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Expression data from longissimus dorsi of backcross Iberian x Landrace individuals

ABSTRACT: The integration of the results of QTL fine-mapping with microarray expression data offers a promising tool for understanding the genetic mechanisms influencing complex traits as fatty acid composition in pigs. The expression level of each probe may be treated as a quantitative trait and the marker genotypes used to map loci with regulatory effect on the gene expression level (eQTL) According to our previous linkage results, we carry out an eQTL scan focused on chromosomal regions showing tissue-consistent effects on fatty acids with Longissimus dorsi gene expression data in order to detect potentional candidate genes underlying the QTL previously detected.

ORGANISM(S): Sus scrofa

PROVIDER: GSE52626 | GEO | 2013/11/22

SECONDARY ACCESSION(S): PRJNA229494

REPOSITORIES: GEO

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Expression data from longissimus dorsi of backcross Iberian x Landrace individuals

Project description:The integration of the results of QTL fine-mapping with microarray expression data offers a promising tool for understanding the genetic mechanisms influencing complex traits as fatty acid composition in pigs. The expression level of each probe may be treated as a quantitative trait and the marker genotypes used to map loci with regulatory effect on the gene expression level (eQTL) According to our previous linkage results, we carry out an eQTL scan focused on chromosomal regions showing tissue-consistent effects on fatty acids with Longissimus dorsi gene expression data in order to detect potentional candidate genes underlying the QTL previously detected. 102 IberianxLandrace backcross pigs were selected for RNA extraction and hybridization on Affymetrix microarrays. An eQTL scan was carried out with the data of 470 probes of the microarray taking into account they were related with fatty acid metabolism

2013-11-22 | E-GEOD-52626 | biostudies-arrayexpress

Proteomic analysis of the Longissimus dorsi muscle of Wannanhua pigs

Project description:4D-Label-free quantitative proteomic analysis of the longissimus dorsi muscle tissue of the Wannanhua pig during the rapid fat deposition stage (120d and 240d)

2024-01-26 | PXD046675 | Pride

Consequences of a low protein diet in the liver and longissimus dorsi transcriptome of Duroc x Iberian crossbred pigs

Project description:Low protein diets supplied during the growing period of pigs can diminish their growth rate and increase the intramuscular fat (IMF) content which affects the sensorial and technological characteristics of the traits. In the present study, the effects of a low protein diet supplied during the growing diet of Duroc x Iberian crossbred pigs on several phenotypic traits and liver and longissimus dorsi transcriptome, were analysed 20 days after the differential treatment was started (EARLY) and at the end of it (FINAL). A total of 20 crossbred pigs were assigned to two different dietary treatments during the growing period: a control diet (C) and a low protein diet (LP) with the same energy and lower levels of raw protein (11%) and lysine (0.60%). The transcriptomes of liver and longissimus dorsi were quantified through RNAseq. A total of 134 differentially expressed annotated genes and new isoforms (DEGs) between C and LP diets in liver of EARLY animals; 480 DEGs in liver of LATE animals, and 128 DEGs and 68 DEGs in longissimus dorsi of EARLY and LATE animals were detected. The functional analyses revealed that low protein diet diminishes the expression in liver of genes codifying for proteins involved in immune system both in EARLY and LATE animals, affects the expression of genes involved in cholesterol homeostasis in liver and in the energy process and growth in longissimus dorsi. Pigs fed with LP diet had not higher IMF content than C ones, although some lipogenesis genes such as FASN, SCD or SREBF1 were higher expressed on their liver. A low protein diet supplied during growing period affects multiple biological process that could compromise the immune and energy state of the Duroc x Iberian crossbred pigs. These results point out that we should be very cautious before implementing this type of regime in Duroc x Iberian pigs.

