title: Transcriptome differences in the rumen of beef steers with variation in feed intake and gain.
abstract: BACKGROUND
  Feed intake and gain are economically important traits in beef production. The rumen wall interacts with feed, microbial populations, and fermentation products important to cattle nutrition. As such, it is likely to be a critical component in the beef steer's ability to utilize feedstuffs efficiently. To identify genes associated with steer feed intake and body weight gain traits, and to gain an understanding of molecules and pathways involved in feed intake and utilization, RNA sequencing (RNA-Seq) was performed on rumen papillae from 16 steers with variation in gain and feed intake. Four steers were chosen from each of the four Cartesian quadrants for gain×feed intake and used to generate individual RNA-Seq libraries.
  
  
  RESULTS
  Normalized read counts from all of the mapped reads from each of the four groups of animals were individually compared to the other three groups. In addition, differentially expressed genes (DEGs) between animals with high and low gain, as well as high and low intake were also evaluated. A total of 931 genes were differentially expressed in the analyses of the individual groups. Eighty-nine genes were differentially expressed between high and low gain animals; and sixty-nine were differentially expressed in high versus low intake animals. Several of the genes identified in this study have been previously associated with feed efficiency. Among those are KLK10, IRX3, COL1A1, CRELD2, HDAC10, IFITM3, and VIM.
  
  
  CONCLUSIONS
  Many of the genes identified in this study are involved with immune function, inflammation, apoptosis, cell growth/proliferation, nutrient transport, and metabolic pathways and may be important predictors of feed intake and gain in beef cattle.
authors.affiliation: USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA. Electronic address: Rebecca.Kern@ARS.USDA.GOV.
authors.forename: Rebecca J
authors.initials: RJ
authors.lastname: Kern
authors.affiliation: USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA. Electronic address: Amanda.Lindholm@ARS.USDA.GOV.
authors.forename: Amanda K
authors.initials: AK
authors.lastname: Lindholm-Perry
authors.affiliation: USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA. Electronic address: Harvey.Freetly@ARS.USDA.GOV.
authors.forename: Harvey C
authors.initials: HC
authors.lastname: Freetly
authors.affiliation: USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA. Electronic address: Warren.Snelling@ARS.USDA.GOV.
authors.forename: Warren M
authors.initials: WM
authors.lastname: Snelling
authors.affiliation: Kern Statistical Services, Sauk Rapids, MN 56379, USA. Electronic address: jkern@kernstat.com.
authors.forename: John W
authors.initials: JW
authors.lastname: Kern
authors.affiliation: Department of Animal Science, University of Wyoming, Laramie, WY 82070, USA. Electronic address: john.keele@ars.usda.gov.
authors.forename: John W
authors.initials: JW
authors.lastname: Keele
authors.affiliation: USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA. Electronic address: Jeremy.Miles@ARS.USDA.GOV.
authors.forename: Jeremy R
authors.initials: JR
authors.lastname: Miles
authors.affiliation: USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA. Electronic address: Andrew.Foote@ars.usda.gov.
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Foote
authors.affiliation: USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA. Electronic address: William.Oliver@ars.usda.gov.
authors.forename: William T
authors.initials: WT
authors.lastname: Oliver
authors.affiliation: USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA. Electronic address: Larry.Kuehn@ars.usda.gov.
authors.forename: Larry A
authors.initials: LA
authors.lastname: Kuehn
authors.affiliation: Department of Animal Science, University of Wyoming, Laramie, WY 82070, USA. Electronic address: Ludden@uwyo.edu.
authors.forename: Paul A
authors.initials: PA
authors.lastname: Ludden
mesh_terms: D000821:Animal Feed; D000818:Animals; D002417:Cattle / Q000523:psychology*; D020869:Gene Expression Profiling; D008297:Male; D053858:Metabolic Networks and Pathways; D012417:Rumen / Q000378:metabolism*; D015430:Weight Gain
keywords: Beef cattle; Feed intake; Gain; RNA-Seq; Rumen