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Comparative transcriptomic analysis to identify differentially expressed genes in fat tissue of adult Berkshire and Jeju Native Pig using RNA-seq

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Abstract

Pork is a major source of animal protein for humans. The subcutaneous, intermuscular and the intramuscular fat are the factors responsible for meat quality. RNA-seq is rapidly adopted for the profiling of the transcriptomes in the studies related to gene regulation. The discovery of differentially expressed genes (DEGs) between adult animals of Jeju Native Pig (JNP) and Berkshire breeds are of particular interest for the current study. RNA-seq was used to investigate the transcriptome profiling in the fat tissue. Sequence reads were obtained from Ilumina HiSeq2000 and mapped to the pig genome using Tophat2. Total 153 DEGs were identified and 71 among the annotated genes, have BLAST matches in the non- redundant database. Metabolic, immune response and protein binding are enriched pathways in the fat tissue. In our study, biological adhesion, cellular, developmental and multicellular organismal processes in fat were up-regulated in JNP as compare to Berkshire. Multicellular organismal process, developmental process, embryonic morphogenesis and skeletal system development were the most significantly enriched terms in fat of JNP and Berkshire breeds (p = 1.17E−04, 0.044, 3.47E−04 and 4.48E−04 respectively). COL10A1, COL11A2, PDK4 and PNPLA3 genes responsible for skeletal system morphogenesis and body growth were down regulated in JNP. This study is the first statistical analysis for the detection of DEGs from RNA-seq data generated from fat tissue sample. This analysis can be used as stepping stone to understand the difference in the genetic mechanisms that might influence the identification of novel transcripts, sequence polymorphisms, isoforms and noncoding RNAs.

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Acknowledgments

This study was supported by a grant from the Next-Generation BioGreen 21 Program (No. PJ009032022012), Rural Development Administration, Republic of Korea, hence the authors are thankful to this organization.

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Authors and Affiliations

  1. Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Ara-1 Dong, Jeju-Do, Jeju, 690-756, South Korea

    Simrinder Singh Sodhi, Mrinmoy Ghosh, Neelesh Sharma, Youn Chul Ryu, Sung Jong Oh & Dong Kee Jeong

  2. Sustainable Agriculture Research Institute (SARI), Jeju National University, Jeju, 690-756, Korea

    Dong Kee Jeong

  3. Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea

    Won Cheoul Park, Jin Nam Kim & Hee Bal Kim

  4. C&K Genomics Main Bldg. #514, SNU Research Park, Seoul National University, Mt.4-2, NakSeoungDae, Gwanakgu, Seoul, 151-919, Korea

    Seo Ae Cho & Hee Bal Kim

  5. Institute for Livestock Promotion, Jeju-do, Jeju, 690-802, Korea

    Kwang Yun Shin & Sang Pyo Hong

  6. Subtropical Animal Experiment Station, National Institute of Animal Science, R.D.A, 175-6, O-deung Dong, Jeju, 690-150, Korea

    In Cheol Cho

  7. Department of Animal Life and Environment Science, Hankyong National University, Ansung, 456-749, Korea

    Sung Hoon Kim

  8. Genomic Informatics Center, Hankyong National University, Ansung, Korea

    Ki-Duk Song

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  1. Simrinder Singh Sodhi
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  2. Won Cheoul Park
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  3. Mrinmoy Ghosh
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Correspondence to Dong Kee Jeong.

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Simrinder Singh Sodhi and Won Cheoul Park have contributed equally to this work.

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Sodhi, S.S., Park, W.C., Ghosh, M. et al. 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, 6305–6315 (2014). https://doi.org/10.1007/s11033-014-3513-y

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