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United States Department of Agriculture

Agricultural Research Service

Research Project: EFFICIENCY OF NUTRIENT USE IN CATTLE:IDENTIFICATION OF CRITICAL PHYSIOLOGIC AND GENOMIC REGULATORY PATHWAYS Title: Characterization of differentially expressed genes in calf rumen epithelium in response to weaning

Authors
item Chung, Hoyoung -
item Baldwin, Ransom
item Li, Congjun
item Connor, Erin

Submitted to: BARC Poster Day
Publication Type: Abstract Only
Publication Acceptance Date: March 28, 2012
Publication Date: April 19, 2012
Citation: Chung, H., Baldwin, R.L., Li, C., Connor, E.E. 2012. Characterization of differentially expressed genes in calf rumen epithelium in response to weaning. BARC Poster Day. p. 05.

Technical Abstract: During weaning, rumen epithelial cell function must transition from a pre-ruminant to a true ruminant state for efficient nutrient absorption and metabolism. During this time, the rumen grows to represent from 30 to 70% of the capacity of the gut, directly impacting net efficiency of feed conversion in growing cattle. To identify and characterize genes, gene pathways, and gene networks affected by weaning in the calf rumen, global gene expression profiles were determined at different stages of development and under different dietary treatments. Holstein bull calves were fed commercial milk replacer only (MRO) up to 42 days of age, then were switched to diets of either milk + orchard grass hay (MH) or milk + grain-based commercial calf starter (MG). Calves were sacrificed at 4 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 RNA extraction from rumen epithelium and subsequent transcript profiling. Gene expression was assessed using a custom bovine whole genome microarray (USDA Bovine 60mer 344-k Array from NimbleGen). Principal components analysis indicated that gene expression patterns were separated by diet but not by developmental stage within diet. Differential expression between MRO at day 42 vs. MG or MH at day 56 was determined using a robust implementation of permutation testing. Lists of differentially expressed genes were selected based on a false discovery rate < 5% and an estimated absolute raw fold change =1.5. A total of 413 differentially expressed genes were identified when the diet changed from MRO at day 42 to that of MH or to MG at day 56. There were 412 transcripts uniquely differentially expressed between the day 42 MRO and day 56 MG groups, and 602 transcripts uniquely differentially expressed between the day 42 MRO and day 56 MH groups. Ingenuity Pathway Analysis indicated that the genes commonly affected by transition to either the MG or MH diets (weaning) function primarily in free-radical scavenging and molecular transport, while those uniquely affected by transition to a grain-based diet function in cell cycle, cellular assembly and organization, and DNA replication. Genes uniquely affected by transition to a hay-based diet function in energy production and lipid metabolism. Results of these analyses will yield molecular markers of rumen development during weaning, as well as identify putative gene networks regulating differentiation and growth of the rumen epithelium. Improving our knowledge of these pathways will aid in identifying targets and methods for improving rumen development and function in the growing calf.

Last Modified: 7/30/2014
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