Abstract
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. 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. 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.
Highlights
The global broiler production was reported to be about 100 million tons in 2019, and the main broiler breeds include Arbor Acres broilers, Avian broilers, Ross 308 broilers, Roman broilers, Cobb broilers, Hubbard broilers
The functional Long non-coding RNA (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 Valgus-varus deformity (VVD), we focused on the following pathways, which are involved in immunity and bone development: the Jak-stat signaling pathway, Tolllike receptor signaling pathway, Wnt-signaling pathway, mTOR signaling pathway, VEGF signaling pathway, Notch signaling pathway, TGF-beta signaling pathway and Fanconi anemia pathway
Summary
The global broiler production was reported to be about 100 million tons in 2019, and the main broiler breeds include Arbor Acres broilers, Avian broilers, Ross 308 broilers, Roman broilers, Cobb broilers, Hubbard broilers. In our previous study of VVD in Hubbard broilers, the incidence was 1.75% [5,6,7]. Previous studies have shown that VVD carries a certain genetic potential, and the incidence of VVD could be reduced by genetic selection [1, 6, 10]. These results suggest that genetic studies will provide a more scientific explanation for the etiology and pathogenesis of VVD. Bone abnormality and leg disease in commercial broiler flocks are increasingly prominent, causing serious economic losses to the broiler breeding industry. There is a paucity of studies on the molecular mechanisms of VVD
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