Stage specific transcriptome analysis of liver tissue from a crossbred Korean Native Pig (KNP × Yorkshire)

서지정보

ㆍ발행기관 : 충북대학교 동물의학연구소 ㆍ수록지정보 : Journal of Biomedical and Translational Research / 19권 / 4호
ㆍ저자명 : Himansu Kumar, Krishnamoorthy Srikanth, Woncheol Park, Kyung-Tai Lee, Bong-Hwan Choi, Jun-Mo Kim, Dajeong Lim, Jong-Eun Park

목차

Introduction
Materials and Methods
Ethical statement and pig rearing
Isolation of RNAs, and RNA sequencing
Quality analysis, mapping, and assembly of sequenced RNA reads
Identification of differentially expressed genes
Gene ontology and KEGG pathway
Validation of differentially expressed genes by qRT-PCR
Results and Discussions
Analysis of sequencing reads
Differentially expressed gene analysis
Pathway analysis
Protein-protein interaction analysis
qRT-PCR analysis to validate the top five DEG genes
Conclusion
References

영어 초록

Korean Native Pig (KNP) has a uniform black coat color, excellent meat quality, white colored fat, solid fat structure and good marbling. However, its growth performance is low, while the western origin Yorkshire pig has high growth performance. To take advantage of the unique performance of the two pig breeds, we raised crossbreeds (KNP × Yorkshire to make use of the heterotic effect. We then analyzed the liver transcriptome as it plays an important role in fat metabolism. We sampled at two stages: 10 weeks and at 26 weeks. The stages were chosen to correspond to the change in feeding system. A total of 16 pigs (8 from each stage) were sampled and RNA sequencing was performed. The reads were mapped to the reference genome and differential expression analysis was performed with edgeR package. A total of 324 genes were found to be significantly differentially expressed (|log2FC| > 1 & q < 0.01), out of which 180 genes were up-regulated and 144 genes were down-regulated. Principal Component Analysis (PCA) showed that the samples clustered according to stages. Functional annotation of significant DEGs (differentially expressed genes) showed that GO terms such as DNA replication, cell division, protein phosphorylation, regulation of signal transduction by p53 class mediator, ribosome, focal adhesion, DNA helicase activity, protein kinase activity etc. were enriched. KEGG pathway analysis showed that the DEGs functioned in cell cycle, Ras signaling pathway, p53 signaling pathway, MAPK signaling pathway etc. Twenty-nine transcripts were also part of the DEGs, these were predominantly Cys2His2-like fold group (C2H2) family of zinc fingers. A protein-protein interaction (PPI) network analysis showed that there were three highly interconnected clusters, suggesting an enrichment of genes with similar biological function. This study presents the first report of liver tissue specific gene regulation in a cross-bred Korean pig.

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