RNA-Seq Analysis of Abdominal Fat Reveals Differences between Modern Commercial Broiler Chickens with High and Low Feed Efficiencies

PLoS One. 2015 Aug 21;10(8):e0135810. doi: 10.1371/journal.pone.0135810. eCollection 2015.


For economic and environmental reasons, chickens with superior feed efficiency (FE) are preferred in the broiler chicken industry. High FE (HFE) chickens typically have reduced abdominal fat, the major adipose tissue in chickens. In addition to its function of energy storage, adipose tissue is a metabolically active organ that also possesses endocrine and immune regulatory functions. It plays a central role in maintaining energy homeostasis. Comprehensive understanding of the gene expression in the adipose tissue and the biological basis of FE are of significance to optimize selection and breeding strategies. Through gene expression profiling of abdominal fat from high and low FE (LFE) commercial broiler chickens, the present study aimed to characterize the differences of gene expression between HFE and LFE chickens. mRNA-seq analysis was carried out on the total RNA of abdominal fat from 10 HFE and 12 LFE commercial broiler chickens, and 1.48 billion of 75-base sequence reads were generated in total. On average, 11,565 genes were expressed (>5 reads/gene/sample) in the abdominal fat tissue, of which 286 genes were differentially expressed (DE) at q (False Discover Rate) < 0.05 and fold change > 1.3 between HFE and LFE chickens. Expression levels from RNA-seq were confirmed with the NanoString nCounter analysis system. Functional analysis showed that the DE genes were significantly (p < 0.01) enriched in lipid metabolism, coagulation, and immune regulation pathways. Specifically, the LFE chickens had higher expression of lipid synthesis genes and lower expression of triglyceride hydrolysis and cholesterol transport genes. In conclusion, our study reveals the overall differences of gene expression in the abdominal fat from HFE and LFE chickens, and the results suggest that the divergent expression of lipid metabolism genes represents the major differences.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Abdominal Fat / chemistry
  • Abdominal Fat / metabolism*
  • Animal Feed / analysis
  • Animals
  • Appetite Regulation / genetics*
  • Chickens / genetics*
  • Chickens / immunology
  • Gene Expression Profiling
  • Gene Expression Regulation
  • Gene Regulatory Networks
  • High-Throughput Nucleotide Sequencing
  • Immunity, Innate
  • Lipid Metabolism / genetics*
  • Lipid Metabolism / immunology
  • Meat / analysis*
  • Molecular Sequence Annotation
  • Multigene Family
  • RNA, Messenger / genetics*


  • RNA, Messenger

Grant support

This work was funded by Delaware Bioscience Center for Advanced Technology and Heritage Breeders, LLC. Phenotypic data were collected at Heritage Breeders, LLC. Maple Leaf Farms, Inc. provided support in the form of salaries for author William R. Lee, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.