title: Transcriptome profile of liver at different physiological stages reveals potential mode for lipid metabolism in laying hens.
abstract: BACKGROUND
  Liver is an important metabolic organ that plays a critical role in lipid synthesis, degradation, and transport; however, the molecular regulatory mechanisms of lipid metabolism remain unclear in chicken. In this study, RNA-Seq technology was used to investigate differences in expression profiles of hepatic lipid metabolism-related genes and associated pathways between juvenile and laying hens. The study aimed to broaden the understanding of liver lipid metabolism in chicken, and thereby to help improve laying performance in the poultry industry.
  
  
  RESULTS
  RNA-Seq analysis was carried out on total RNA harvested from the liver of juvenile (n = 3) and laying (n = 3) hens. Compared with juvenile hens, 2567 differentially expressed genes (1082 up-regulated and 1485 down-regulated) with P ≤ 0.05 were obtained in laying hens, and 960 of these genes were significantly differentially expressed (SDE) at a false discovery rate (FDR) of ≤0.05 and fold-change ≥2 or ≤0.5. In addition, most of the 198 SDE novel genes (91 up-regulated and 107 down-regulated) were discovered highly expressed, and 332 SDE isoforms were identified. Gene ontology (GO) enrichment and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis showed that the SDE genes were most enrichment in steroid biosynthesis, PPAR signaling pathway, biosynthesis of unsaturated fatty acids, glycerophospholipid metabolism, three amino acid pathways, and pyruvate metabolism (P ≤ 0.05). The top significantly enriched GO terms among the SDE genes included lipid biosynthesis, cholesterol and sterol metabolic, and oxidation reduction, indicating that principal lipogenesis occurred in the liver of laying hens.
  
  
  CONCLUSIONS
  This study suggests that the majority of changes at the transcriptome level in laying hen liver were closely related to fat metabolism. Some of the SDE uncharacterized novel genes and alternative splicing isoforms that were detected might also take part in lipid metabolism, although this needs further investigation. This study provides valuable information about the expression profiles of mRNAs from chicken liver, and in-depth functional investigations of these mRNAs could provide new insights into the molecular networks of lipid metabolism in chicken liver.
authors.affiliation: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China. lihong19871202@163.com.
authors.forename: Hong
authors.initials: H
authors.lastname: Li
authors.affiliation: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China. 15286833615@163.com.
authors.forename: Taian
authors.initials: T
authors.lastname: Wang
authors.affiliation: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China. xclmu521@163.com.
authors.forename: Chunlin
authors.initials: C
authors.lastname: Xu
authors.affiliation: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China. wdd13938406174@163.com.
authors.forename: Dandan
authors.initials: D
authors.lastname: Wang
authors.affiliation: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China. 862758007@qq.com.
authors.forename: Junxiao
authors.initials: J
authors.lastname: Ren
authors.affiliation: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China. 15138656629@163.com.
authors.forename: Yanmin
authors.initials: Y
authors.lastname: Li
authors.affiliation: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China. ydtian111@163.com.|Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China. ydtian111@163.com.
authors.forename: Yadong
authors.initials: Y
authors.lastname: Tian
authors.affiliation: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China. ybwang2008@126.com.|Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China. ybwang2008@126.com.
authors.forename: Yanbin
authors.initials: Y
authors.lastname: Wang
authors.affiliation: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China. 2397981088@qq.com.|Institute of Animal Husbandry and Veterinary Medicine, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China. 2397981088@qq.com.
authors.forename: Yuping
authors.initials: Y
authors.lastname: Jiao
authors.affiliation: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China. xtkang2001@263.net.|Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China. xtkang2001@263.net.|International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou, 450002, China. xtkang2001@263.net.
authors.forename: Xiangtao
authors.initials: X
authors.lastname: Kang
authors.affiliation: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China. xjliu2008@hotmail.com.|Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China. xjliu2008@hotmail.com.|International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou, 450002, China. xjliu2008@hotmail.com.
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Liu
mesh_terms: D000818:Animals; D002645:Chickens / Q000235:genetics* / Q000254:growth & development; D002784:Cholesterol / Q000235:genetics / Q000378:metabolism; D004531:Eggs; D005260:Female; D020869:Gene Expression Profiling; D050356:Lipid Metabolism / Q000235:genetics*; D008099:Liver / Q000378:metabolism*; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics; D015398:Signal Transduction; D059467:Transcriptome / Q000235:genetics*
chemical_list: D012333:RNA, Messenger; D002784:Cholesterol