2021-07-01 | GSE163513 | GEO

Transcriptome changes following castration of Korean cattle bulls in longissimus dorsi muscle

Project description:Transcripome of longissimus dorsi muscle was compared between Korean cattle bulls and steers by using a customized bovine Combimatrix microarray containing 10,199 genes. A customized bovine Combimatrix microarray containing 10,199 genes were constructed, and transcripome of longissimus dorsi muscle was compared between Korean cattle bulls (3 bulls) and steers (3 high-marbled and 3 low-marbled steers) by using the microarray hybridzation.

2013-06-30 | E-GEOD-35085 | biostudies-arrayexpress

Expression data from longissimus dorsi muscle of Shaziling pig at 25-days old and longissimus dorsi musle of Yorkshire pig at 25-days old

Project description:To characterize the mechanism of porcine skeletal muscle development, transcriptome analysis of longissimus dorsi muscle between Shaziling and Yorkshire pig breeds

2016-06-23 | GSE70673 | GEO

Early postmortem gene expression and its relationship to composition and quality traits in pig Longissimus dorsi muscle

Project 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. 59 Longissimus Dorsi samples from 59 LD/LW x Duroc cross. A total of 33 traits on composition, conformation and meat quality and compositional traits were recorded in the left Longissimus dorsi muscle.

2011-09-19 | E-GEOD-32179 | biostudies-arrayexpress

Expression data from Northeastern Indigenous and Large White longissimus dorsi

Project description:To understand the molecular basis of distinct pork quality in Chinese indigenous and Western breed, longissimus dorsi samples were collected from three adult Northeastern Indigenous and from three adult Large White. Total RNA was extracted and subjected to porcine Affymetrix Genechip. The study helps to elucidate the genetic mechnism of divergent pork quality and provide the theory basis for selection and genetic improvement of meat quality traits in porcine. Six longissimus dorsi samples were collected from three Northeastern Indigenous and from three Large White. Three Large White were control samples. Total RNA was extracted from each sample.Gene-expression profiling was performed for each RNA sample separately on the GeneChipÂ® Porcine Genome Array at CapitalBio Corporation (Beijing, China).

2016-09-02 | E-GEOD-24192 | biostudies-arrayexpress

Comparison of transcriptome profiles between bulls and steers in the longissimus dorsi muscle of Korean cattle

Project description:Purpose: The goals of this study are to determine effects of castration on gene expression in longissimus dorsi muscle by comparing transcriptome profiles and to search candidate genes related with beef quality like flavor, tenderness, juiciness and fat deposition Methods: longissimus dorsi muscle mRNA profiles of 3 bulls and 3 steers of Korean cattles were generated by RNA sequencing using Illumina NextSeq 500. After quality checking, Tophat2 software was used for read mapping, and EdgeR was used to identify differentially expressed genes (DEGs) between bulls and steers. Gene ontology pathway analysis on DEGs was conducted with DAVID tool for categorization of DEGs. Results: Using an optimized data analysis workflow, we mapped about 58 million sequence reads per sample to the bovine genome (build UMD3.1) and identified 18,027 expressed genes in the longissimus dorsi muscle of bulls and steers with TopHat2 workflow. RNA-seq data confirmed 1,146 differentially expressed genes (adjusted p-value, FDR <0.05). Conclusions: We comparatively analyzed the transcriptome profile from longissimus dorsi muscle of bulls and steers of Korean cattles using NGS and identified DEGs between bulls and steers. The functional annotation analysis of DEGs found that transcriptome profile difference in longissimus dorsi muscle by castration.

2020-03-07 | GSE95789 | GEO

Transcriptome changes following castration of Korean cattle bulls in longissimus dorsi muscle

Project description:Transcripome of longissimus dorsi muscle was compared between Korean cattle bulls and steers by using a customized bovine Combimatrix microarray containing 10,199 genes.

2013-06-30 | GSE35085 | GEO

Spatial transcriptome data of Longissimus dorsi muscle from 3 pigs

Project description:This study takes pig longissimus dorsi muscle as the object. Through spatial transcriptome research, we clarified the gene expression distribution of different types of muscle fibers in the tissue, and their corresponding marker genes were identified.

2022-05-17 | GSE203094 | GEO

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