The first comprehensive description of the expression profile of genes involved in differential body growth and the immune system of the Jeju Native Pig and miniature pig
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Sus scrofa provides a major source of animal protein for humans as well as being an excellent biomedical model. This study was carried out to understand, in detail, the genetic and functional variants of Jeju Native Pigs and miniature pigs through differential expression profiling of the genes controlling their immune response, growth performance, and meat quality. The Illumina HiSeq 2000 platform was used for generating 1.3 billion 90 bp paired-end reads, which were mapped to the S. scrofa genome using TopHat2. A total of 2481 and 2768 genes were differentially expressed with 8-log changes in muscle and liver samples, respectively. Five hundred forty-eight genes in muscle and 642 genes in liver samples had BLAST matches within the non-redundant database. GO process and pathway analyses showed enhanced biological processes related to the extracellular structural organization and skeletal muscle cell differentiation in muscle tissue, whereas the liver tissue shares functions related to the inflammatory response. Herein, we identify inflammatory regulatory genes in miniature pigs and growth response genes in Jeju Native Pigs, information which can provide a stronger base for the selection of breeding stock and facilitate further in vitro and in vivo studies for therapeutic purposes.
KeywordsDifferentially expressed genes Livestock improvement Principal component analysis Sus scrofa domestica Ttranscriptome sequencing
Acid phosphatase 5
Collagen type XXI alpha 1
C-X-C Motif Chemokine Ligand 13
Database for Annotation, Visualization and Integrated Discovery
Differentially expressed genes
Fatty acid-binding proteins
Fatty acid-binding protein 6
False discovery rate
Jeju Native Pig
Kyoto encyclopedia of genes and genomes
Myosin binding protein H
Macrophage receptor with collagenous
Principal component analysis
Patatin-like phospholipase domain-containing protein 3
SPENCD with immune dysregulation
This study was supported by a grant from the Next-Generation BioGreen 21 Program (No. PJ01316701; PJ01117401, and PJ0099272014), Rural Development Administration, Republic of Korea, hence the authors are thankful for this organization. Author MG also thankful to Lovely Professional University for provide necessary requirements.
DKJ and MG contributed to the design the conception and designed the project; MG contributed to design, analysis, and interpretation of data; MG, NK, and JZ contributed to the collected, harvested and mRNA analyses; DCK, DH, KTD and TK contributed to collect the field samples; DKJ, KD contributed to the evaluation of intellectual contents; KKP contributed to further literature corrections; DKJ and NS contributed to revising the manuscript critically for important intellectual content; HKL and KDS contributed to the additional validation and data analysis; DKJ contributed to the final approval of the manuscript. All authors provided critical input in manuscript completion and approved the final version of the manuscript.
Compliance with ethical standards
Conflict of interest
The authors declare we have no known conflicts of interest in this work.
All procedures performed in this experiment were approved by the regional Ethical Committee (Jeju National University Animal Bioethics committee permit number: 2013-0009). The animals were handled in accordance with proper animal welfare guidelines.
Written and intellectual contents of this article were obtained from all the authors listed in the study. All authors have been contributed to conception, design, interpretation of data and analysis.
- Andrade EL, Bento AF, Cavalli J, Oliveira SK, Schwanke RC, Siqueira JM, Freitas CS, Marcon R, Calixto JB (2016) Non-clinical studies in the process of new drug development-Part II: good laboratory practice, metabolism, pharmacokinetics, safety and dose translation to clinical studies. Braz J Med Biol Res 49(12):e5646CrossRefPubMedPubMedCentralGoogle Scholar
- Briggs TA, Rice GI, Daly S, Urquhart J, Gornall H, Bader-Meunier B, Baskar K, Baskar S, Baudouin V, Beresford MW, Black GC (2011) Tartrate-resistant acid phosphatase deficiency causes a bone dysplasia with autoimmunity and a type I interferon expression signature. Nat Genet 43(2):127–131CrossRefPubMedGoogle Scholar
- deLange CFM (2012) New NRC (2012) nutrient requirements of Swine. Adv Pork Product: 17-28Google Scholar
- Ghadimi M, Ried T, Yfantis HG, Lee DH, Maitra A, Hanna N, Alexander HR, Hussain SP (2013) Integration of metabolomics and transcriptomics revealed a fatty acid network exerting growth inhibitory effects in human pancreatic cancer. Clin Cancer Res 19(18):4983–4993CrossRefPubMedPubMedCentralGoogle Scholar
- Ghosh M, Sodhi SS, Song KD, Kim JH, Mongre RK, Sharma N, Singh NK, Kim SW, Lee HK, Jeong DK (2015) Evaluation of body growth and immunity-related differentially expressed genes through deep RNA sequencing in the piglets of Jeju Native Pig and Berkshire. Anim Genet 46(3):255–264CrossRefPubMedGoogle Scholar
- Gunawan A, Sahadevan S, Neuhoff C, Große-Brinkhaus C, Gad A, Frieden L, Tesfaye D, Tholen E, Looft C, Uddin MJ, Schellander K, Cinar MU (2013) RNA Deep sequencing reveals novel candidate genes and polymorphisms in boar testis and liver tissues with divergent androstenone levels. PLoS One 8(5):e63259CrossRefPubMedPubMedCentralGoogle Scholar
- Hara H, Koike N, Long C, Piluek J, Roh DS, SundarRaj N, Funderburgh JL, Mizuguchi Y, Isse K, Phelps CJ, Ball SF (2011) Initial in vitro investigation of the human immune response to corneal cells from genetically engineered pigs. Invest Ophthalmol Vis Sci 52(8):5278–5286CrossRefPubMedPubMedCentralGoogle Scholar
- Kayan A (2011) Identification of positional and functional candidate genes for meat and carcass quality in F2 Duroc x Pietrain resource population. Dissertation, Bonn UniversityGoogle Scholar
- Sodhi SS, Park WC, Ghosh M, Kim JN, Sharma N, Shin KY, Cho IC, Ryu YC, Oh SJ, Kim SH, Song KD (2014a) Comparative transcriptomic analysis to identify differentially expressed genes in fat tissue of adult Berkshire and Jeju Native Pig using RNA-seq. Mol Biol Rep 41(9):6305–6315CrossRefPubMedGoogle Scholar
- Sodhi SS, Song KD, Ghosh M, Sharma N, Lee SJ, Kim JH, Kim N, Mongre RK, Adhikari P, Young KJ, Pyo HS, Sung OhJ, Jeong DK (2014b) Comparative transcriptomic analysis by RNA-seq to discern differential expression of genes in liver and longissimus dorsi muscle tissues of adult Berkshire and Jeju Native Pig. Gene 546(2):233–242CrossRefPubMedGoogle Scholar