The expression profiles of longissimus dorsi muscle from six Laiwu pigs (three with extremely high and three with extremely low intramuscular fat content).
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PROVIDER: PRJNA854631 | ENA |
REPOSITORIES: ENA
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Project description:To understand the role of message RNA (mRNAs, lncRNAs and circRNAs) in regulation of intramuscular fat deposition, the expression profiles of longissimus dorsi muscle from six Laiwu pigs were sequenced based on rRNA-depleted library construction. We then performed gene expression profiling analysis using data obtained from RNA-seq.
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Project description:The Laiwu pig is famous for its excessively higher level of IMF content, however, the exact regulatory mechanism is still unknown. The intramuscular fat content (IMF) is an economically important traits in pigs, which is controlled by multiple genes and biological pathways. In the present study, we performed an integrated transcriptome-assisted label-free quantitative proteomic analysis of longissimus dorsi (LD) muscle in Laiwu pigs at the fastest IMF deposition stage. A total of 5074 unique proteins were identified and 191 were differentially abundant proteins (DAPs) (> 1.2-fold cutoff, p < 0.05), which were hierarchically clustered in the LD muscle over two developmental stages from 120 d to 240 d. Proteins participating in the regulation of lipolysis in adipocytes and AMPK signaling pathway were identified. Six proteins were analyzed using parallel reaction monitoring (PRM) to confirm the reliability of the TMT proteomic analysis. Association networks of differentially abundant proteins revealed that these DAPs were mainly involved in ribosome biosynthesis in eukaryotic species. A comparasion between transcriptomic (mRNA) and proteomic data revealed seven differentially expressed genes corresponding to DAPs. This study, for the first time, provides some data for the elucidation of the molecular mechanism of IMF deposition in pigs.
2020-01-09 | PXD011718 | Pride
Project description:The content of intramuscular fat (IMF) is closely related to meat quality traits. In this study, in order to explore the candidate genes related to IMF content, the longissimus dorsi muscle of Guangling donkey was measured for intramuscular fat content. According to its intramuscular fat content, it was divided into two groups, the low fat group (L , N=3) and high-fat group (H, n=3), using RNA-seq to identify differentially expressed genes (DGEs) on the longissimus dorsi muscle tissue of Guangling donkey with high and low intramuscular fat content to reveal the possibility Gene network and metabolic pathways that help increase intramuscular fat content. A total of 167 DEGs (|log2Fold Change|>=1 and FDR<0.05) were detected in the high (H) and low (L) groups of Guangling donkeys, of which 64 were up-regulated genes and 103 were down-regulated genes. The GO enrichment and KEGG pathway analysis showed that these differential genes were enriched in several biological processes and pathways related to adipocyte differentiation, lipid biosynthesis, and neutral lipid metabolism. These results will help to further explore the molecular mechanism of IMF deposition in donkeys and provide a theoretical basis for the molecular breeding of Guangling donkeys.
2021-09-01 | GSE156840 | GEO
Project description:The intramuscular fat (IMF) content of different beef cattle breeds varies greatly, which plays an important role in taste and nutritional value. However, the molecular mechanism of fat metabolism and deposition in beef cattle is still not very clear. In this study, the meat quality traits of Angus cattle and Chinese Simmental cattle were compared, the transcriptome of the longissimus dorsi muscle (LD) between Angus cattle and Chinese Simmental cattle was then analyzed to identify key genes related to fat metabolism and adipogenesis by high-throughput RNA-seq technology. In the current study conducted a comprehensive analysis on the transcriptome of the longissimus dorsi muscle (LD) of Angus and Simmental cattle, and identified differentially expressed genes related to lipid metabolism，which may have a great impact on on the formation of IMF.
2022-04-30 | GSE171876 | GEO
Project description:The proteomic data presented in this article are associated with the research article entitled "Longissimus dorsi muscle label-free quantitative proteomic reveals biological mechanisms associated with intramuscular fat deposition" published in Journal of Proteomics [1]. In this article, we characterized the proteomic profile of bovine Longissimus dorsi muscle from Nelore steers and identified differentially abundant proteins associated with the intramuscular fat (IMF) content. An integrated transcriptome-assisted label-free quantitative proteomic approach by High Definition Mass Spectrometry (HDMSE) was employed to identify and quantify the proteins. A functional enrichment analysis using the differentially abundant proteins list was performed to understand the biological processes involved in IMF deposition. Moreover, to explore and clarify the biological mechanisms that influence IMF content, the mRNA data for the same trait from Cesar and collaborators [2] obtained by RNA-sequencing technology was compared with proteomic data. The mRNA data is deposited in the European Nucleotide Archive (ENA) repository (EMBL-EBI), under accession PRJEB13188.
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Project description:Intramuscular fat (IMF) deposition is a physiological process in cattle and is highly variable among breeds suggesting a large influence of genetic factors besides environmental factors. In order to elucidate molecular pathways underlying the genetic variation in this trait we compared transcriptomes of Musculus longissimus dorsi (MLD) in steers of Japanese Black and Holstein Friesian cattle breeds fed a high energy diet typically applied in Japan to achieve maximum IMF content. We identified a total of 569 differentially expressed genes (DEGs) with the majority (433) up-regulated in Japanese Black cattle. This breed is characterized by an extreme capacity for IMF deposition. Subsequent Ingenuity Pathway Analysis (IPA) revealed a gene network linking parameters of cell morphology and maintenance with lipid metabolism. The data from this study were deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE75348. We provide here a dataset which is of potential value to dissect molecular pathways influencing differences in fat deposition under high-energy nutrition.
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Project description:Laiwu black goat kid liver mRNA expression profile were sequenced with novaSeq 6000. The liver tissues were procured at 5-time points from the Laiwu black goats of 1 day, 2 weeks, 4 weeks, 8 weeks, and 12 weeks of age, respectively with 5 goats per time point, for a total of 25 goats.
