title: Transcriptome profiling of the rumen epithelium of beef cattle differing in residual feed intake.
abstract: Feed efficient cattle consume less feed and produce less environmental waste than inefficient cattle. Many factors are known to contribute to differences in feed efficiency, however the underlying molecular mechanisms are largely unknown. Our study aimed to understand how host gene expression in the rumen epithelium contributes to differences in residual feed intake (RFI), a measure of feed efficiency, using a transcriptome profiling based approach.
  
  
  
  The rumen epithelial transcriptome from highly efficient (low (L-) RFI, n = 9) and inefficient (high (H-) RFI, n = 9) Hereford x Angus steers was obtained using RNA-sequencing. There were 122 genes differentially expressed between the rumen epithelial tissues of L- and H- RFI steers (p < 0.05) with 85 up-regulated and 37 down-regulated in L-RFI steers. Functional analysis of up-regulated genes revealed their involvement in acetylation, remodeling of adherens junctions, cytoskeletal dynamics, cell migration, and cell turnover. Additionally, a weighted gene co-expression network analysis (WGCNA) identified a significant gene module containing 764 genes that was negatively correlated with RFI (r = -0.5, p = 0.03). Functional analysis revealed significant enrichment of genes involved in modulation of intercellular adhesion through adherens junctions, protein and cell turnover, and cytoskeletal organization that suggest possible increased tissue morphogenesis in the L-RFI steers. Additionally, the L-RFI epithelium had increased expression of genes involved with the mitochondrion, acetylation, and energy generating pathways such as glycolysis, tricarboxylic acid cycle, and oxidative phosphorylation. Further qPCR analysis of steers with different RFI (L-RFI, n = 35; M-RFI, n = 34; H-RFI, n = 35) revealed that the relative mitochondrial genome copy number per cell of the epithelium was positively correlated with RFI (r = 0.21, p = 0.03).
  
  
  
  Our results suggest that the rumen epithelium of L-RFI (efficient) steers may have increased tissue morphogenesis that possibly increases paracellular permeability for the absorption of nutrients and increased energy production to support the energetic demands of increased tissue morphogenesis compared to those of H-RFI (inefficient) animals. Greater expression of mitochondrial genes and lower relative mitochondrial genome copy numbers suggest a greater rate of transcription in the rumen epithelial mitochondria of L-RFI steers. Understanding how host gene expression profiles are associated with RFI could potentially lead to identification of mechanisms behind this trait, which are vital to develop strategies for the improvement of cattle feed efficiency.
authors: Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, 416F, Edmonton, AB, T6G 2P5, Canada.
authors: Rebecca S G
authors: RS
authors: Kong
authors: Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, 416F, Edmonton, AB, T6G 2P5, Canada.
authors: Guanxiang
authors: G
authors: Liang
authors: Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, 416F, Edmonton, AB, T6G 2P5, Canada.
authors: Yanhong
authors: Y
authors: Chen
authors: Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, 416F, Edmonton, AB, T6G 2P5, Canada.
authors: Paul
authors: P
authors: Stothard
authors: Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, 416F, Edmonton, AB, T6G 2P5, Canada. lguan@ualberta.ca.
authors: Le Luo
authors: le L
authors: Guan
mesh_terms: D000821:Animal Feed; D000818:Animals; D002170:Canada; D002417:Cattle; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D004272:DNA, Mitochondrial; D005753:Gastric Mucosa / Q000378:metabolism*; D018628:Gene Dosage; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D053858:Metabolic Networks and Pathways; D058977:Molecular Sequence Annotation; D015203:Reproducibility of Results; D012417:Rumen / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D004272:DNA, Mitochondrial
keywords: Beef cattle; Feed efficiency; RNA-sequencing; Residual feed intake; Rumen epithelium; Transcriptome