression differences found were identified by calculating the regulatory impact factors (RIF). Sixteen TF were found, some of them with known relationship with muscle development (MSTN, SIX4), adipogenesis (CEBPD, PPARGC1B), or extracellular matrix processes (MAX, MXI1). Correlation among the expression of these TF and DE genes show relevant differences between genetic types. Conclusion: The results contribute valuable information about molecular mechanisms determining the phenotypic differences of growth and meat quality between the genetic types studied, mainly related to the development and function of the extracellular matrix and also to some metabolic processes as proteolysis and lipid metabolism. 28 male piglets were employed. 14 animals coming for pure Iberian parents and 14 coming from the crossing of Duroc boars with Iberian sows. Animals were sacrificed at 28 d of age. At the sacrifice, longissimus dorsi muscle tissue was sampled from each animal.
2014-06-11 | E-GEOD-53029 | biostudies-arrayexpress
Project description:We studied the influence of the oleic acid content of the diet on adipose tissue transcriptome. Iberian pigs were fed a standard (C) or a high oleic sunflower oil enriched (HO) diet. Transcriptome analyses were performed in adipose tissue samples (inner layer) obtained at slaughter (110 kg live weight) employing the Affymetrix porcine GeneChip. Normalized and filtered microarray expression data (background corrected and base-2 logarithmic-transformed) were analyzed through Bayesian inference using the GEAMM v.1.6 program. Statistically significant expression differences (FDR<0.10) between C and HO groups were observed for a total of ten probes corresponding to nine different known genes. Six genes were overexpressed in the HO group and three were overexpressed in the C group. Expression differences between groups ranged from 1.38 to 2.75-fold. The two most significantly DE genes were related with immune defense (TCRB and GPR183) and others were related with nutrient metabolism as glicerolipid metabolism (GK), phospholipid and sphingolipid metabolism (PPM1L), carbohydrate metabolism (FBP2) aminoacid metabolism and energy homeostasis (PRSS35 and CKB) and gene expression regulation and adipogenesis (RXRG). 15 Iberian castrated male pigs were adscribed to one of two experimental groups at 28 kg live weight (7 animals in Control group and 8 animals in High Oleic group). Nutritional treatment was maintained until sacrifice of the animals at 110 kg of live weight. At the sacrifice, backfat adipose tissue was sampled from each animal at the level of the last rib.
2013-06-14 | E-GEOD-47941 | biostudies-arrayexpress
Project description:Background: Supplementing farm animals diet with functional ingredients may improve the nutritional quality of meat products. Diet composition has been also demonstrated to influence the gene expression with effect on biological processes and pathways. However, the knowledge on the effect of nutrients at the molecular level is scant. In particular, studies on the effects of antioxidants and polyphenols dietary supplementation have been investigated mainly in rodents, and only scarcely in farm animals so far. RNA-seq with next-generation sequencing (NGS) is increasingly the method of choice for studying changes in the transcriptome and it has been recently employed also in pig nutrigenomics studies to identify diet-induced changes in gene expression. The present study aimed to investigate the effect of diets enriched with functional ingredients (linseed, vitamin E and plant extracts) on the transcriptome of pig Longissimus thoracis to elucidate the role of these compounds in influencing genes involved in muscle physiology and metabolism compared to a standard diet. Results: 893 significant differentially expressed genes (DEGs) (FDR adjusted P-value < 0.05) were detected by RNA-seq analysis in the three diet comparisons (D2-D1, D3-D1, D4-D1). The functional analysis of DEGs showed that the diet enriched with n-3 PUFA from linseed (D2) mostly downregulated genes, compared to the standard diet (D1) included in pathways and biological processes (BPs) involved in muscle development, contraction, and glycogen metabolism. The diet supplemented with linseed and vitamin E/Selenium (D3) compared to D1 mostly downregulated genes linked to oxidative phosphorylation. Only few genes were upregulated by the D3 and involved in extracellular matrix (ECM) organization. Finally, the comparison D4-D1 showed that the diet supplemented with linseed and plant extracts (D4) upregulated the majority of genes compared to D1 that were included in a complex network of pathways and BPs all connected by hub genes. In particular, IGF2 was a hub gene connecting protein metabolism, ECM organization, immune system and lipid biosynthesis pathways. Conclusion: The supplementation of pig diet with n-3 PUFA from linseed, antioxidants and plant-derived polyphenols can influence the expression of a relevant number of genes in Longissimus thoracis muscle that are involved a variety of biochemical pathways linked to muscle function and metabolism.
2019-06-29 | E-MTAB-7131 | biostudies-arrayexpress