Identification of molecular mechanisms related with fatness in pig at transcriptome and miRNAome level
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ABSTRACT:
PROVIDER: PRJNA506427 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8235030.fastq.gz | Fastqsanger.gz | |||
| SRR8235040.fastq.gz | Fastqsanger.gz | |||
| SRR8235050.fastq.gz | Fastqsanger.gz | |||
| SRR8235060.fastq.gz | Fastqsanger.gz | |||
| SRR8235031.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: The aim of present research was to identify miRNAs potentially related with fattness traits in pigs Methods: miRNA-seq analysis was performed on subcutaneous fat samples collected from 22 pigs representing two sire-line breeds – Pietrain and Hampshire and one dam-line – Large White. Based on dissection data, pigs were selected from a larger population in terms of fatness traits to obtain the most extreme groups in each breed. The cDNA libraries were constructed form 300 ng of total RNA with the use NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA, United States) according to the protocol. The quantification of obtained libraries was performed on Qubit 2.0 (Invitrogen, Life Technologies) and TapeStation 2200 (D1000 ScreenTape; Agilent). The RNA-seq was performed in 36 single-end cycles on HiScanSQ platform (Illumina) with the use of ruSeq SR Cluster Kit v3- CBOT-HS and TruSeq SBS Kit v 3 - HS (Illumina). Each library was sequences in 4 technical replications. The DEGs were detected using DESEq2 software and validation was performed by qPCR. Results: RNA-seq approach allowed to identify miRNAs differentially expressed between pigs with various fatness traits in each analyzed breeds: 64 for Pietrain pigs; 41 for Hampshire and 46 for Large White pigs (pvalue <0.05; fold change≤1.5). The comparison of obtained miRNAs sets showed 13 miRNAs identified in all three breeds. The Gene Ontology analysis (mirPath v.3.0 DIANA Tools web with DIANA—TarBase v7.0 as a reference) confirmed that detected miRNAs were involved in fatty acid biosynthesis (pvalue <1e-325); fatty acid metabolism (pvalue 6.661338e-16); ECM-receptor interaction (pvalue <1e-325). The most important targeted genes regulated by identified miRNAs were: fatty acid synthase – FASN; Acetyl-CoA carboxylase 1 – ACACA; Malonyl CoA-acyl carrier protein transacylase – MCAT and acetyl-CoA acyltransferase 1 and 2 (ACAA1 and ACAA2 genes). Conclusions: Obtained results allow to propose the panel of miRNAs, which can be related with fatness in pig. Such analysis can be the basis of future research in terms of identification of molecular mechanisms related with adipogenesis and fatness traits in pigs.
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Project description:Domestication of pig results in modifications of many traits, including fatness traits, which are important in pig production since they have effect on meat quality, fattening efficiency, reproduction and immunity.In this study, we investigate 3D genome organization and transcriptomic characterization of adipose tissues (ATs) between wild boars and Bama pig, a typical indigenous domestic pig in China, to uncover molecular mechanisms of fatness-phenotypic shifts.
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Project description:Fat deposition and growth rate are closely related to pork quality and fattening efficiency. The next-generation sequencing (NGS) approach for transcriptome and miRNAome massive parallel sequencing of adipocyte tissue was applied to search for a molecular network related to fat deposition in pigs. Pigs were represented by three breeds (Large White, Pietrain, and Hampshire) that varied in fat content within each breed. The obtained results allowed for the detection of significant enrichment of Gene Ontology (GO) terms and pathways associated directly and indirectly with fat deposition via regulation of fatty acid metabolism, fat cell differentiation, inflammatory response, and extracellular matrix (ECM) organization and disassembly. Moreover, the results showed that adipocyte tissue content strongly affected the expression of leptin and other genes related to a response to excessive feed intake. The findings indicated that modification of genes and miRNAs involved in ECM rearrangements can be essential during fat tissue growth and development in pigs. The identified molecular network within genes and miRNAs that were deregulated depending on the subcutaneous fat level are proposed as candidate factors determining adipogenesis, fatness, and selected fattening characteristics in pigs.
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Project description:Identification of genes and causal mutations regulating growth and fatness traits in pig.
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Project description:Purpose: Identification of genes regulating growth and fatness traits in pig. Methods: Hypothalamic transcriptome analysis through RNA-seq and differential expression analysis of divergent pigs for growth and fatness traits. Results: Characterization of the transcripts expressed in the porcine hypothalamus and identification of differentially expressed genes, some of them located within previously described QTL regions. Conclusions: Characterization of porcine hypothalamic transcriptome and identification of relevant genes and transcription factors related to the traits of interest. Transcriptome sequencing of 10 hypothamic samples of two groups of divergent pigs for growth and fatness (five per group).
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