Integration of Long Non-Coding RNA and mRNA Profiling Reveals the Mechanisms of Different Dietary NFC/NDF Ratios Induced Rumen Development in Calves

SIMPLE SUMMARY: Altering carbohydrate source and form affects the development of the rumen epithelium. Calves fed diets with one of three different ratios of non-fibrous carbohydrate to neutral detergent fiber (NFC/NDF) was conducted to reveal putative mechanisms and pathways affected by and responsible for rumen development. Calves in the high NFC/NDF ratio (1.10) group had higher average daily gain, and ruminal papillae developed flatter than calves in the low NFC/NDF ratio (0.60) group. Transcriptomics identified that a large number of differentially expressed genes were significantly enriched in pathways related to rumen epithelia development including focal adhesion, Wnt signaling pathway, thyroid hormone signaling pathway, regulation of actin cytoskeleton and cGMP-PKG signaling pathway. The lncRNA-mRNA network analysis revealed that some target genes including XLOC_068691 and monoamine oxidase B (MOAB), XLOC_023657 and dickkopf homolog 2 (DKK2), XLOC_064331 and protein phosphatase 1 regulatory subunit 12A (PPP1R12A) were affected by the NCF/NDF ratios fed. The pathways and affected genes may serve as markers for the further investigation into the mechanisms regulating dietary and luminal factors impacting rumen development in growing ruminants. ABSTRACT: The aim of the present study was to explore the effects of dietary non-fibrous carbohydrate to neutral detergent fiber (NFC/NDF) ratios on rumen development of calves, and to investigate the mechanisms by integrating of lncRNA and mRNA profiling. Forty-five weaned Charolais hybrid calves [body weight = 94.38 ± 2.50 kg; age = 70 ± 2.69 d] were randomly assigned to 1 of 3 treatment groups with different dietary NFC/NDF ratios: 1.10 (H group), 0.94 (M group) and 0.60 (L group), respectively. The ventral sac of the rumen was sampled for morphological observation and transcriptional sequencing. The average daily gain of calves in the high NFC/NDF ratio group was significantly higher than that in other groups (p < 0.05). Papillae width was largest in high NFC/NDF ratio group calves (p < 0.05). Identified differentially expressed genes that were significantly enriched in pathways closely related to rumen epithelial development included focal adhesion, Wingless-int signaling pathway, thyroid hormone signaling pathway, regulation of actin cytoskeleton and cGMP-PKG signaling pathway. The lncRNA-mRNA network included XLOC_068691 and MOAB, XLOC_023657 and DKK2, XLOC_064331 and PPP1R12A which we interpret to mean they have important regulatory roles in calve rumen development. These findings will serve as a theoretical basis for further analysis of the molecular genetic mechanism of dietary factors affecting rumen development in calves.