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Abstract

This study aimed to analyze the genetic diversity of the sambar deer (Cervus unicolor) population through mitochondrial D-loop DNA sequencing. The findings provide valuable insights into the conservation status of this vulnerable species in the region and inform future management strategies for Cervus unicolor. Blood samples from 10 individual sambar deer, consisting of 8 females and two male deer, were amplified using PCR and then sequenced. Data analysis of the genetic diversity of sambar deer was carried out using the genome sequencing method from NCBI, Bioedit 7.7.1 software, DNAsp 5.1, and MEGA 11 Software. The results of this study were that the DNA concentration test in sambar deer had an average of 12.375 ng/uL, with an average DNA purity test = 1.34, with 10 samples divided into 3 haplotypes. The level of genetic diversity of sambar deer from all samples is π = 0.01745 ± 0.00380, and haplotype diversity of Hd = 1,000 ± 0.045. Based on the phylogenetic tree, there are two parts: the Asian and Kalimantan regions. The conclusion of the current study showed that sequencing analysis of Sambar deer shows relatively high diversity and is a reasonable basis for performance selection and development of modern Sambar deer breeding.

Keywords

Cervus unicolor brookei D-loop mitochondrial DNA Genetic diversity Haplotipe

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How to Cite
Jofaturrahmah, A., Fanani, A. F., Wibowo, A., Indana, K., Putra, W. P. B., & Suhardi, S. (2025). Genetic Diversity Analysis of Sambar Deer (Cervus unicolor) Based on Mitochondrial DNA D-loop Sequence. Jurnal Sain Peternakan Indonesia, 20(1), 61–69. https://doi.org/10.31186/jspi.id.20.1.61-69
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References

