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United States Department of Agriculture

Agricultural Research Service

Research Project: IMPROVED NUTRIENT EFFICIENCY OF BEEF CATTLE AND SWINE

Location: Nutrition and Environmental Management Research

Title: An evaluation of the differences in the rumen transcriptome among beef steers with extreme feed efficiency phenotypes

Authors
item Lindholm-Perry, Amanda
item Kern, Rebecca
item Kuehn, Larry
item Miles, Jeremy
item Freetly, Harvey
item Snelling, Warren
item Ludden, Paul

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: December 3, 2013
Publication Date: January 1, 2014
Citation: Lindholm-Perry, A.K., Kern, R.J., Kuehn, L.A., Miles, J.R., Freetly, H.C., Snelling, W.M., Ludden, P.A. 2014. An evaluation of the differences in the rumen transcriptome among beef steers with extreme feed efficiency phenotypes. Plant & Animal Genome XXII Conference, January 11-15, 2014, San Diego, CA. Abstract No. W155.

Technical Abstract: Feed is the largest variable cost in beef production and the rumen likely has a critical role in an animal’s ability to efficiently utilize feed. We identified differentially expressed transcripts in animals with extreme differences in postweaning feed intake and gain. Rumen papillae RNA samples were collected from 16 steers with extreme feed efficiency phenotypes for RNA-Seq. A negative binomial test using edgeR and an analysis by Cofactor Genomics were used to identify differentially expressed genes by phenotypic extreme. EdgeR analysis identified 26 differentially expressed transcripts, while 171 were identified by Cofactor analysis. Approximately 38% (n=26) of edgeR and 48% (n=23) of Cofactor identified transcripts were validated with real-time RTPCR. Exons differentially expressed between animals with high and low feed intake included LPO, CAV1, ATP6V1C2 and others involved antimicrobial, signaling, cell membrane and ion transport categories, while genes including COL1A1, SOX2, and PHGDH involved in macromolecule metabolism, mitochondrial, development, and nucleotide binding gene categories were correlated to gain. Three genes (KLK10, KLK12 and ARHGAP27) were identified in both analyses. DNA variants (n=199) in the 26 differentially expressed edgeR genes were detected in sequence from 250 USMARC bulls. These SNPs were genotyped on over 1000 steers with feed efficiency phenotypes to determine whether they segregate with gain or feed intake. In summary, we identified differentially expressed rumen genes that may have effects on feed efficiency; resulting SNPs or pathway analysis may contribute to future selection tools.

Last Modified: 10/25/2014
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