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Transcriptome differences in the rumen of beef steers with variation in feed intake and gain

Rebecca J. Kern, Amanda K. Lindholm-Perry, Harvey C. Freetly, Warren M. Snelling, John W. Kern, John W. Keele, Jeremy R. Miles, Andrew P. Foote, William T. Oliver, Larry A. Kuehn, Paul A. Ludden
Gene 2016 v.586 no.1 pp. 12-26
RNA, apoptosis, beef, beef cattle, biochemical pathways, feed conversion, feed intake, feeds, gene expression regulation, genes, genomics, immunologic diseases, meat production, metabolic diseases, mortality, nucleotide sequences, phenotype, quantitative polymerase chain reaction, rumen, ruminant nutrition, statistical analysis, steers, transcriptome, volatile fatty acids
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.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.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.