title: A global view of porcine transcriptome in three tissues from a full-sib pair with extreme phenotypes in growth and fat deposition by paired-end RNA sequencing.
abstract: BACKGROUND
  Elucidation of the pig transcriptome is essential for interpreting functional elements of the genome and understanding the genetic architecture of complex traits such as fat deposition, metabolism and growth.
  
  
  RESULTS
  Here we used massive parallel high-throughput RNA sequencing to generate a high-resolution map of the porcine mRNA and miRNA transcriptome in liver, longissimus dorsi and abdominal fat from two full-sib F2 hybrid pigs with segregated phenotypes on growth, blood physiological and biochemical parameters, and fat deposition. We obtained 8,508,418-10,219,332 uniquely mapped reads that covered 78.0% of the current annotated transcripts and identified 48,045-122,931 novel transcript fragments, which constituted 17,085-29,499 novel transcriptional active regions in six tested samples. We found that about 18.8% of the annotated genes showed alternative splicing patterns, and alternative 3' splicing is the most common type of alternative splicing events in pigs. Cross-tissue comparison revealed that many transcriptional events are tissue-differential and related to important biological functions in their corresponding tissues. We also detected a total of 164 potential novel miRNAs, most of which were tissue-specifically identified. Integrated analysis of genome-wide association study and differential gene expression revealed interesting candidate genes for complex traits, such as IGF2, CYP1A1, CKM and CES1 for heart weight, hemoglobin, pork pH value and serum cholesterol, respectively.
  
  
  CONCLUSIONS
  This study provides a global view of the complexity of the pig transcriptome, and gives an extensive new knowledge about alternative splicing, gene boundaries and miRNAs in pigs. Integrated analysis of genome wide association study and differential gene expression allows us to find important candidate genes for porcine complex traits.
authors: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045, Nanchang, China.
authors: Congying
authors: C
authors: Chen
authors: Huashui
authors: H
authors: Ai
authors: Jun
authors: J
authors: Ren
authors: Wanbo
authors: W
authors: Li
authors: Pinghua
authors: P
authors: Li
authors: Ruimin
authors: R
authors: Qiao
authors: Jing
authors: J
authors: Ouyang
authors: Ming
authors: M
authors: Yang
authors: Junwu
authors: J
authors: Ma
authors: Lusheng
authors: L
authors: Huang
mesh_terms: D050153:Abdominal Fat / Q000378:metabolism*; D017398:Alternative Splicing; D000818:Animals; D005260:Female; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D008099:Liver / Q000378:metabolism; D035683:MicroRNAs / Q000235:genetics; D058977:Molecular Sequence Annotation; D018482:Muscle, Skeletal / Q000378:metabolism; D010641:Phenotype; D017423:Sequence Analysis, RNA / Q000379:methods*; D034421:Sus scrofa / Q000235:genetics* / Q000254:growth & development*; D059467:Transcriptome
chemical_list: D035683:MicroRNAs