title: Messenger RNA sequencing and pathway analysis provide novel insights into the biological basis of chickens' feed efficiency.
abstract: BACKGROUND
  Advanced selection technologies have been developed and continually optimized to improve traits of agricultural importance; however, these methods have been primarily applied without knowledge of underlying biological changes that may be induced by selection. This study aims to characterize the biological basis of differences between chickens with low and high feed efficiency (FE) with a long-term goal of improving the ability to select for FE.
  
  
  RESULTS
  High-throughput RNA sequencing was performed on 23 breast muscle samples from commercial broiler chickens with extremely high (n = 10) and low (n = 13) FE. An average of 34 million paired-end reads (75 bp) were produced for each sample, 80% of which were properly mapped to the chicken reference genome (Ensembl Galgal4). Differential expression analysis identified 1,059 genes (FDR < 0.05) that significantly divergently expressed in breast muscle between the high- and low-FE chickens. Gene function analysis revealed that genes involved in muscle remodeling, inflammatory response and free radical scavenging were mostly up-regulated in the high-FE birds. Additionally, growth hormone and IGFs/PI3K/Akt signaling pathways were enriched in differentially expressed genes, which might contribute to the high breast muscle yield in high-FE birds and partly explain the FE advantage of high-FE chickens.
  
  
  CONCLUSIONS
  This study provides novel insights into transcriptional differences in breast muscle between high- and low-FE broiler chickens. Our results show that feed efficiency is associated with breast muscle growth in these birds; furthermore, some physiological changes, e.g., inflammatory response and oxidative stress, may occur in the breast muscle of the high-FE chickens, which may be of concern for continued selection for both of these traits together in modern broiler chickens.
authors.affiliation: Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA. nanzhou@udel.edu.
authors.forename: Nan
authors.initials: N
authors.lastname: Zhou
authors.affiliation: Maple Leaf Farms LLC, Leesburg, IN, 46538, USA. BillLee@mapleleaffarms.com.
authors.forename: William R
authors.initials: WR
authors.lastname: Lee
authors.affiliation: Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA. abasht@udel.edu.
authors.forename: Behnam
authors.initials: B
authors.lastname: Abasht
mesh_terms: D000821:Animal Feed; D000824:Animal Nutritional Physiological Phenomena / Q000235:genetics*; D000818:Animals; D002645:Chickens / Q000235:genetics* / Q000378:metabolism; D015536:Down-Regulation; D016166:Free Radical Scavengers / Q000378:metabolism; D016678:Genome; D013006:Growth Hormone / Q000235:genetics / Q000378:metabolism; D051795:Hypoxia-Inducible Factor 1, alpha Subunit / Q000235:genetics / Q000378:metabolism; D007334:Insulin-Like Growth Factor I / Q000235:genetics / Q000378:metabolism; D007335:Insulin-Like Growth Factor II / Q000235:genetics / Q000378:metabolism; D008297:Male; D018482:Muscle, Skeletal / Q000378:metabolism; D018384:Oxidative Stress / Q000235:genetics; D010641:Phenotype; D019869:Phosphatidylinositol 3-Kinases / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D015398:Signal Transduction / Q000235:genetics; D059467:Transcriptome; D015854:Up-Regulation
chemical_list: D016166:Free Radical Scavengers; D051795:Hypoxia-Inducible Factor 1, alpha Subunit; D012333:RNA, Messenger; D007334:Insulin-Like Growth Factor I; D007335:Insulin-Like Growth Factor II; D013006:Growth Hormone; D019869:Phosphatidylinositol 3-Kinases