  1. Agisimanto, D., Supriyanto, A. 2007. Keragaman Genetik Pamelo Indonesia Berdasarkan Primer Random Amplified Polymorphic DNA. Jurnal Hortikultura, 17(1), 1–7.
  2. Ando, S., Komiyama, T., Sudo, M., Higaki, Y., Ishida, K., Costello, J. T., & Katayama, K. 2020. The interactive effects of acute exercise and hypoxia on cognitive performance: A narrative review. Scandinavian Journal of Medicine and Science in Sports, 30(3), 384–398. https://doi.org/10.1111/sms.13573
  3. Aulia, S. L., Suwignyo, R. A., & Hasmeda, M. 2021. Optimasi Suhu Annealing untuk Amplifikasi Dna Padi Hasil Persilangan Varietas Tahan Terendam dengan Metode Polymerase Chain Reaction. Sainmatika: Jurnal Ilmiah Matematika Dan Ilmu Pengetahuan Alam, 18(1), 44. https://doi.org/10.31851/sainmatika.v17i3.5805
  4. Avise, J. C., Arnold, J., Ball, R. M., Bermingham, E., Lamb, T., Neigel, J. E., Reeb, C. A., & Saunders, N. C. 1987. INTRASPECIFIC PHYLOGEOGRAPHY: The Mitochondrial DNA Bridge Between Population Genetics and Systematics. Annual Review of Ecology and Systematics, 18(1), 489–522. https://doi.org/10.1146/annurev.es.18.110187.002421
  5. Balakrishnan, C. N., Monfort, S. L., Gaur, A., Singh, L., & Sorenson, M. D. 2003. Phylogeography and conservation genetics of Eld’s deer (Cervus eldi). Molecular Ecology, 12(1), 1–10. https://doi.org/10.1046/j.1365-294X.2003.01751.x
  6. Dauzery, E., & Randi, E. 1997. The mitochondrial control region of Cervidae: Evolutionary patterns and phylogenetic content. Molecular Biology and Evolution, 14(11), 1154–1166. https://doi.org/10.1093/oxfordjournals.molbev.a025725
  7. Ghazi, M. G., Hussain, S. A., & Gupta, S. K. 2021. Detection of 40 bp tandem repeat motif and associated insertions and deletions (INDEL) in the mitochondrial DNA control region of Sambar deer (Rusa unicolor). Molecular Biology Reports, 48(5), 4129–4135. https://doi.org/10.1007/s11033-021-06426-6
  8. Hasibuan, F. E. B., Mantiri, F. R., & Rumende, R. R. . 2017. KAJIAN VARIASI SEKUNES INTRASPESIES DAN FILOGENETIK MONYET HITAM SULAWESI (Macaca nigra) DENGAN MENGGUNAKAN GEN COI. Jurnal Ilmiah Sains, 17(1), 59–67. https://doi.org/10.35799/jis.17.1.2017.15558
  9. Hisheh, S., Westerman, M., & Schmitt, L. H. 1998. Biogeography of the Indonesian archipelago: Mitochondrial DNA variation in the fruit bat, Eonycteris spelaea. Biological Journal of the Linnean Society, 65(3), 329–345. https://doi.org/10.1006/bijl.1998.0244
  10. Hobbs, J. P. A., Frisch, A. J., Ford, B. M., Thums, M., Saenz-Agudelo, P., Furby, K. A., & Berumen, M. L. 2013. Taxonomic, Spatial and Temporal Patterns of Bleaching in Anemones Inhabited by Anemonefishes. PLoS ONE, 8(8), 1–12. https://doi.org/10.1371/journal.pone.0070966
  11. Hu, J., Fang, S. G., & Wan, Q. H. 2006. Genetic diversity of Chinese water deer (Hydropotes inermis inermis): Implications for conservation. Biochemical Genetics, 44(3–4), 161–172. https://doi.org/10.1007/s10528-006-9020-7
  12. Liu, B., Tao, W., Feng, D., Wang, Y., Heizatuola, N., Ahemetbai, T., & Wu, W. 2022. Revealing Genetic Diversity and Population Structure of Endangered Altay White-Headed Cattle Population Using 100 k SNP Markers. Animals, 12(22), 1–17. https://doi.org/10.3390/ani12223214
  13. Liu, R. Y., Lei, C. Z., Liu, S. H., & Yang, G. S. 2007. Genetic diversity and origin of Chinese domestic goats revealed by complete mtDNA D-loop sequence variation. Asian-Australasian Journal of Animal Sciences, 20(2), 178–183. https://doi.org/10.5713/ajas.2007.178
  14. Liu, R. Y., Yang, G. S., & Lei, C. Z. 2006. The genetic diversity of mtDNA D-loop and the origin of Chinese goats. Acta Genetica Sinica, 33(5), 420–428. https://doi.org/10.1016/S0379-4172(06)60069-3
  15. Martins, R. F., Schmidt, A., Lenz, D., Wilting, A., & Fickel, J. 2018. Human-mediated introduction of introgressed deer across Wallace’s line: Historical biogeography of Rusa unicolor and R. timorensis. Ecology and Evolution, 8(3), 1465–1479. https://doi.org/10.1002/ece3.3754
  16. Nei, M. 1972. Chapter 9: Genetic Distance Between Populations. Molecular Evolutionary Genetics, 106(949), 283–292. https://doi.org/10.7312/nei-92038-010
  17. Nei, M. 1987. The Molecular Approach (Vol. 237, Issue 1984).
  18. Nicholls, T. J., & Minczuk, M. 2014. In D-loop: 40 years of mitochondrial 7S DNA. Experimental Gerontology, 56, 175–181. https://doi.org/10.1016/j.exger.2014.03.027
  19. Pereira, F., Pereira, L., Van Asch, B., Bradley, D. G., & Amorim, A. 2005. The mtDNA catalogue of all Portuguese autochthonous goat (Capra hircus) breeds: High diversity of female lineages at the western fringe of European distribution. Molecular Ecology, 14(8), 2313–2318. https://doi.org/10.1111/j.1365-294X.2005.02594.x
  20. Rahayu, S. E. 2010. Keragaman Genetik Pandan Asal Jawa Barat. Makara Sains, 14(2), 158–162.
  21. Rianti, P., Hutapea, A. L., Rahman, D. A., & Santosa, Y. 2021. Primer design of D-loop region for wild population genetics of Rusa timorensis in Indonesia. IOP Conference Series: Earth and Environmental Science, 948(1), 1–13. https://doi.org/10.1088/1755-1315/948/1/012017
  22. S. Blair Hedges, Julie Marin, Michael Suleski, M. P., & and Sudhir Kumara. 1925. Title: Tree of life reveals clock-like speciation and diversification S. Blair Hedges. 1–23.
  23. Suparningtyas, J. F., Dwi Pramudyawardhani, O., Purwoko, D., & Tajuddin, T. 2018. Analisis filogenetik beberapa Klon Karet dengan Marka AFLP. Jurnal Bioteknologi Dan Biosains Indonesia, 5(1), 8–19. http://ejurnal.bppt.go.id/index.php/JBBI
  24. Taylor, R. W., & Turnbull, D. M. 2005. Mitochondrial DNA mutations in human disease. Nature Reviews Genetics, 6(5), 389–402. https://doi.org/10.1038/nrg1606
  25. Utami, S. D., Utaminingsih, S., & Sophian, A. 2023. Analisis DNA Hasil Isolasi Pada Produk Pangan Olahan Ikan (Surimi Ikan) Menggunakan Nano Photometer. JRST (Jurnal Riset Sains Dan Teknologi), 7(1), 9–13. https://doi.org/10.30595/jrst.v7i1.15180
  26. Whitehead, G. K. 1993. Whitehead encyclopedia of deer. 704. https://doi.org/10.3/JQUERY-UI.JS
  27. Wirdateti. 2012. Keragaman Genetik Rusa Sambar (Rusa unicolor), Pemanfaatan dan Implikasinya Untuk Konservasi. Jurnal Biologi Indonesia, 8(1), 131–139.
  28. Wu, H. L., & Fang, S. G. 2005. Mitochondrial DNA genetic diversity of black muntjac (Muntiacus crinifrons), an endangered species endemic to China. Biochemical Genetics, 43(7–8), 407–416. https://doi.org/10.1007/s10528-005-6779-x
  29. Wu, H., Wan, Q. H., & Fang, S. G. 2004. Two genetically distinct units of the Chinese sika deer (cervus nippon): Analyses of mitochondrial DNA variation. Biological Conservation, 119(2), 183–190. https://doi.org/10.1016/j.biocon.2003.10.027
  30. Y, Y., Widayanti, R., & Artama, T. 2014. Analisis Genetika Molekuler Kuda Sumba Berdasarkan Urutan D-Loop Mitokondria. Jurnal Kedokteran Hewan - Indonesian Journal of Veterinary Sciences, 8(1), 23–26. https://doi.org/10.21157/j.ked.hewan.v8i1.1250
  31. Yuliati, S., Helmi, T. Z., Rinidar, Balqis, U., Erwin, & Rosmaidar. 2019. Kajian Molekuler Karakteristik Gen Calpastatin (Cast) Pada Kambing Boerka (Capra Hircus). Jimvet, 3(4), 206–216. http://www.etd.unsyiah.ac.id/index.php?p=show_detail&id=40853
  32. Zein, M. S. 2009. Keragaman Daerah Kontrol DNA Mitokondria Rusa Timor (Cervus timorensis timorensis) di Pulau Timor, Alor, dan Pantar. Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati, 12(3), 138–144. https://doi.org/10.24002/biota.v12i3.2799

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