Transcriptomic profiling of duodenal epithelium reveals temporally dynamic impacts of direct duodenal starch-infusion during dry period of dairy cattle

Authors: Li, Congjun - Cj; LIN, SHUDAI - South China Agricultural University; RANILLA-GARCIA, MARIA - University Of Leon; Baldwin, Ransom - Randy

Submitted to: Frontiers in Veterinary Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/14/2019
Publication Date: 7/2/2019
Citation: Li, C., Lin, S., Ranilla-Garcia, M.J., Baldwin, R.L. 2019. Transcriptomic profiling of duodenal epithelium reveals temporally dynamic impacts of direct duodenal starch-infusion during dry period of dairy cattle. Frontiers in Veterinary Science. 6:214. https://doi.org/10.3389/fvets.2019.00214.
DOI: https://doi.org/10.3389/fvets.2019.00214

Interpretive Summary: Cattle intestine is a major component of digestion system. However, the genetic profiling has never been done. In this report, we using Next Generation Sequencing technology and direct biopsy, we assembled the transcriptome of cattle intestinal epithelia. We also used direct infusion of single nutrient (starch hydrolysate) to study the genetic response of intestinal epithelial gene expression. We found the digestive system developemt and function are among the major functions of the genes induced by starch infusion. We also identified the primary transcription regulators for future focus.

Technical Abstract: Previous research has demonstrated a positive relationship between dietary MEI and increased maintenance energy costs associated with the visceral tissues. This experiment was conducted with a single nutrient (starch hydrolysate) infused (7 d) directly into the intestine to mimic typical changes in post-ruminal starch delivery in dairy production settings. Duodenal epithelial samples collected via biopsy were evaluated using next-generation sequencing technology (RNA-Seq) to profile and compare the transcriptome of cattle intestinal epithelial tissues. Samples of intestinal epithelial tissue were collected during the infusion on the day before the infusion, and day 1, day 3 and day 7 during the infusion. Samples were also collected on day 1 and day 7 after infusion was discontinued (Day 8 and Day14 of the experiment). RNA-seq data revealed significant dynamic changes of global gene expression during infusion. On day 7 of the infusion, 1490 genes were found to be significantly differentially expressed (DE) compared to the day 0 control samples with FDR p-value < 0.05, versus 105 genes on day 1 and 246 genes on Day 3. After infusion was terminated however, on day 8, only 428 genes were differentially expressed compared to day 0 and only107 genes on Day 14. Thus, differential expression of these genes is putatively a result of the starch infusion. By performing function and pathway analysis of DE genes using IPA, we found that digestive system development and function are among the primary functions of the DE genes. Furthermore, primary transcription regulators such as PTH, JUN, WNT, and TNFRSF11B were identified as the activated upstream regulators for future focus.