Integration of Non-Coding RNA and mRNA Profiles Reveals the Mechanisms of Rumen Development Induced by Different Types of Diet in Calves

Selecting suitable feed types and understanding the gastrointestinal digestive mechanism are helpful for the growth and health of calves in intensive dairy farming. However, the effects on rumen development of changing the molecular genetic basis and the regulatory mechanism by using different feed types are still unclear. Nine 7-day-old Holstein bull calves were randomly divided into GF (concentrate), GFF (alfalfa: oat grass = 3:2) and TMR (concentrate: alfalfa grass: oat grass: water = 0.30:0.12:0.08:0.50) diet experiment groups. Rumen tissue and serum samples were collected for physiological and transcriptomic analysis after 80 days. The results showed that serum α-amylase content and ceruloplasmin activity were significantly higher in the TMR group, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis ncRNAs and mRNAs were significantly enriched in the pathways of rumen epithelial development and stimulated rumen cell growth, including the Hippo signaling pathway, Wnt signaling pathway, thyroid hormone signaling pathway, ECM–receptor interaction and the absorption of protein and fat. The circRNAs/lncRNA-miRNAs-mRNA networks constructed, including novel_circ_0002471, novel_circ_0012104, TCONS_00946152, TCONS_00960915, bta-miR-11975, bta-miR-2890, PADI3 and CLEC6A, participated in metabolic pathways of lipid, immune system, oxidative stress and muscle development. In conclusion, the TMR diet could improve rumen digestive enzyme activities, stimulate rumen nutrient absorption and stimulate the DEGs related to energy homeostasis and microenvironment balance, and is thus better than the GF and GFF diets for promoting rumen growth and development.