Journal of Animal Production, Print ISSN: 2008-6776., Online ISSN: 2382-994X

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

Document Type : Research Paper

Authors

Bizhan Mahmoudi 1
Hedayatollah Roshanfekr 1
Mohsen Sari 2
Mohammad Reza Bakhtiarizadeh 3

1 Department of Animal science, Agricultural Sciences and Natural Resources University of Khuzestan, Ahvaz, Iran

2 Animal Science Department, Agricultural Sciences and Natural Resources University of Khuzestan, Ahvaz, Iran.

3 Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran

https://doi.org/10.22059/jap.2020.291923.623463
Abstract
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.

Keywords

Gene expression pattern
Illumine
LncRNA
Sequencing
Signaling
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Journal of Animal Production, Print ISSN: 2008-6776., Online ISSN: 2382-994X
Volume 22, Issue 3
Summer 2020
Pages 337-348

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