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

被引:0
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作者
Simrinder Singh Sodhi
Won Cheoul Park
Mrinmoy Ghosh
Jin Nam Kim
Neelesh Sharma
Kwang Yun Shin
In Cheol Cho
Youn Chul Ryu
Sung Jong Oh
Sung Hoon Kim
Ki-Duk Song
Sang Pyo Hong
Seo Ae Cho
Hee Bal Kim
Dong Kee Jeong
机构
[1] Jeju National University,Department of Animal Biotechnology, Faculty of Biotechnology
[2] Jeju National University,Sustainable Agriculture Research Institute (SARI)
[3] Seoul National University,Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences
[4] Seoul National University,C&K Genomics Main Bldg. #514, SNU Research Park
[5] Institute for Livestock Promotion,Subtropical Animal Experiment Station
[6] National Institute of Animal Science,Department of Animal Life and Environment Science
[7] Hankyong National University,Genomic Informatics Center
[8] Hankyong National University,undefined
来源
Molecular Biology Reports | 2014年 / 41卷
关键词
RNA-seq; Jeju Native Pig (JNP); Berkshire; Fat; Differentially expressed genes (DEGs);
D O I
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中图分类号
学科分类号
摘要
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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页码:6305 / 6315
页数:10
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