Functional & Integrative Genomics

, Volume 13, Issue 1, pp 133–142 | Cite as

Gene expression in bovine rumen epithelium during weaning identifies molecular regulators of rumen development and growth

  • Erin E. ConnorEmail author
  • Ransom L. BaldwinVI
  • Cong-jun Li
  • Robert W. Li
  • Hoyoung Chung
Original Paper


During weaning, epithelial cell function in the rumen transitions in response to conversion from a pre-ruminant to a true ruminant environment to ensure efficient nutrient absorption and metabolism. To identify gene networks affected by weaning in bovine rumen, Holstein bull calves were fed commercial milk replacer only (MRO) until 42 days of age, then were provided diets of either milk + orchardgrass hay (MH) or milk + grain-based calf starter (MG). Rumen epithelial RNA was extracted from calves sacrificed at four time points: day 14 (n = 3) and day 42 (n = 3) of age while fed the MRO diet and day 56 (n = 3/diet) and day 70 (n = 3/diet) while fed the MH and MG diets for transcript profiling by microarray hybridization. Five two-group comparisons were made using Permutation Analysis of Differential Expression® to identify differentially expressed genes over time and developmental stage between days 14 and 42 within the MRO diet, between day 42 on the MRO diet and day 56 on the MG or MH diets, and between the MG and MH diets at days 56 and 70. Ingenuity Pathway Analysis (IPA) of differentially expressed genes during weaning indicated the top 5 gene networks involving molecules participating in lipid metabolism, cell morphology and death, cellular growth and proliferation, molecular transport, and the cell cycle. Putative genes functioning in the establishment of the rumen microbial population and associated rumen epithelial inflammation during weaning were identified. Activation of transcription factor PPAR-α was identified by IPA software as an important regulator of molecular changes in rumen epithelium that function in papillary development and fatty acid oxidation during the transition from pre-rumination to rumination. Thus, molecular markers of rumen development and gene networks regulating differentiation and growth of rumen epithelium were identified for selecting targets and methods for improving and assessing rumen development and function, particularly in the growing calf.


Cattle Growth Microarray Rumen Weaning 



The authors acknowledge the excellent technical support of Marsha Campbell, Dennis Hucht, Mary Niland, Donald Carbaugh, Mary Bowman, Jim Piatt, and the Research Support Services staff at the Beltsville Agricultural Research Center who contributed to this project. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture (USDA). The USDA is an equal opportunity provider and employer.

Supplementary material

10142_2012_308_MOESM1_ESM.docx (79 kb)
Table S1 (DOCX 78.5 kb)
10142_2012_308_MOESM2_ESM.pdf (102 kb)
Table S2 (PDF 101 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg (outside the USA) 2013

Authors and Affiliations

  • Erin E. Connor
    • 1
    Email author
  • Ransom L. BaldwinVI
    • 1
  • Cong-jun Li
    • 1
  • Robert W. Li
    • 1
  • Hoyoung Chung
    • 2
  1. 1.Bovine Functional Genomics Laboratory, Agricultural Research ServiceUSDABeltsvilleUSA
  2. 2.Animal Genomics and Bioinformatics DivisionNational Institute of Animal ScienceSuwonSouth Korea

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