Identification of candidate genes and regulatory factors underlying intramuscular fat content through longissimus dorsi transcriptome analyses in heavy Iberian pigs
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ABSTRACT:
PROVIDER: PRJNA480676 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7511290_1.fastq.gz | Fastqsanger.gz | |||
| SRR7511290_2.fastq.gz | Fastqsanger.gz | |||
| SRR7511281_1.fastq.gz | Fastqsanger.gz | |||
| SRR7511281_2.fastq.gz | Fastqsanger.gz | |||
| SRR7511291_1.fastq.gz | Fastqsanger.gz |
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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: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: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
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: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.
2022-08-31 | GSE207279 | GEO
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:We studied the influence of genetic type (pure Iberian pigs vs crossbred with Duroc) on l.dorsi transcriptome Background: The two main genetic types in Iberian pig production show important phenotypic differences in growth, fattening and tissue composition since early developmental stages. The objective of this work was the evaluation of muscle transcriptome profile in young animals of both genetic types, in order to identify genes, pathways and transcription factors responsible of their phenotypic differences. Contemporary families coming from pure Iberian pigs (IB) or from crossing with Duroc boars (DUxIB) were generated. Piglets (14 from each genetic type) were sacrificed at weaning (28 days) and longissimus dorsi muscle was sampled for composition and gene expression studies. RNA was obtained and hybridized to Affymetrix Porcine Genechip expression arrays. Results: Loin muscle composition showed significant differences between genetic types in intramuscular fat content (6% vs. 4.2% in IB and DUxIB animals, respectively, P=0.009) and in saturated and monounsaturated fatty acid contents (P=0.019 and P=0.044, respectively). Statistical analysis of gene expression data allowed the identification of 256 differentially expressed (DE) genes between genetic types (FDR<0.10), 102 upregulated in IB and 154 upregulated in DUxIB. The size of the effects ranged between 1.2x and 7.8x. Transcript differences were validated for a subset of DE genes by qPCR. Some candidate genes with known effects on muscle growth were found among the DE genes upregulated in DUxIB (IGF2, collagens, integrins). Genes related to lipid metabolism and proteolysis were found among the genes upregulated in IB (ME1, ELOVL6, caspases, catepsins, ubiquitination proteins). We observed alteration in biological functions related to extracellular matrix organization, cellular adhesion, muscle growth and lipid metabolism. Transcription factors (TF) potentially involved in the expression differences found were identified by calculating the regulatory impact factors (RIF). Sixteen TF were found, some of them with known relationship with muscle development (MSTN, SIX4), adipogenesis (CEBPD, PPARGC1B), or extracellular matrix processes (MAX, MXI1). Correlation among the expression of these TF and DE genes show relevant differences between genetic types. Conclusion: The results contribute valuable information about molecular mechanisms determining the phenotypic differences of growth and meat quality between the genetic types studied, mainly related to the development and function of the extracellular matrix and also to some metabolic processes as proteolysis and lipid metabolism. 28 male piglets were employed. 14 animals coming for pure Iberian parents and 14 coming from the crossing of Duroc boars with Iberian sows. Animals were sacrificed at 28 d of age. At the sacrifice, longissimus dorsi muscle tissue was sampled from each animal.
2014-06-11 | E-GEOD-53029 | biostudies-arrayexpress
Project description:10 + 10 Holstein x Charolais F2 cattle were assigned to 2 groups with high and low IMF content, respectively; Musculus longissimus dorsi mRNA expression was determined by microarray analysis
2015-12-02 | GSE75347 | GEO
Project description:One of the most important determinants of meat quality is the intramuscular fat (IMF) content. 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 present study were to analyze the longissimus dorsi transcriptome of purebred Iberian pigs divergent for their IMF breeding value to identify differential expressed genes and regulatory factors affecting gene expression. RNA-seq allowed identifying ?10,000 of the 25,878 annotated genes in the analyzed samples. In addition to this, 42.46% of the identified transcripts corresponded to newly predicted isoforms. Differential expression analyses revealed a total of 221 DE annotated genes and 116 DE new isoforms. Functional analyses identified an enrichment of overexpressed genes involved in lipid metabolism (FASN, SCD, ELOVL6, DGAT2, PLIN1, CIDEC, and ADIPOQ) in animals with a higher content of IMF and an enrichment of overexpressed genes related with myogenesis and adipogenesis (EGR1, EGR2, EGR3, JUNB, FOSB, and SEMA4D) in the animals with a lower content of IMF. In addition to this, potential regulatory elements of these DE genes were identified. Co-expression networks analyses revealed six long non-coding RNAs (lncRNAs) (ALDBSSCG0000002079, ALDBSSCG0000002093, ALDBSSCG0000003455, ALDBSSCG0000004244, ALDBSSCG0000005525, and ALDBSSCG0000006849) co-expressed with SEMA4D and FOSB genes and one (ALDBSSCG0000004790) with SCD, ELOVL6, DGAT2, PLIN1, and CIDEC. Analyses of the regulatory impact factors (RIFs) revealed 301 transcriptionally regulatory factors involved in expression differences, with five of them involved in adipogenesis (ARID5B, CREB1, VDR, ATF6, and SP1) and other three taking part of myogenesis and development of skeletal muscle (ATF3, KLF11, and MYF6). The results obtained provide relevant insights about the genetic mechanisms underlying IMF content in purebred Iberian pigs and a set of candidate genes and regulatory factors for further identification of polymorphisms susceptible of being incorporated in a selection program.
| S-EPMC6288315 | biostudies-literature
Project description:Transcriptome Profiling of Longissimus Dorsi Muscle of Donkeys with High and Low Intramuscular Fat Content
| PRJNA659228 | ENA