title: Comparative transcriptomic analysis by RNA-seq to discern differential expression of genes in liver and muscle tissues of adult Berkshire and Jeju Native Pig.
abstract: RNA-seq is being rapidly adopted for the profiling of the transcriptomes in different areas of biology, especially 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 of Sus scrofa, is of particular interest for the current study. For the better understanding of the gene expression profiles of the liver and longissimus dorsi muscle, DEGs were identified via RNA-seq. Sequence reads were obtained from Illumina HiSeq2000 and mapped to the pig reference genome (Sscrofa10.2) using Tophat2. We identified 169 and 39 DEGs in the liver and muscle of JNP respectively, by comparison with Berkshire breed. Out of all identified genes, 41 genes in the liver and 9 genes in the muscle have given significant expression. Gene ontology (GO) terms of developmental process and KEGG pathway analysis showed that metabolic, immune response and protein binding were commonly enriched pathways in the two tissues. Further the heat map analysis by ArrayStar has shown the different levels of expression in JNP with respect to the Berkshire breed. The validation through real time PCR and western blotting also confirmed the differential expression of genes in both breeds. Genes pertaining to metabolic process and inflammatory and immune system are more enriched in Berkshire breed. This comparative transcriptome analysis of two tissues suggests a subset of novel marker genes which expressed differently between the JNP and Berkshire.
authors.affiliation: Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea.
authors.forename: Simrinder Singh
authors.initials: SS
authors.lastname: Sodhi
authors.affiliation: The Animal Genomics and Breeding Center, Hankyong National University, Anseong-si, Gyeonggi-do 456-749, South Korea.
authors.forename: Ki-Duk
authors.initials: KD
authors.lastname: Song
authors.affiliation: Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea.
authors.forename: Mrinmoy
authors.initials: M
authors.lastname: Ghosh
authors.affiliation: Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea.
authors.forename: Neelesh
authors.initials: N
authors.lastname: Sharma
authors.affiliation: Department of Animal Biotechnology, College of Animal Bioscience and Technology, Kangwon National University, Chuncheon 200-701, South Korea.
authors.forename: Sung Jin
authors.initials: SJ
authors.lastname: Lee
authors.affiliation: Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea.
authors.forename: Jeong Hyun
authors.initials: JH
authors.lastname: Kim
authors.affiliation: Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea.
authors.forename: Nameun
authors.initials: N
authors.lastname: Kim
authors.affiliation: Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea.
authors.forename: Raj Kumar
authors.initials: RK
authors.lastname: Mongre
authors.affiliation: Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea.
authors.forename: Pradeep
authors.initials: P
authors.lastname: Adhikari
authors.affiliation: Institute for Livestock Promotion, Jeju-do, Jeju 690-802, South Korea.
authors.forename: Jin Young
authors.initials: JY
authors.lastname: Kim
authors.affiliation: Institute for Livestock Promotion, Jeju-do, Jeju 690-802, South Korea.
authors.forename: Sang Pyo
authors.initials: SP
authors.lastname: Hong
authors.affiliation: Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea.
authors.forename: Sung Jong
authors.initials: SJ
authors.lastname: Oh
authors.affiliation: Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea; Sustainable Agriculture Research Institute (SARI), Jeju National University, Jeju 690-756, South Korea. Electronic address: dkjeong@jejunu.ac.kr.
authors.forename: Dong Kee
authors.initials: DK
authors.lastname: Jeong
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000502:physiology*; D008099:Liver / Q000378:metabolism*; D018482:Muscle, Skeletal / Q000378:metabolism*; D013552:Swine / Q000378:metabolism*; D059467:Transcriptome / Q000502:physiology*
keywords: Differentially expressed genes (DEGs); Gene ontology (GO); Liver; Longissimus dorsi muscle; RNA-seq