Liver gene expression patterns in pigs as indicators of serum plasma levels and meat quality atributes
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ABSTRACT:
ORGANISM(S): Sus scrofa
PROVIDER: GSE48992 | GEO | 2014/01/01
SECONDARY ACCESSION(S): PRJNA212535
REPOSITORIES: GEO
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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: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: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.
2010-03-01 | GSE19275 | GEO
Project description:In pigs, adipose tissue is one of the principal organs involved in the regulation of lipid metabolism. It is particulary involved in the overall fatty acid synthesis with consequences in other lipid-target organs such as muscles and the liver. With this in mind, we have used massive, parallel high-throughput sequencing technologies to characterize the porcine adipose tissue transcriptome architecture in six Iberian x Landrace crossbred pigs showing extreme phenotypes for intramuscular fatty acid composition (three per group). High-throughput RNA sequencing was used to generate a whole characterization of adipose tissue (backfat) transcriptome. A total of 4,130 putative unannotated protein-coding sequences were identified in the 20% of reads which mapped in intergenic regions. Furthermore, 36% of the unmapped reads were represented by interspersed repeats, SINEs being the most abundant elements. Differential expression analyses identified 396 candidate genes among divergent animals for intramuscular fatty acid composition. Sixty-two percent of these genes (247/396) presented higher expression in the group of pigs with higher content of intramuscular SFA and MUFA, while the remaining 149 showed higher expression in the group with higher content of PUFA. Pathway analysis related these genes to biological functions and canonical pathways controlling lipid and fatty acid metabolisms. In concordance with the phenotypic classification of animals, the major metabolic pathway differentially modulated between groups was de novo lipogenesis, the group with more PUFA being the one that showed lower expression of lipogenic genes. These results will help in the identification of genetic variants at loci that affect fatty acid composition traits. The implications of these results range from the improvement of porcine meat quality traits to the application of the pig as an animal model of human metabolic diseases. The supplementary files contains the five arrays reported in the paper. Backfat from five animals were assayed with high-density oligonucleotide microarray chips (GeneChipM-BM-. Porcine) from Affymetrix, in order to validate RNA-Seq data.
2014-03-31 | E-GEOD-52012 | biostudies-arrayexpress
Project description:In pigs, adipose tissue is one of the principal organs involved in the regulation of lipid metabolism. It is particulary involved in the overall fatty acid synthesis with consequences in other lipid-target organs such as muscles and the liver. With this in mind, we have used massive, parallel high-throughput sequencing technologies to characterize the porcine adipose tissue transcriptome architecture in six Iberian x Landrace crossbred pigs showing extreme phenotypes for intramuscular fatty acid composition (three per group). High-throughput RNA sequencing was used to generate a whole characterization of adipose tissue (backfat) transcriptome. A total of 4,130 putative unannotated protein-coding sequences were identified in the 20% of reads which mapped in intergenic regions. Furthermore, 36% of the unmapped reads were represented by interspersed repeats, SINEs being the most abundant elements. Differential expression analyses identified 396 candidate genes among divergent animals for intramuscular fatty acid composition. Sixty-two percent of these genes (247/396) presented higher expression in the group of pigs with higher content of intramuscular SFA and MUFA, while the remaining 149 showed higher expression in the group with higher content of PUFA. Pathway analysis related these genes to biological functions and canonical pathways controlling lipid and fatty acid metabolisms. In concordance with the phenotypic classification of animals, the major metabolic pathway differentially modulated between groups was de novo lipogenesis, the group with more PUFA being the one that showed lower expression of lipogenic genes. These results will help in the identification of genetic variants at loci that affect fatty acid composition traits. The implications of these results range from the improvement of porcine meat quality traits to the application of the pig as an animal model of human metabolic diseases. The supplementary files contains the five arrays reported in the paper.
2014-03-31 | GSE52012 | GEO
Project description:Backfat thickness is one of the most important traits of commercially raised pigs. Meishan pigs are renowned for having thicker backfat than Landrace pigs. To examine the genetic factors responsible for the differences, we first produced female crossbred pig lines by mating Landrace (L) × Large White (W) × Duroc (D) females (LWD) with Landrace (L) or Meishan (M) boars (i.e., LWD × L = LWDL for Landrace offspring and LWD × M = LWDM of the Meishan offspring). We confirmed that LWDM pigs indeed had a thicker backfat than LWDL pigs. Next, we performed gene expression microarray analysis (in both genetic lines) to examine differentially expressed genes (DEGs) in energy metabolism-related tissues, subcutaneous adipose (fat), liver, and longissimus dorsi muscle tissues. We analyzed the annotation of DEGs (2-fold cutoff) to functionally categorize them by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways. The number of DEGs in muscle tissues of both lines was much less than that in fat and liver tissues, indicating that DEGs was much lesser in muscle tissues (in both genetic lines) than in fat and liver tissues, thus indicating that DEGs in muscle tissues may not contribute much to differences in backfat thickness. In contrast, several genes related to muscle (in fat tissue) and fatty acid and glucose metabolism (in the liver) were more upregulated in LWDM pigs than LWDL pigs, indicating that those DEGs might be responsible for differences in backfat thickness. The different genome-wide, gene expression profiles in the fat, liver, and muscle tissues between breeds can provide useful information for pig breeders.