2022-01-28 | GSE194190 | GEO
Project description:One of the most important determinants of meat quality is the intramuscular fat content (IMF). The development of high-throughput techniques as RNA-seq allows identifying gene pathways and networks with a differential expression (DE) between groups of animals divergent for a particular trait. The Iberian pig is characterized by having an excellent meat quality and a high content of intramuscular fat. The objectives of the current study were to analyze the longissimus dorsi transcriptome of purebred Iberian pigs divergent for IMF breeding value to identify differential expressed genes and regulatory factors affecting gene expression. RNA-seq technique allowed identifying in the samples analyzed around 10,000 of the 25,878 annotated genes. In addition to this, the 42.46% of the identified transcripts corresponded to newly predicted isoforms. The differential expression analyses revealed a total of 221 DE annotated genes and 116 DE newly isoforms. Functional analyses identified an enrichment of overexpressed genes in animals with a higher content of IMF involved in lipid metabolism (FASN, SCD, ELOVL6, DGAT2, PLIN1, CIDEC and ADIPOQ) and an enrichment of overexpressed genes related with myogenesis and adipogenesis (EGR1, EGR2, EGR3, JUNB, FOSB and SEMA4D) in the groups of animals with a lower content of IMF. In addition to this, potential regulatory elements of these DE genes were identified. On the one hand, co-expression networks analyses revealed six lncRNAs (ALDBSSCG0000002079, ALDBSSCG0000002093, ALDBSSCG0000003455, ALDBSSCG0000004244, ALDBSSCG0000005525, ALDBSSCG0000006849) co-expressed with SEMA4D and FOSB genes and one (ALDBSSCG0000004790) with SCD, ELOVL6, DGAT2, PLIN1 and CIDEC. The computation of the regulatory impact factors (RIFs) revealed a total of 301 transcriptionally regulatory factors involved in the expression differences, some of them have a role in adipogenesis (ARID5B, CREB1, VDR, ATF6 and SP1) and other ones take part of myogenesis and development of skeletal muscle (ATF3, KLF11 and MYF6). The results obtained provide a relevant insight about the knowledge of the genetics mechanisms underlying IMF content in purebred Iberian pigs and a set of candidate genes and regulatory factors is proposed for a further identification of polymorphisms susceptible of integrate in a selection program.
2018-07-12 | GSE116951 | GEO
Project description:In this study, we examined the role of mRNAs and miRNAs in variations in intramuscular fat content in the longissimus dorsi muscle in Xinjiang brown cattle. Two groups of Xinjiang brown cattle with extremely different intramuscular fat content in the longissimus dorsi were selected for combined of miRNA and mRNA analysis using an RNA-Seq. In total, 296 mRNAs and 362 miRNAs were significantly differentially expressed, including 155 newly predicted miRNAs, 275 significantly upregulated genes, 252 significantly upregulated miRNAs, 21 significantly downregulated genes and 110 significantly downregulated miRNAs. The combined miRNA and mRNA analysis identified 96 differentially expressed miRNAs and 27 differentially expressed mRNAs. In all, 47 upregulated miRNAs had a regulatory effect on 14 differentially downregulated target genes, and 49 downregulated miRNAs had a regulatory effect on 13 upregulated target genes. To verify the sequencing results, 10 differentially expressed genes (DEGs) and 10 differentially expressed miRNAs were selected for qRT-PCR. The qRT-PCR results confirmed the sequencing results. The results of this study shed light on the molecular regulation of bovine adipose tissue, which might help with the development of new strategies for improving meat quality and animal productivity in beef cattle to provide healthier meat products for consumers.
| S-EPMC6226300 | biostudies-literature
Project description:BackgroundThe intramuscular fat content (IMF) refers to the amount of fat within muscles, including the sum of phospholipids mainly found in cell membranes, triglycerides and cholesterol, and is determined both by hyperplasia and hypertrophy of adipocyte during the development of pigs. The IMF content is an important economic trait that is genetically controlled by multiple genes. The Laiwu pig is an indigenous fatty pig breed distributed in North China, characterized by excessively higher level of IMF content (9%~12%), therefore, is suitable for the identification of genes controlling IMF variations. To identify genes underlying IMF deposition, we performed genome-wide transcriptome and methylome analyses on longissimus dorsi (LD) muscle in Laiwu pigs across four developmental stages.ResultsA total of 22,524 expressed genes were detected and 1158 differentially expressed genes (DEGs) were hierarchically clustered in the LD muscle over four developmental stages from 60 d to 400 d. These genes were significantly clustered into four temporal expression profiles, and genes participating in fat cell differentiation and lipid biosynthesis processes were identified. From 120 d to 240 d, the period with the maximum IMF deposition rate, the lipid biosynthesis related genes (FOSL1, FAM213B and G0S2), transcription factors (TFs) (EGR1, KLF5, SREBF2, TP53 and TWIST1) and enriched pathways (steroid biosynthesis and fatty acid biosynthesis) were revealed; and fat biosynthesis relevant genes showing differences in DNA methylation in gene body or intergenic region were detected, such as FASN, PVALB, ID2, SH3PXD2B and EGR1.ConclusionsThis study provides a comprehensive landscape of transcriptome of the LD muscle in Laiwu pigs ranging from 60 to 400 days old, and methylome of the LD muscle in 120 d and 240 d Laiwu pigs. A set of candidate genes and TFs involved in fat biosynthesis process were identified, which were probably responsible for IMF deposition. The results from this study would provide a reference for the identification of genes controlling IMF variation, and for exploring molecular mechanisms underlying IMF deposition in pigs.
| S-EPMC5639760 | biostudies-literature