Amino Acids

, Volume 51, Issue 3, pp 495–511 | Cite as

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

  • Mrinmoy Ghosh
  • Neelesh Sharma
  • Meeta Gera
  • Nameun Kim
  • Simrinder Singh Sodhi
  • KrishnaKanth Pulicherla
  • Do Huynh
  • Dae Cheol Kim
  • Jiaojiao Zhang
  • Taeho Kwon
  • Kyung Tak Do
  • Hak Kyo Lee
  • Ki-Duk Song
  • DongKee JeongEmail author
Original Article


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.


Differentially expressed genes Livestock improvement Principal component analysis Sus scrofa domestica Ttranscriptome sequencing 



Alveolar macrophage


Alpha-1-microglobulin/bikunin precursor


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


Gene ontology


Jeju Native Pig


Kyoto encyclopedia of genes and genomes


Myosin binding protein H


Macrophage receptor with collagenous


Next-generation sequencing


Protegrin 3


Principal component analysis


Principal component




Pancreatic lipase


Patatin-like phospholipase domain-containing protein 3




SPENCD with immune dysregulation


Single variations



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.

Author contributions

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.

Ethical approval

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.

Informed consent

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.

Supplementary material

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Supplementary material 1 (DOCX 427 kb)
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Supplementary material 2 (DOCX 25 kb)
726_2018_2685_MOESM3_ESM.xlsx (22.8 mb)
Supplementary material 3 (XLSX 23339 kb)
726_2018_2685_MOESM4_ESM.xlsx (20.5 mb)
Supplementary material 4 (XLSX 21011 kb)


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Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2018

Authors and Affiliations

  • Mrinmoy Ghosh
    • 1
    • 2
  • Neelesh Sharma
    • 3
  • Meeta Gera
    • 1
  • Nameun Kim
    • 1
  • Simrinder Singh Sodhi
    • 4
  • KrishnaKanth Pulicherla
    • 5
  • Do Huynh
    • 1
  • Dae Cheol Kim
    • 6
  • Jiaojiao Zhang
    • 1
  • Taeho Kwon
    • 1
  • Kyung Tak Do
    • 1
  • Hak Kyo Lee
    • 7
  • Ki-Duk Song
    • 7
  • DongKee Jeong
    • 1
    Email author
  1. 1.Department of Animal Biotechnology, Faculty of BiotechnologyJeju National UniversityJejuRepublic of Korea
  2. 2.Department of Biotechnology, Division of Research and DevelopmentLovely Professional UniversityPhagwaraIndia
  3. 3.Department of Veterinary Medicine, Faculty of Veterinary Science and Animal HusbandrySher-e-Kashmir University of Agricultural Sciences and Technology of JammuJammuIndia
  4. 4.Department of Veterinary and Animal Husbandry Extension EducationGuru Angad Dev Veterinary and Animal Sciences UniversityLudhianaIndia
  5. 5.Department of Science and TechnologyTechnology Development TransferNew DelhiIndia
  6. 6.Livestock Promotion Institute, Jeju Special Self-governing ProvinceJejuRepublic of Korea
  7. 7.Department of Animal BiotechnologyChonbuk National UniversityJeonjuRepublic of South Korea

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