Integrative analysis of long non-coding RNA and mRNA in broilers with valgus-varus deformity.

Abstract

BACKGROUND:

Bone abnormality and leg disease in commercial broiler flocks are increasingly prominent, causing serious economic losses to the broiler breeding industry. Valgus-varus deformity (VVD) is a common deformity of the long bone in broilers that manifests as an outward or inward deviation of the tibiotarsus or tarsometatarsus. There is a paucity of studies on the molecular mechanisms of VVD.

RESULTS:

In this study, 6 cDNA libraries were constructed from spleen samples from VVD birds and normal birds. A total of 1951 annotated lncRNAs, 7943 novel lncRNAs and 30252 mRNAs were identified by RNA-sequencing. In addition, 420 differentially expressed (DE) mRNAs and 124 differentially expressed lncRNAs (adjusted P-value < 0.05) were obtained. A total of 16 dysregulated genes were confirmed by qPCR to be consistent with the results of the RNA-Seq. The functional lncRNA-mRNA co-expression network was constructed using differentially expressed mRNAs and target genes of the differentially expressed lncRNAs. 11 DE genes were obtained from the analysis. In order to gain insight into the interactions of genes, lncRNAs and pathways associated with VVD, we focused on the following pathways, which are involved in immunity and bone development: the Jak-stat signaling pathway, Toll-like receptor signaling pathway, Wnt-signaling pathway, mTOR signaling pathway, VEGF signaling pathway, Notch signaling pathway, TGF-beta signaling pathway and Fanconi anemia pathway. All together, 30 candidate DE genes were obtained from these pathways. We then analyzed the interaction between the DE genes and their corresponding lncRNAs. From these interaction network analyses we found that GARS, NFIC, PIK3R1, BMP6, NOTCH1, ACTB and CREBBP were the key core nodes of these networks.

CONCLUSION:

This study showed that differentially expressed genes and signaling pathways were related to immunity or bone development. These results increase the understanding of the molecular mechanisms of VVD and provide some reference for the etiology and pathogenesis of VVD.

• Authors: Hehe Tang, Yaping Guo, Zhenzhen Zhang, Zhuanjian Li, Yanhua Zhang, Yuanfang Li, Xiangtao Kang, Ruili Han
• Journal: PloS one (PLoS One) Vol. 15 Issue 9 Pg. e0239450 ( 2020) ISSN: 1932-6203 [Electronic] United States
• PMID: 32970714 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)

Chemical References

• RNA, Long Noncoding
• RNA, Messenger

Topics

• Animals
• Bone Development (genetics)
• Bone Diseases (genetics, pathology)
• Chickens (genetics)
• Chromosomes (genetics)
• Cluster Analysis
• Down-Regulation
• Gene Library
• Gene Regulatory Networks
• Poultry Diseases (genetics, pathology)
• RNA, Long Noncoding (chemistry, metabolism)
• RNA, Messenger (chemistry, metabolism)
• Sequence Analysis, RNA
• Spleen (metabolism)
• Transcriptome
• Up-Regulation