Reclassification of velvet antler portions following transcriptomic analysis
Tao Qin
A , Guanning Wei C , Haiping Zhao A , Yong Li D , Hengxing Ba A E and Chunyi Li A B E
A Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, 4899 JuYe Street, Nanguan District, Changchun City, Jilin 130112, China.
B Changchun Sci-Tech University, 1699 DongHua Street, Shuangyang District, Changchun, Jilin 130022, China.
C School of Life Sciences, Jilin University, Qianwei Campus of Jilin University, 2699 Qianjin Street, Chaoyang District, Hangchun, Jilin Province, China.
D Tangshan Eighth Hospital, 16 Xiyao Road, Tangshan City, Hebei 063020, China.
E Corresponding author. Email: lichunyi1959@163.com; bahengxing@caas.cn
Animal Production Science 60(10) 1364-1367 https://doi.org/10.1071/AN19482
Submitted: 13 September 2019 Accepted: 19 March 2020 Published: 1 May 2020
Abstract
Context: Commercially, velvet antlers along the longitudinal axis are divided into four portions, namely, wax-like (WL), blood-colour (BC), honeycomb-like (HL) and bone (B) slices from the top to the base. However, there is no evidence at a molecular level showing the accuracy of this classification.
Aims: The aim of the present study was to take transcriptional approach to assess the accuracy of the traditional classification for these four portions of velvet antler, and to link the expressed mRNAs of each portion with possible functions by using bioinformatics analysis.
Methods: Three sticks of three-branched velvet antlers of sika deer were harvested from three anaesthetised 4-year-old sika deer. On the basis of the traditional methods used commercially, the velvet antler sticks were divided into the four portions of WL, BC, HL and B. Transcriptome sequencing was performed using Illumina HiSeq × Ten at BGI (Shenzheng, China).
Key results: In total, 5647 genes were obtained from the four portions. Spearman correlation analysis grouped these four portions into three clusters (WL, BC, HL+B). C-means analysis further confirmed a similar trend, indicating the accuracy of the new classification based on transcriptome analysis. Further functional analysis showed that highly expressed genes in WL, BC and HL+B were mainly related to cell cycle, cartilage development, and bone development respectively.
Conclusions: Four-portion classification based on traditional methods should be replaced by three-portion classification based on the mRNA expression levels.
Implications: We believe that this new classification can contribute to velvet antler industry, providing more accuracy in the use of velvet antlers as pharmaceuticals.
Additional keywords: blood-colour slice, bone slice, honeycomb-like slice, RNA-seq, wax-like slice.
References
Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biology 11, R106| Differential expression analysis for sequence count data.Crossref | GoogleScholarGoogle Scholar | 20979621PubMed |
Ba H, Jia B, Wang G, Yang Y, Kedem G, Li C (2017) Genome-wide SNP discovery and analysis of genetic diversity in farmed sika deer (Cervus nippon) in northeast China using double-digest restriction site-associated DNA sequencing. G3 7, 3169–3176.
| Genome-wide SNP discovery and analysis of genetic diversity in farmed sika deer (Cervus nippon) in northeast China using double-digest restriction site-associated DNA sequencing.Crossref | GoogleScholarGoogle Scholar | 28751500PubMed |
Clark DE, Lord EA, Suttie JM (2006) Expression of VEGF and pleiotrophin in deer antler. The Anatomical Record. Part A, Discoveries in Molecular, Cellular, and Evolutionary Biology 288A, 1281–1293.
| Expression of VEGF and pleiotrophin in deer antler.Crossref | GoogleScholarGoogle Scholar |
Gong R, Wang Y, Wang Y, Chen B, Gao K, Sun Y (2018) Simultaneous determination of N(ε)-(carboxymethyl) lysine and N(ε)-(carboxyethyl) lysine in different sections of antler velvet after various processing methods by UPLC–MS/MS. Molecules 23, 3316
| Simultaneous determination of N(ε)-(carboxymethyl) lysine and N(ε)-(carboxyethyl) lysine in different sections of antler velvet after various processing methods by UPLC–MS/MS.Crossref | GoogleScholarGoogle Scholar |
Gong RZ, Wang YH, Gao K, Zhang L, Liu C, Wang ZS, Wang YF, Sun YS (2019) Quantification of furosine (N(epsilon)-(2-furoylmethyl)-l-lysine) in different parts of velvet antler with various processing methods and factors affecting its formation. Molecules 24,
| Quantification of furosine (N(epsilon)-(2-furoylmethyl)-l-lysine) in different parts of velvet antler with various processing methods and factors affecting its formation.Crossref | GoogleScholarGoogle Scholar | 30935092PubMed |
Hu P, Wang T, Liu H, Xu J, Wang L, Zhao P, Xing X (2019) Full-length transcriptome and microRNA sequencing reveal the specific gene-regulation network of velvet antler in sika deer with extremely different velvet antler weight Molecular Genetics and Genomics 294, 431–443.
