title: Global liver gene expression differences in Nelore steers with divergent residual feed intake phenotypes.
abstract: BACKGROUND
  Efficiency of feed utilization is important for animal production because it can reduce greenhouse gas emissions and improve industry profitability. However, the genetic basis of feed utilization in livestock remains poorly understood. Recent developments in molecular genetics, such as platforms for genome-wide genotyping and sequencing, provide an opportunity to identify genes and pathways that influence production traits. It is known that transcriptional networks influence feed efficiency-related traits such as growth and energy balance. This study sought to identify differentially expressed genes in animals genetically divergent for Residual Feed Intake (RFI), using RNA sequencing methodology (RNA-seq) to obtain information from genome-wide expression profiles in the liver tissues of Nelore cattle.
  
  
  RESULTS
  Differential gene expression analysis between high Residual Feed Intake (HRFI, inefficient) and low Residual Feed Intake (LRFI, efficient) groups was performed to provide insights into the molecular mechanisms that underlie feed efficiency-related traits in beef cattle. A total of 112 annotated genes were identified as being differentially expressed between animals with divergent RFI phenotypes. These genes are involved in ion transport and metal ion binding; act as membrane or transmembrane proteins; and belong to gene clusters that are likely related to the transport and catalysis of molecules through the cell membrane and essential mechanisms of nutrient absorption. Genes with functions in cellular signaling, growth and proliferation, cell death and survival were also differentially expressed. Among the over-represented pathways were drug or xenobiotic metabolism, complement and coagulation cascades, NRF2-mediated oxidative stress, melatonin degradation and glutathione metabolism.
  
  
  CONCLUSIONS
  Our data provide new insights and perspectives on the genetic basis of feed efficiency in cattle. Some previously identified mechanisms were supported and new pathways controlling feed efficiency in Nelore cattle were discovered. We potentially identified genes and pathways that play key roles in hepatic metabolic adaptations to oxidative stress such as those involved in antioxidant mechanisms. These results improve our understanding of the metabolic mechanisms underlying feed efficiency in beef cattle and will help develop strategies for selection towards the desired phenotype.
authors.affiliation: Embrapa Southeast Livestock, São Carlos, SP, Brazil. ptizioto@gmail.com.|Division of Animal Sciences, University of Missouri Columbia, Columbia, MO, USA. ptizioto@gmail.com.
authors.forename: Polyana C
authors.initials: PC
authors.lastname: Tizioto
authors.affiliation: Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil. llcoutinho@usp.br.
authors.forename: Luiz L
authors.initials: LL
authors.lastname: Coutinho
authors.affiliation: Division of Animal Sciences, University of Missouri Columbia, Columbia, MO, USA. DeckerJE@missouri.edu.
authors.forename: Jared E
authors.initials: JE
authors.lastname: Decker
authors.affiliation: Division of Animal Sciences, University of Missouri Columbia, Columbia, MO, USA. schnabelr@missouri.edu.
authors.forename: Robert D
authors.initials: RD
authors.lastname: Schnabel
authors.affiliation: Department of Animal Science, State University of Sao Paulo, Jaboticabal, SP, Brazil. oliveira.kamila@ymail.com.
authors.forename: Kamila O
authors.initials: KO
authors.lastname: Rosa
authors.affiliation: Department of Genetics and Evolution, Federal University of Sao Carlos, São Carlos, SP, Brazil. priscilaneuberndeoliveira@gmail.com.
authors.forename: Priscila S N
authors.initials: PS
authors.lastname: Oliveira
authors.affiliation: Department of Genetics and Evolution, Federal University of Sao Carlos, São Carlos, SP, Brazil. mm.rissato@gmail.com.
authors.forename: Marcela M
authors.initials: MM
authors.lastname: Souza
authors.affiliation: Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil. gbmourao@usp.br.
authors.forename: Gerson B
authors.initials: GB
authors.lastname: Mourão
authors.affiliation: Embrapa Southeast Livestock, São Carlos, SP, Brazil. rymer.tullio@embrapa.br.
authors.forename: Rymer R
authors.initials: RR
authors.lastname: Tullio
authors.affiliation: Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil. amalia7l@yahoo.com.br.
authors.forename: Amália S
authors.initials: AS
authors.lastname: Chaves
authors.affiliation: Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil. dplanna@usp.br.
authors.forename: Dante P D
authors.initials: DP
authors.lastname: Lanna
authors.affiliation: Embrapa Agricultural Informatics, Campinas, SP, Brazil. adhemar.zerlotini@embrapa.br.
authors.forename: Adhemar
authors.initials: A
authors.lastname: Zerlotini-Neto
authors.affiliation: Embrapa Southeast Livestock, São Carlos, SP, Brazil. mauricio.mudadu@embrapa.br.
authors.forename: Mauricio A
authors.initials: MA
authors.lastname: Mudadu
authors.affiliation: Division of Animal Sciences, University of Missouri Columbia, Columbia, MO, USA. taylorjerr@missouri.edu.
authors.forename: Jeremy F
authors.initials: JF
authors.lastname: Taylor
authors.affiliation: Embrapa Southeast Livestock, São Carlos, SP, Brazil. luciana.regitano@embrapa.br.
authors.forename: Luciana C A
authors.initials: LC
authors.lastname: Regitano
mesh_terms: D000821:Animal Feed; D000818:Animals; D002417:Cattle / Q000235:genetics* / Q000378:metabolism; D004063:Digestion; D008099:Liver / Q000378:metabolism*; D008460:Meat / Q000191:economics; D010641:Phenotype; D059467:Transcriptome