RNA-Seq Reveals Gastrointestinal Transcriptome Dynamics in Preweaning Yak Calves Fed Concentrate Supplements

The objective of this study was to investigate the effects of supplemental starter feeding on the development of the ruminal epithelium in suckling yak calves using transcriptomic analysis. Twenty healthy one-month-old male yak calves with similar body weights were selected and randomly assigned to two groups. The pre-feeding adaptation period lasted 14 days, followed by a 120-day experimental feeding period. At the end of the trial, five calves from each group were slaughtered, and samples of abomasum tissue and ruminal contents were collected for subsequent analyses. The results demonstrated that early concentrate supplementation markedly increased the final body weight and ruminal NH3-N concentration of calves in the RAS group compared with the control (RA) group (p < 0.05). Similarly, dry matter intake and ruminal microbial protein (MCP) content were significantly higher in the RAS group (p < 0.05). In contrast, the concentration of acetic acid in ruminal fluid was significantly higher in the RA group, whereas valeric acid concentration was higher in the RAS group. Furthermore, ruminal TNF-α, TNF-γ, and IL-2 concentrations were significantly elevated in the RAS group (p < 0.05), suggesting enhanced ruminal immune function. Transcriptomic analysis revealed that both up- and down-regulated gene expression contributed to the morphological development and overall health of the ruminal epithelium. Up-regulated genes were enriched in pathways related to chemical carcinogenesis, cytochrome P450 metabolism, steroid hormone biosynthesis, retinol metabolism, ascorbate and aldarate metabolism, drug metabolism-cytochrome P450, pentose and glucuronate interconversions, ovarian steroidogenesis, and porphyrin and chlorophyll metabolism. Conversely, down-regulated genes were mainly associated with cytokine–cytokine receptor interactions, mineral absorption, arachidonic acid metabolism, and viral protein interactions with cytokine receptors. Overall, early supplementation with concentrate feed enhanced the expression of genes associated with ruminal epithelial development, improved immune responses, and promoted better growth performance in suckling yak calves.