Identification of Potential Disease Biomarkers in the Ovaries of Dolang Sheep from Xinjiang using Transcriptomics and Bioinformatics Approaches

DOI: 10.18805/ijar.B-1265    | Article Id: B-1265 | Page : 412-419
Citation :- Identification of Potential Disease Biomarkers in the Ovaries of Dolang Sheep from Xinjiang using Transcriptomics and Bioinformatics Approaches.Indian Journal of Animal Research.2021.(55):412-419
WH Chang, ZL Cui, JH Wang changweihua112@163.com
Address : College of Animal Science, Tarim University, Alar City, Xinjiang 843300, PR China.
Submitted Date : 18-03-2020
Accepted Date : 5-07-2020


Background: The Dolang sheep is a well-known indigenous breed from the Xinjiang region of China. The most important characteristics of these sheep are a year-round estrus and a strong resistance to a variety of diseases. Although the molecular regulatory mechanisms governing the year-round estrus and adaptability in health and disease are well studied in various animals, the related information is limited for sheep, particularly, the Dolang variety. 
Methods: To identify differentially expressed genes (DEGs) that might be responsible for the year-round estrus and that are expressed under different physiological conditions in Dolang sheep, samples from ovaries collected at different reproductive periods were analyzed using high-throughput sequencing and subsequent transcriptomics and bioinformatics analyses. 
Result: We identified 28,717 expressed genes by RNA-Seq analysis and from a list of 987 candidate genes, we identified 308 that were differentially expressed in the ovaries of non-pregnant Dolang sheep in estrus and anestrus phases and those in the gestation phase. The genes DQA, DQB and LOC101106374 were upregulated during the gestation period. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that these three genes may improve immunity and prevent the occurrence of abortion, brucellosis, toxoplasmosis and globidiosis and can be used to monitor sheep health during pregnancy. Thus, DQA, DQB and LOC101106374 may serve as potential biomarkers for monitoring disease progression as well as abortion risk during pregnancy in sheep.


