Dataset Information

Identification and functional prediction of long noncoding RNAs related to intramuscular fat content in Laiwu pigs.

ABSTRACT:

Objective

Intramuscular fat (IMF) is a critical economic indicator of pork quality. Studies on IMF among different pig breeds have been performed via high-throughput sequencing, but comparisons within the same pig breed remain unreported.

Methods

This study was performed to explore the gene profile and identify candidate long noncoding RNA (lncRNAs) and mRNAs associated with IMF deposition among Laiwu pigs with different IMF contents. Based on the longissimus dorsi muscle IMF content, eight pigs from the same breed and management were selected and divided into two groups: a high IMF (>12%, H) and low IMF group (<5%, L). Whole-transcriptome sequencing was performed to explore the differentially expressed (DE) genes between these two groups.

Results

The IMF content varied greatly among Laiwu pig individuals (2.17% to 13.93%). Seventeen DE lncRNAs (11 upregulated and 6 downregulated) and 180 mRNAs (112 upregulated and 68 downregulated) were found. Gene Ontology analysis indicated that the following biological processes played an important role in IMF deposition: fatty acid and lipid biosynthetic processes; the extracellular signal-regulated kinase cascade; and white fat cell differentiation. In addition, the peroxisome proliferator-activated receptor, phosphatidylinositol-3-kinase-protein kinase B, and mammalian target of rapamycin pathways were enriched in the pathway analysis. Intersection analysis of the target genes of DE lncRNAs and mRNAs revealed seven candidate genes associated with IMF accumulation. Five DE lncRNAs and 20 DE mRNAs based on the pig quantitative trait locus database were identified and shown to be related to fat deposition. The expression of five DE lncRNAs and mRNAs was verified by quantitative real time polymerase chain reaction (qRT-PCR). The results of qRT-PCR and RNA-sequencing were consistent.

Conclusion

These results demonstrated that the different IMF contents among pig individuals may be due to the DE lncRNAs and mRNAs associated with lipid droplets and fat deposition.

SUBMITTER: Wang L

PROVIDER: S-EPMC8738936 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundLong non-coding RNAs (lncRNAs) regulate adipocyte differentiation and metabolism, However, their function on subcutaneous and intramuscular adipose tissues in pigs is unclear. Intramuscular fat (IMF) is an important indicator for evaluating meat quality. Breeds with high IMF content are often accompanied by high subcutaneous fat (SCF), which severely affects the meat rate of pigs. It is of great significance for porcine breeding to study the mechanism of lncRNA related to adipogenesis and lipid metabolism.MethodsWe identified differentially expressed lncRNAs, miRNAs and mRNAs in subcutaneous and intramuscular adipose tissues in three female Laiwu pigs by deep RNA-sequencing(|log2foldchange|≥1, P_value ≤ 0.05). The gene expression profiles of IMF and SCF in Laiwu pigs were comparatively analyzed by Bioinformatics methods to identify key lncRNAs, miRNAs, and mRNAs associated with lipid metabolism and adipogenesis.ResultsA total of 1209 lncRNAs (DElncRNAs), 286 miRNAs (DEmiRNAs), and 1597 mRNAs (DEgenes) were differentially expressed between two types of adipose. Among them, 17 DElncRNAs and 103 target genes play a role in the co-expression network, as well as 59 DElncRNAs, 44 DEmiRNAs, and 88 DEgenes involved in ceRNA network. In GO(Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis of DElncRNAs their target genes involved in many adipogenesis and lipid metabolism biological processes and signaling pathways, such as PPAR signaling pathway, Wnt signaling pathway, MAPK signaling pathway.ConclusionsBy constructing co-expression and ceRNAs network we found that Wnt signaling pathway play a critical regulatory role in intramuscular adipogenesis and lipid accumulation in Laiwu pigs. TCONS_00006525, TCONS_00046551 and TCONS_00000528 may target WNT5A, WNT10B and FDZ3 in co-expression network, TCONS_00026517 and other lncRNAs regulate the expression of PPARG, RXRG and SCD in ceRNA network, and were involved in Wnt signaling pathway. This study provides a theoretical basis for further understanding the post-transcriptional regulation mechanism of meat quality formation, predicting and treating diseases caused by ectopic fat.