2018-09-06 | GSE97711 | GEO
Project description:Breed, gender and diet are factors affecting porcine metabolism. The aim of this study has been to investigate the gene expression patterns of the major sites for lipid metabolism, liver and fat, conditional on gender and on a moderate feeding restriction in Iberian pigs, as a model of obese porcine breed. Our results show that tissue effect account for more differentially expressed genes than gender or feeding restriction. The results obtained from the comparison between tissues support the studies showing adipose tissue is not only a fat-storage depot, we report a high number of upregulated genes in adipose tissue which represent relevant biological functions such as carbohydrate and energy metabolisms and endocrine function. Besides, key genes implicated in lipid metabolism are specifically overrepresented in liver or fat, particularly the differentially expressed genes related to fatty acid synthesis support previous studies showing that in pig, as in cattle or sheep, this process largely occurs in fat. We identified metabolic differences between genders such as oxidation capacity or response to toxins, reflected at gene expression level in liver but no in adipose tissue, contrarily to previous studies. Finally, our results seem to indicate that a moderate feeding restriction does not have large effects on liver or fat gene expression of obese pigs. Although the list of differentially expressed genes due to the effect of feeding restriction is limited, we could identify expression differences in genes related to antiageing mechanisms associated with feeding restriction as enhancement of immune response and anticoagulation and the balance between prosurvival and cell-death. Breed, gender and diet are factors affecting porcine metabolism. The aim of this study has been to investigate the gene expression patterns of the major sites for lipid metabolism, liver and fat, conditional on gender and on a moderate feeding restriction in Iberian pigs, as a model of obese porcine breed. Our results show that tissue effect account for more differentially expressed genes than gender or feeding restriction. The results obtained from the comparison between tissues support the studies showing adipose tissue is not only a fat-storage depot, we report a high number of upregulated genes in adipose tissue which represent relevant biological functions such as carbohydrate and energy metabolisms and endocrine function. Besides, key genes implicated in lipid metabolism are specifically overrepresented in liver or fat, particularly the differentially expressed genes related to fatty acid synthesis support previous studies showing that in pig, as in cattle or sheep, this process largely occurs in fat. We identified metabolic differences between genders such as oxidation capacity or response to toxins, reflected at gene expression level in liver but no in adipose tissue, contrarily to previous studies. Finally, our results seem to indicate that a moderate feeding restriction does not have large effects on liver or fat gene expression of obese pigs. Although the list of differentially expressed genes due to the effect of feeding restriction is limited, we could identify expression differences in genes related to antiageing mechanisms associated with feeding restriction as enhancement of immune response and anticoagulation and the balance between prosurvival and cell-death. 16 liver and subcutaneous backfat samples from eight animals at slaughter, 211 days old, four males and four females, four under high feeding level and four under 20% restriction
2010-06-08 | E-GEOD-21952 | biostudies-arrayexpress
Project description:Transcript abundance in adipose and liver tissues was used to map expression quantitative trait loci (eQTL) underlying fat accretion, weight gain and liver weight. Gonadal fat and liver tissues were used from 48 individuals F2 selected from a cohort (1,200 mice) originated from a cross between M16i and MB2 mice. A complex polygenic architecture within the MB2 locus was observed which was comprised of several locally regulated eQTL (cis-eQTL) with significant correlations to obesity traits. Total RNA obtained from isolated gonadal fat and liver tissues were used to mesured transcript abundance in order to detect expression QTLs.
2010-09-15 | E-GEOD-20724 | biostudies-arrayexpress
Project description:Transcriptional profiling in peritoneal adipose tissue of 48 pigs (132 days of age) originated from two lines divergently selected for residual feed intake (RFI) : low-RFI pigs (RFIneg), high-RFI pigs (RFIpl). Both lines were offered isocaloric and isoproteic diets with contrasted energy source and nutrients: low fat, low fiber (LF) diet or a high fat, high fiber (HF)diet during 10 weeks. Effects of RFI selection, diet and interaction between diet and line were investigated. Four experimental groups: low-RFI pigs fed high fat, high fiber diet (HF_RFIneg), high-RFI pigs fed high fat, high fiber diet(HF_RFIpl), low-RFI pigs fed low fat, low fiber diet (LF_RFIneg) and high-RFI pigs fed low fat, low fiber diet(LF_RFIpl). 12 pigs per condition. One replicate per array.
2016-07-01 | E-GEOD-70837 | biostudies-arrayexpress
Project description:Transcriptional profiling in subcutaneous adipose tissue of 48 pigs aged (132 days of age) originated from two lines divergently selected for residual feed intake (RFI) : low-RFI pigs (RFIneg), high-RFI pigs (RFIpl). Both lines were offered isocaloric and isoproteic diets with contrasted energy source and nutrients: low fat, low fiber (LF) diet or a high fat, high fiber (HF)diet during 10 weeks. Effects of RFI selection, diet and interaction between diet and line were investigated. Four experimental groups: low-RFI pigs fed high fat, high fiber diet (HF_RFIneg), high-RFI pigs fed high fat, high fiber diet(HF_RFIpl), low-RFI pigs fed low fat, low fiber diet (LF_RFIneg) and high-RFI pigs fed low fat, low fiber diet(LF_RFIpl). 12 pigs per condition. One replicate per array.
2016-07-01 | E-GEOD-70836 | biostudies-arrayexpress