Liver and fat transcriptomic changes related to fat content in pigs
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ABSTRACT:
PROVIDER: PRJNA673196 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12937428_1.fastq.gz | Fastqsanger.gz | |||
| SRR12937428_2.fastq.gz | Fastqsanger.gz | |||
| SRR12937429_1.fastq.gz | Fastqsanger.gz | |||
| SRR12937429_2.fastq.gz | Fastqsanger.gz | |||
| SRR12937430_1.fastq.gz | Fastqsanger.gz |
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Project description:Intramuscular (i.m.) fat content influencing consumer’s acceptability of pork is considered as a limiting factor for meat quality. To gain insight into the biological basis of individual variability in i.m. fat content, both gene expression profiling and proteomic investigation were associated in pig longissimus muscle (LM). Keywords: intramuscular fat, gene expression, pigs, proteomics, microarray, pork meat
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Project description:Intramuscular (i.m.) fat content influencing consumerâs acceptability of pork is considered as a limiting factor for meat quality. To gain insight into the biological basis of individual variability in i.m. fat content, both gene expression profiling and proteomic investigation were associated in pig longissimus muscle (LM). Keywords: intramuscular fat, gene expression, pigs, proteomics, microarray, pork meat Animals were sampled from a population of 1,000 pigs generated as an F2 intercross between two production sire lines: FH016 (Pietrain type, France Hybrides SA, St Jean de Braye, France) and FH019 (Synthetic line, from Duroc, Hampshire and Large White founders, France Hybrides SA, St Jean de Braye, France).
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Project description:Intramuscular fat (IMF) content is the determining factor for meat taste. To reveal the genetic basis of IMF content, genetic studies have made some progress in lean-type pig breeds, but fewer studies have been conducted in Chinese fat-type pigs. The Luchuan pig is a fat-type local breed in southern China that is famous for its desirable meat quality. In the present study, we measured the IMF content for 265 crossed pigs of Duroc x Luchuan pigs, from which individuals with extremely high (6.03% ± 0.58%, n = 12) and low (1.67% ± 0.42%, n = 12) IMF contents were selected to identify differentially expressed genes (DEGs) related to IMF content in the longissimus dorsi. RNA sequencing for 24 samples in total identified 312 differentially expressed transcripts that were significantly enriched in triglyceride biosynthesis- and metabolism-related processes (p-value ≤ 0.05 and fold change ≥ 1.5). Functional enrichment analysis revealed that the PPAR signaling pathway was the most significantly enriched pathway (p-value = 0.024, represented by ADIPOQ, FABP3, FABP4, LPL, PLIN4 and SCD). When a more stringent condition was applied (gene-based q-value ≤ 0.2 and fold change ≥ 1.5), only 17 transcripts remained to be differentially expressed, including LEP, ATP6V1F, SDR16C5, TUSC5, MPZ, PRX, PTPN4, BEX1, MVB12B, ZFP62, P4HA2, IDH2, THOC7, KRT14, FCGRT, MYPN and LPL. Among these DEGs, TUSC5 was significantly upregulated in the group of high IMF contents (log2FC = 1.114, p-value = 3.02E-5) and was suspected as a strong new candidate gene affecting porcine IMF content since it was the target gene of PPAR-gamma. The present study provided new data and candidate genes for the genetic study of porcine IMF content.
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Project description:Intramuscular fat content (IMF) is a complex trait influencing the technological and sensorial features of meat products and determining pork quality. Thus, we aimed at analysing through RNA-sequencing the Semimembranosus muscle transcriptome of Italian Large White pigs in order to study the gene networks associated with IMF deposition. Two groups of samples were used; each one was composed of six unrelated pigs with extreme and divergent IMF content (0.67 ± 0.09% in low IMF vs. 6.81 ± 1.17% in high IMF groups) that were chosen from 950 purebred individuals. Paired-end RNA sequences were aligned to Sus scrofa genome assembly 11.1 and gene counts were analysed using WGCNA and DeSeq2 packages in R environment. Interestingly, among the 58 differentially expressed genes (DEGs), several were related to primary cilia organelles (such as Lebercilin 5 gene), in addition to the genes involved in the regulation of cell differentiation, in the control of RNA-processing, and in G-protein and ERK signalling pathways. Together with cilia-related genes, we also found in high IMF pigs an over-expression of Fibroblast Growth Factor 2 (FGF2) gene, which in other animal species was found to be a regulator of ciliogenesis. Four WGCNA gene modules resulted significantly associated with IMF deposition: grey60 (P = 0.003), darkturquoise (P = 0.022), skyblue1 (P = 0.022), and lavenderblush3 (P = 0.030). The genes comprised in the significant modules confirmed the results obtained for the DEGs, and the analysis with CytoHubba indicated genes controlling RNA splicing and cell differentiation as hub genes. Among the complex molecular processes affecting muscle fat depots, genes involved in primary cilia may have an important role, and the transcriptional reprogramming observed in high IMF pigs may be related to an FGF-related molecular cascade and to ciliogenesis, which in the literature have been associated with fibro-adipogenic precursor differentiation.
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