Biological pathways related to known intergenic lncRNAs in calf ruminal samples affected with acidosis

The objective of this study was to identify known intergenic lncRNAs related to biological pathways of acidosis in Holstein calves using ruminal tissue. Two groups of healthy calves (N=3) and affected by acidosis (N=3) were compared. Paired-end sequencing method was performed using the Hiseq2500 illumine platform. Hisat2 software was used to align reads to the bovine reference genome and StringTie software package was used to assemble read files into transcripts. Using next generation sequencing, 1636 genes belonging to known intergenic lncRNAs were identified, of which 56 genes showed significant differential expression (P≤0.05). Neighbor genes of known intergenic lncRNAs were determined on bovine genome. Analysis of biological pathways and molecular function showed that five biological pathways were significantly (P≤0.05) enriched. These pathways were Apelin signaling pathway, Gap junction, Glucagon signaling pathway, Renin secretion, and AGE-RAGE signaling pathway. Moreover, two molecular functions including gap junction channel activity, and phosphatidyl inositol phospholipase C activity were significantly (P≤0.05) enriched. Some lncRNAs have different expression in healthy and acidosis samples, and the decreased pH acts as a stimulus to activate some biological signaling pathways. In conclusion, it was indicated that lncRNAs with differential expression between the control group and the group affected by acidosis are associated with pathways related to rumen energy metabolism and signaling. Identified differentially expressed lncRNAs could be used as prognostic in acidosis and biomarkers or promising candidates in animal breeding.