Adaptability Biomarkers Dolang sheep Next-generation RNA sequencing


  1. Chang, W.H., Yong, Z*., Wang, J.H., Ma, Y.J., Zhao, X.X., Zhang, C.R. (2015). Identification of novel and differentially expressed microRNAs in ovine ovary and testis tissues using solexa sequencing and bioinformatics[J]. Journal of Integrative Agriculture. 14(8): 1604-1616.
  2. Chang, W.H., Wang, J.H., Zhang Y., Wu, J.Y. (2018). Discovery of two novel miRNAs from the Ovis aries by a combinatorial approach of experiments and bioinformatics. Indian J. Anim. Res. 52(8): 1155-1161.
  3. Chen, C., Ai, H., Ren, J., Li, W., Li, P., Ma, J., Huang, L. (2011). A global view of porcinetranscriptome in three tissues from a full-sib pair with extreme phenotypesin growth and fat deposition by pairedend RNA sequencing. BMC Genomics. 12: 448. Doi: 10.1186/1471-2164-12-448.
  4. Chalmel F. and Rolland, A.D. (2015). Linkingtranscriptomics and proteomics inspermatogenesis. Reproduction. 150: 66 R149-R157.
  5. Conrad, T., Kniemeyer, O., Henkel, S.G., Brakhage, A.A., Vlaic, S., Linde, J. (2018). Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin. BMC Syst Biol. 12: 88. Doi: 10.1186/s 12918-018-0620-8.
  6. Diana, D.M, Eileen, A.L, Diane, G, Jorge, O. (2016). Genetic Variation at Exon 2 of the MHC Class II DQB Locus in Blue Whale (Balaenoptera musculus) from the Gulf of California. PLOS One, 1. DOI:10.1371/journal.pone.0141296.
  7. Fan, Y.X., Wu, R.B., Qiao, X., Zhang, Y.J., Li, J.Q. (2015). Hair follicle transcriptome profiles during the transition from anagen to catagen in Cashmere goat (Capra hircus). Genet. Mol. Res., 14(4): 17904-17915 
  8. Fan, Z.B., Zhang, H.F., Rong, M., Meng, D.M., Jiang, L.L., Jiang, P.H. (2019). Molecular Cloning and Bioinformatics Analysis of DQA Gene from Mink (Neovison vison). International Journal of Molecular Sciences. 20: 1037. doi:10.3390/ijms20051037
  9. Gui, D., Jia, K.T., Xia, J., Yang, L.L., Wu, Y.P., Yi, M.S. (2013). De novo assembly of the indo-pacific humpback dolphin leucocyte transcriptome to identify putative genes involved in the aquatic adaptation and immune response.PLoS One. 8. Doi:10.1371/journal.pone.0072417.
  10. Juul-Madsen, H., Dalgaard, T.S., Afanassieff, M. (2000). Molecular characterization of major and minor MHC class I and II genes in B21-like haplotypes in chickens. Anim. Genet. 31: 252-261
  11. Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 40: D109-D114.
  12. Kordonowy, L. and MacManes, M. (2017). Characterizing the reproductive transcriptomic correlates of acute dehydration in males in the desert-adapted rodent, Peromyscus eremicus. BMC Genomics.18: 473. Doi: 10.1186 /s12864-017- 3840-1.
  13. Liu, W., Chen, M.S., Bai, L.J. (2017). Comprehensive transcriptomics and proteomics analyses of pollinated and parthenocarpic litchi (Litchi chinensisSonn.) fruits during early development. Scientific Reports. 7: 5401. Doi:10.1038/s41598-017-05724-z.
  14. Marguerat, S. and Bähler, J. (2010). RNA-seq: from technology to biology. Cell Mol Life Sci. 67: 569-579.
  15. Najafi, S., Mohammadzadeh, M., Bidoki, A.Z., Meighani, Rezaei, N. (2016). HLA-DRB and HLA-DQB Allele and Haplotype Frequencies in Iranian Patients with Recurrent Aphthous Stomatitis. Iran J Allergy Asthma Immunol. 15(4): 289-295.
  16. Qian, X., Ba, Y., Zhuang, Q. F., Zhong, G. F. (2014). RNA-Seq technology and its application in fish transcriptomics. OMICS. 18: 98-110.
  17. Ramayo-Caldas, Y., Mach, N., Esteve-Codina, A., Corominas, J., Folch, J.M. (2012). Liver transcriptome profile in pigs with extremephenotypes of intramuscular fatty acid omposition. BMC Genomics. 13: 547. Doi: 10.1186/1471-2164-13-547.
  18. Rani, B., Sharma, V.K. (2017). Transcriptome profiling: methods and applications-A review. Agricultural Reviews. 38(4): 271-281.
  19. Ruan, R., Guo, A.H., Hao, Y.J., Zheng, J.S., Wang, D. (2015). Novo assembly and characterization of narrow-ridged finless porpoise renal transcriptome and identification of candidate genes involved in osmoregulation. Int J Mol Sci. 16: 2220-2238.
  20. Shukla, P., Rajput, R., Kumar R., Verma, M. (2019). Biochemical composition of amniotic fluid during different stages of gestation in Gaddi sheep. Indian J. Anim. Res. 53 (2): 178-180.
  21. Sun, X.J., Liu, Z.H., Wu, B., Zhou, L.Q., Wang, Q., Wu, W., Yang, A.G. (2018). Differences between fast and slow muscles in scallops revealed through proteomics and transcriptomics. BMC Genomics. 19. Doi.org/10.1186/s12864-018-4770-2.
  22. Tian, F., Liu, S.J., Shi, J.Q., Qi, H.F., Zhao, K., Xie, B.S. (2019). Transcriptomic profiling reveals molecular regulation of seasonal reproduction in Tibetan highland fish, Gymnocypris przewalskii. BMC Genomics, 20. Doi.org/ 10.1186/s12864- 018-5358-6.
  23. Wickramasinghe, S., Cánovas, A., Rincón, G., Juan, F. (2014). Medrano. RNA-sequencing: a tool to explore new frontiers in animal genetics. Livestock Science. 166: 206-216.
  24. Wang, X., Cao, X.D., Zhang, W.J., Zhang, EI-Ashram, S., Wu, J.D., Chen, C.F.(2018). Association of human leukocyte antigens-DQB2/DPA1/DPB1 polymorphism and pulmonary tuberculosis in the Chinese Uygur population. Molecular genetics and Genomic Medicine. DOI:10.1002/mgg 3.544
  25. Xie, H.J., Zhao, J., Zhuo-Ma, D., Zhan-Dui, N., Er-Bu, A., Tserinq, T. (2019). Inhibiting tumour metastasis by DQA modified paclitaxel plus ligustrazine micelles in treatment of non-small-cell lung cancer. Artif Cells Nanomed Biotechnol. 47(1): 3465-3477.
  26. Xing, F., Gao, Q.H., Qi, X., Li, Q.J., Li, C. (2019). Cloning and expression of Lin28A gene in the onset of pugerty in Duolang sheep. Acta Veterinaria et Zootechnica Sinica. 50(01): 78-85.
  27. Yang, H., Xu, X.L., Ma, H.M., Jiang, J. (2016). Integrative analysis of transcriptomics and proteomics of skeletal muscles of the Chinese indigenous Shaziling pig compared with the Yorkshire breed. BMC Genetics. 17. Doi:10.1186 /s12863-016- 0389-y.
  28. Zhang, S.F.,Zhao, F.P.,Wei, C.H., Sheng, X.H., Ren, H.X., Du, L.X. 2013. Identification and Characterization of the miRNA Transcriptome of Ovis aries. PLOS ONE. 8(3): e58905. https://doi.org/10.1371/journal.pone.0058905.
  29. Zheng, X., Wang, J., Chen, Y.G., Wei, Y. (2018). Comprehensive analysis of transcriptional and proteomic profiling reveals silver nanoparticles-induced toxicity to bacterial denitrification. Journal of Hazardous Materials. 344: 291-298.

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