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GSE19275
Sus scrofa
67 Downloadable Samples
Affymetrix Porcine Genome Array (porcine)
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 -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.
Publication Title
Muscle transcriptomic profiles in pigs with divergent phenotypes for fatness traits.
Sample Metadata Fields
Age, Specimen part
View Samples- Sus scrofa
- 56 Downloadable Samples
- Affymetrix Porcine Genome Array (porcine)
Description
A mRNA expression study has been performed 20-25 minutes postmortem obtained samples from Longissimus dorsi muscle of 59 Duroc x LD/LW pigs to search for gene sequences related to meat quality (pH24, pH45, Lab colour coordinates, curing yield and exudation at three different times) or to meat composition (intramuscular fat, content of several fatty acid (C16:0, C18:0, C18:1 and C18:2), ratio of saturated, monounsaturated and polyunsaturated fatty acids, and protein and humidity contents) traits in order to find targets for selection. Gene ontology analysis, biological pathways and gene networks studies all show, that many more differentially expressed genes (506 vs 279) are related to meat quality (Group P, or perimortem characters) than to meat composition traits (Group L, or whole life traits). The difference between the number of GO terms annotated, biological pathways and gene networks in groups P and L is notable due to the differences in the complexity of the generation process of P-traits and the involvement of other tissues or organs in the generation of variability of L-traits. Also, interactions between a list of differentially expressed genes were found in ECM-receptor interaction, TGF-beta signaling pathway, fatty acid elongation in mitochondria and adipocytokine signalling pathway indicating that a substantial fraction of the gene networks could be associated with interactions between differential expressed genes related to traits under study. A high number of the most overexpressed genes are related to muscle development and functionality and repair mechanisms; they could be good candidates for breeding programs whose main goal is to enhance meat quality.
Publication Title
Early postmortem gene expression and its relationship to composition and quality traits in pig Longissimus dorsi muscle.
Sample Metadata Fields
Age, Specimen part
View Samples- Sus scrofa
- 36 Downloadable Samples
- Affymetrix Porcine Genome Array (porcine)
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.
Publication Title
No associated publication
Sample Metadata Fields
Age, Specimen part
View Samples- Sus scrofa
- 19 Downloadable Samples
- Affymetrix Porcine Genome Array (porcine)
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.
Publication Title
No associated publication
Sample Metadata Fields
Age, Specimen part
View Samples