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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from porcine red and white muscle

ABSTRACT: In meat animal production, favourable meat traits such as color and, in the pig in particular, tenderness have been found to closely associate with the greater abundance of red or highly oxidative fibres. Red muscles possess higher lipid concentration (intra- and inter-fibre fat) which is associated with more tender and juicy meat. In addition, individuals with muscles that are abundant in oxidative type I fibres are associated with favourable metabolic health, and are less likely to predispose to obesity and insulin resistance. Collectively, understanding the molecular processes that govern the expression of specific fiber types and the phenotypic characteristics of muscles is important in agricultural and medical fields. In this study, a genome-wide investigation of the porcine differential expression between two red (soleus, SE) and white (longissimus dorsi, LD) muscle was conducted using the Affymetrix GeneChip® Porcine Genome Array containing oligonucleotides representing approximately 24123 transcripts from 20201 S. scrofa genes Three meishan gilts from the same litter were slaughtered at the 150 days of age by electrical stunning and exsanguination, in compliance with national regulations applied in commercial slaughtering. Immediately after slaughter, two muscles with different locations, functions, and biochemical properties were sampled: the longissimus at the last rib level, a fast twitch glycolytic muscle involved in voluntary movements of the back, and the deep portion of the SE, a oxydolytic muscle.

ORGANISM(S): Sus scrofa

SUBMITTER: Bo Zuo

PROVIDER: E-GEOD-19975 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data from porcine red and white muscle

Project description:In meat animal production, favourable meat traits such as color and, in the pig in particular, tenderness have been found to closely associate with the greater abundance of red or highly oxidative fibres. Red muscles possess higher lipid concentration (intra- and inter-fibre fat) which is associated with more tender and juicy meat. In addition, individuals with muscles that are abundant in oxidative type I fibres are associated with favourable metabolic health, and are less likely to predispose to obesity and insulin resistance. Collectively, understanding the molecular processes that govern the expression of specific fiber types and the phenotypic characteristics of muscles is important in agricultural and medical fields. In this study, a genome-wide investigation of the porcine differential expression between two red (soleus, SE) and white (longissimus dorsi, LD) muscle was conducted using the Affymetrix GeneChip® Porcine Genome Array containing oligonucleotides representing approximately 24123 transcripts from 20201 S. scrofa genes

2011-01-29 | GSE19975 | GEO

Expression data from longissimus dorsi muscle of Meishan pigs

Project description:The skeletal muscle growth and development is a very complicated but precisely regulated process with interwoven molecular mechanisms. Skeletal muscle is a very heterogeneous tissue that is made up of a large variety of functionally diverse fiber types. Muscle mass is therefore largely determined by the number and size of those fibres. These fibre characteristics are determined by hyperplasia before birth and by hypertrophy after. Around 65 dpc and three postnatal stages (newborn, 3 days; young, 60 days; and mature, 120 days) are key time points in swine skeletal muscle growth and development. We used microarrays to detail the global programme of gene expression underlying porcine skeletal muscle growth and development. Porcine longissimus dorsi muscles were selected at four stages of development for RNA extraction and hybridization on Affymetrix microarrays. We sought to investigate the global gene expression patterns accompanying the skeletal muscle development. To that end, we selected longissimus dorsi muscles at four time-points: 65 days post coitus, 3 days, 60 days and 120 days afterbirth.

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Porcine intramuscular fat content and composition are regulated by quantitative trait loci with muscle-specific effects

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.

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Whole Genome Bisulfite Sequencing of Longissimus Dorsi Muscles between Japanese Black (Wagyu) and Chinese Red Steppes Cattle

Project description:We performed a comparative genome-wide methylation analysis of longissimus dorsi muscles between the Japanese Black (Wagyu) and Chinese Red Steppes cattle, which exhibit significant differences in meat quality traits. This will allow us to better understand the correlation between DNA methylation variants and meat quality traits.

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The miRNA Transcriptome directly Reflect the Physiological and Biochemical Differences between Red, White and Intermediate Muscle Fiber Types

Project description:MicroRNAs (miRNAs) are small non-coding RNAs that can regulate the expression of their target genes at post-transcriptional level. Skeletal muscle comprises different ï¬?ber types that can be broadly classified as red, intermediate and white fiber types. Recently, a set of miRNAs were identified to be expressed on a fiber type-specific manner between red and white fiber types. Nonetheless, an integral explanation of the miRNA transcriptome differences in all three fiber types is long overdue. Herein, we collected 15 kinds of porcine skeletal muscles from different anatomic locations, which were then clearly divided into red, white and intermediate fiber type based on the hierarchical clustering analysis for the ratios of myosin heavy chain (MHC) isoforms. We further illustrated that three muscles, which typically represented each muscle fiber type (i.e. red: peroneal longus (PL), intermediate: psoas major muscle (PMM), white: longissimus dorsi muscle (LDM)), have distinct metabolic patterns of mitochondrial and glycolytic enzyme levels. In addition, we constructed the small RNA libraries for PL, PMM and LDM using deep sequencing approach. Results showed that, the differentially expressed miRNAs were mainly enriched in PL and played a vital role in myogenesis and energy metabolism. Overall, this comprehensive analysis will contribute to a better understanding of the miRNA regulatory mechanism for the phenotypic diversity of skeletal muscles. 3 sample

2015-12-23 | E-GEOD-64523 | biostudies-arrayexpress

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Proteomic analysis of the Longissimus dorsi muscle of Wannanhua pigs

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Identification of novel markers of beef sensory quality and muscle growth potential

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PROTEOMICS AND METABOLOMICS PROFILING OF MEAT EXUDATE TO UNDERSTAND THE IMPACT OF POSTMORTEM AGING ON OXIDATIVE STABILITY OF BEEF MUSCLES

Project description:The objective of this study was to characterize the major proteomes and metabolites present in beef exudate and determine their relationship with the color and oxidative quality of beef muscles. Beef loin (longissimus lumborum; LD) and tenderloin (psoas major; PM) muscles were cut into sections, individually vacuum-packaged, and aged for 9, 16 and 23 days. Following aging, the meat exudates were collected and analyzed for both proteomics and metabolomics profiles. Both analyses demonstrated that distinct proteins and metabolites clustered by different muscle types and aging times were detected from meat exudate, however, metabolomics profiling presented a greater capability in identifying different aging periods. The proteome profile of PM exudate exhibited a greater concentration of oxidative metabolism enzymes, while the LD exudate contained a higher abundance of glycolytic metabolism enzymes. Greater lipid, nucleotide, carnitine and glucoside metabolites were observed in LD and 23d exudates, further explaining potential postmortem energy metabolism. HSP70 and laminin proteins, together with glucosides metabolites identified in the exudates were correlated (P<0.1 and |r|>0.5) to muscle oxidative stability. The results indicated that meat exudate could be a viable analytical matrix to further understand postmortem metabolism and potentially generate unique biomarker combinations to predict meat quality attributes.

2022-08-24 | MSV000090195 | MassIVE

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