| Full-length transcriptome and microRNA sequencing reveal the specific gene-regulation network of velvet antler in sika deer with extremely different velvet antler weightCrossref | GoogleScholarGoogle Scholar | 30539301PubMed |
Jeon B, Kim S, Lee S, Park P, Sung S, Kim J, Moon S (2009) Effect of antler growth period on the chemical composition of velvet antler in sika deer (Cervus nippon). Mammalian Biology 74, 374–380.
| Effect of antler growth period on the chemical composition of velvet antler in sika deer (Cervus nippon).Crossref | GoogleScholarGoogle Scholar |
Kumar L, Futschik ME (2007) Mfuzz. A software package for soft clustering of microarray data. Bioinformation
| Mfuzz. A software package for soft clustering of microarray data.Crossref | GoogleScholarGoogle Scholar | 18084642PubMed |
Lai AKW, Hou WL, Verdon DJ, Nicholson L F B, Barling PM (2007) The distribution of the growth factors FGF-2 and VEGF, and their receptors, in growing red deer antler. Tissue & Cell 39, 35–46.
| The distribution of the growth factors FGF-2 and VEGF, and their receptors, in growing red deer antler.Crossref | GoogleScholarGoogle Scholar |
Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10, R25
| Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.Crossref | GoogleScholarGoogle Scholar | 19261174PubMed |
Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323
| RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.Crossref | GoogleScholarGoogle Scholar | 21816040PubMed |
Li C (2013) Histogenetic aspects of deer antler development. Frontiers in Bioscience E5, 479–489.
| Histogenetic aspects of deer antler development.Crossref | GoogleScholarGoogle Scholar |
Li C, Clark DE, Lord EA, Stanton JA, Suttie JM (2002) Sampling technique to discriminate the different tissue layers of growing antler tips for gene discovery. The Anatomical Record 268, 125–130.
| Sampling technique to discriminate the different tissue layers of growing antler tips for gene discovery.Crossref | GoogleScholarGoogle Scholar | 12221718PubMed |
Li C, Yang F, Sheppard A (2009) Adult stem cells and mammalian epimorphic regeneration: insights from studying annual renewal of deer antlers. Current Stem Cell Research & Therapy 4, 237–251.
| Adult stem cells and mammalian epimorphic regeneration: insights from studying annual renewal of deer antlers.Crossref | GoogleScholarGoogle Scholar |
Pita-Thomas W, Fernandez-Martos C, Yunta M, Maza RM, Navarro-Ruiz R, Lopez-Rodriguez MJ, Reigada D, Nieto-Sampedro M, Nieto-Diaz M (2010) Gene expression of axon growth promoting factors in the deer antler. PLoS One 5, e15706
| Gene expression of axon growth promoting factors in the deer antler.Crossref | GoogleScholarGoogle Scholar | 21187928PubMed |
Tseng S, Sung C, Chen L, Lai Y, Chang W, Sung H, Wang C (2014) Comparison of chemical compositions and osteoprotective effects of different sections of velvet antler. Journal of Ethnopharmacology 151, 352–360.
| Comparison of chemical compositions and osteoprotective effects of different sections of velvet antler.Crossref | GoogleScholarGoogle Scholar | 24212078PubMed |
Wu F, Li H, Jin L, Li X, Ma Y, You J, Li S, Xu Y (2013) Deer antler base as a traditional Chinese medicine: a review of its traditional uses, chemistry and pharmacology. Journal of Ethnopharmacology 145, 403–415.
| Deer antler base as a traditional Chinese medicine: a review of its traditional uses, chemistry and pharmacology.Crossref | GoogleScholarGoogle Scholar | 23246455PubMed |
Yang ZQ, Zhang HL, Duan CC, Geng S, Wang K, Yu HF, Yue ZP, Guo B (2017) IGF1 regulates RUNX1 expression via IRS1/2: implications for antler chondrocyte differentiation. Cell Cycle (Georgetown, Tex.) 16, 522–532.
| IGF1 regulates RUNX1 expression via IRS1/2: implications for antler chondrocyte differentiation.Crossref | GoogleScholarGoogle Scholar |
Yao B, Zhao Y, Wang Q, Zhang M, Liu M, Liu H, Li J (2012a) De novo characterization of the antler tip of Chinese sika deer transcriptome and analysis of gene expression related to rapid growth. Molecular and Cellular Biochemistry 364, 93–100.
| De novo characterization of the antler tip of Chinese sika deer transcriptome and analysis of gene expression related to rapid growth.Crossref | GoogleScholarGoogle Scholar | 22198337PubMed |
Yao B, Zhao Y, Zhang H, Zhang M, Liu M, Liu H, Li J (2012b) Sequencing and de novo analysis of the Chinese sika deer antler-tip transcriptome during the ossification stage using Illumina RNA-Seq technology. Biotechnology Letters 34, 813–822.
| Sequencing and de novo analysis of the Chinese sika deer antler-tip transcriptome during the ossification stage using Illumina RNA-Seq technology.Crossref | GoogleScholarGoogle Scholar | 22212490PubMed |
Zhou R, Li S (2009) In vitro antioxidant analysis and characterisation of antler velvet extract. Food Chemistry 114, 1321–1327.
| In vitro antioxidant analysis and characterisation of antler velvet extract.Crossref | GoogleScholarGoogle Scholar |
