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Full-length transcriptome and microRNA sequencing reveal the specific gene-regulation network of velvet antler in sika deer with extremely different velvet antler weight

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Abstract

Velvet antler displays the fastest and most robust tissue proliferation in the animal world, it is a model for a complete organ development/regeneration, and alternative medicine, tonic made from velvet antler, was beneficial for human. The weight of velvet antler had high biomedical and economic value, but the related regulation mechanisms controlling velvet antler weight remain unclear. In this study, extremely heavy and light velvet antler groups were selected from a sika deer population of 100 individuals with extreme velvet antler weight. A combination of full-length transcriptome sequencing and microRNA sequencing to the proliferation zone in the tip of velvet antler was applied. A total of 55306 transcripts and 1082 microRNAs were identified. Some highly expressed genes (COL1A1, COL1A2, COL3A1, FN1, and ATP6) and microRNAs (miR-21, let-7i, and miR-27b) were highly correlated with the physiological and growth characteristics of velvet antlers. Among the 334 differentially expressed genes, we found that most of the genes were located in the developmental process, especially animal organ development process. It is exciting to see that more blood vessels were found in the growing tip of heavy velvet antler through histological observation, and GO term of blood vessel development was also significant different between two groups. The combination analysis with mRNA and microRNA data in velvet antler showed a specific regulation network involved in the development of bone, mesenchyme, cartilage, and blood vessel, and helped us clearly find out the candidate 14 genes and 6 microRNAs, which could be used for selecting significant DNA markers of velvet antler weight.

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Data availability

All raw sequence reads were deposited in NCBI Sequence Read Archive (SRA, http://www.ncbi.nlm.nih.gov/Traces/sra) with SRA accession: SRP145255.

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Acknowledgements

Thanks are due to Changchun Dongda deer Industry Co., Ltd. for its support in sample collection. This study was funded by the Agricultural Science and Technology Innovation Program of China [grant number CAAS-ASTIP-201X-ISAPS]; and the Special Economic Animals Sharing Platform in China.

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Author notes

  1. Pengfei Hu and Tianjiao Wang contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory for Molecular Biology of Special Economic Animals, Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China

    Pengfei Hu, Tianjiao Wang, Huamiao Liu, Jiaping Xu, Lei Wang, Pei Zhao & Xiumei Xing

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  1. Pengfei Hu
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  2. Tianjiao Wang
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Correspondence to Xiumei Xing.

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Conflict of interest

Pengfei Hu declares that he/she has no conflict of interest. Tianjiao Wang declares that he/she has no conflict of interest. Huamiao Liu declares that he/she has no conflict of interest. Jiaping Xu declares that he/she has no conflict of interest. Lei Wang declares that he/she has no conflict of interest. Pei Zhao declares that he/she has no conflict of interest. Xiumei Xing declares that he/she has no conflict of interest.

Ethical approval

All procedures concerning animals were organized to accord with the guidelines of care and use of experimental animals established by the Ministry of Agriculture of China, and all protocols were approved by the Institutional Animal Care and Use Committee of Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China.

Additional information

Communicated by S. Hohmann.

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Figure S1

Category of annotated genes and microRNAs. A, The overall length distributions of small RNA in heavy and light velvet antler group; B, The species distribution map of annotated genes; C, The species distribution map of annotated known microRNAs (TIF 739 KB)

Figure

S2 Statistics of the enriched KEGG categories for the differentially expressed genes. The differentially expressed genes were grouped into 12 signal pathways, among them, PI3K-Akt-signaling pathway was most relevant to velvet antler development (TIF 654 KB)

Figure S3

Validation of sequencing results by quantitative real-time RT-PCR. Transcript levels of 12 genes and 4 microRNAs, of which involve in animal organ development, in qRT-PCR analysis. The y-axis shows the relative gene expression levels analyzed by qRT-PCR. The bars represent SE (n=3). L group, light velvet antler group; H group, heavy velvet antler group (TIF 898 KB)

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Hu, P., Wang, T., Liu, H. et al. Full-length transcriptome and microRNA sequencing reveal the specific gene-regulation network of velvet antler in sika deer with extremely different velvet antler weight. Mol Genet Genomics 294, 431–443 (2019). https://doi.org/10.1007/s00438-018-1520-8

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