Assembly and analysis of changes in transcriptomes of dairy cattle rumen epithelial during lactation and dry periods

Authors: Baldwin, Ransom - Randy; Li, Congjun - Cj; Li, Robert

Submitted to: Agricultural Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/28/2018
Publication Date: 5/31/2018
Citation: Baldwin, R.L., Li, C., Li, R.W. 2018. Assembly and analysis of changes in transcriptomes of dairy cattle rumen epithelial during lactation and dry periods. Agricultural Sciences. 9:619-638. https://doi.org/10.4236/as.2018.95043.
DOI: https://doi.org/10.4236/as.2018.95043

Interpretive Summary: Milk production in cows substantially increases their dietary nutrient and energy requirements to support milk synthesis. Therefore, the metabolism of the cow must adapt to milk production-associated challenges that require major functional adjustments of the rumen and digestive system. The vast dynamics of gene expression occurring in the rumen during both the milking and non-milking periods of the production cycle were characterized using next-generation sequencing technology. Information generated from the work supports our understanding of functional adaptation of rumen metabolism to meet the nutritional demands of lactation and promotes future advances in ruminant nutrition and feeding.

Technical Abstract: Lactation in dairy cattle is coupled with increased nutrient requirements for milk synthesis. Therefore, dairy cattle metabolism has to adapt to meet lactation-associated challenges and requires major functional adjustments of the rumen and whole digestive system. This report describes the use of next-generation sequencing technology for assembly and profiling of the transcriptome of cattle rumen epithelial tissues from cattle in both dry and lactation periods. Transcriptomics profiling and comparison revealed extensive changes in gene expression related to metabolism in rumen epithelial tissue during the adaptation to lactation. Ruminal epithelial adaptation to the challenges of metabolism and high nutrient requirements during lactation are primary triggers for these alterations in gene expression. Principal component analysis (PCA) indicated that the gene expression profiles of the rumen epithelia from dry and lactating cattle fall into two very distinct clusters. Gene Ontology (GO) enrichment analysis revealed that the most GO terms were related to various metabolic processes in lactating cattle. The most significantly enriched GO term in biological processes was ‘carbohydrate derivative metabolic process,’ followed by ‘nucleoside metabolic process.’ Up-stream regulators, such as PPARA, and up-regulated genes of molecular transporters are the focal points of this report.