Haplogroups determination from RNR1 and RNR2 regions of mitochondrial DNA

Shahrul Hisham Zainal Ariffin; Rus Dina Rus Din; Rohaya Megat Abdul Wahab; Siti Nur Zahidah Zahari; Hanis Nabilah Mohd Nazman; Intan Zarina Zainol Abidin

doi:10.53730/ijhs.v6nS7.13058

Authors

Shahrul Hisham Zainal Ariffin Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
Rus Dina Rus Din Forensic Science Program, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
Rohaya Megat Abdul Wahab Centre of Family Dental Health, Faculty of Dentistry, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz 50300 Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
Siti Nur Zahidah Zahari Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
Hanis Nabilah Mohd Nazman Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
Intan Zarina Zainol Abidin
intanzarina@cyberjaya.edu.my
Centre for Research and Graduate Studies, University of Cyberjaya, 63000 Cyberjaya, Selangor, Malaysia

Keywords:

Haplogroup determination, hypervariation regions, mitochondrial DNA

Abstract

Mitochondrial DNA (mtDNA) has two regions, i.e. coding and control regions which are also known as hypervariation (HV) regions. Analysis of hypervariation regions or the entire human mtDNA genome is an important element that could be used during human evolutionary, forensic or phylogenetic studies. Although most human phylogenetics studies often use HV regions; the lack of information from those regions can complicate the process of haplogroup determination. Therefore, in this study, the human mtDNA coding regions such as MT-RNR1 and MT-RNR2 genes were used as an alternative to determine the haplogroups. A total of four primer pairs were designed based on MT-RNR1 and MT-RNR2 genes using the Primer Designing Tool software. The human mtDNA sequence from the National Center for Biotechnology Information (NCBI) database (accession number NC_012920.1) was used as a reference. These primers were used in the PCR amplification approach using DNA genomic samples isolated from human peripheral blood. Polymorphism analysis of MT-RNR1 and MT-RNR2 regions using the Mitomaster database was performed to determine haplogroups. The results indicated that three haplogroups were identified which are N11a, H2a and H1. In conclusion, the primers designed from mitochondrial RNR1 and RNR2 genes can be used for human haplogroup identification.

Downloads

Download data is not yet available.

References

Achilli, A., Rengo, C., Magri, C., Battaglia, V., Olivieri, A., Scozzari, R., Cruciani, F., Zeviani, M., Briem, E., Carelli, V., Moral, P., Dugoujon, J.M., Roostalu, U., Loogväli, E.L., Kivisild, T., Bandelt, H.J., Richards, M., Villems, R., Silvana Santachiara-Benerecetti, A., Semino, O. & Torroni, A. 2004. The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool. American Journal of Human Genetics 75(5): 910–918.

Amorim, A., Fernandes, T. & Taveira, N. 2019. Mitochondrial DNA in human identification: A review. PeerJ 7(2019): e7314.

Drobná, D. & Celec, P. 2018. Mitochondrial DNA. In Gvozdjáková, A., Cornelissen-Guillaume, G.G. & Singh, R.B. (ed.) Recent Advances in Mitochondrial Medicine and Coenzyme Q, pp: 81–100. New York: Nova Science Publisher, Inc.

Duan, M., Tu, J. & Lu, Z. 2018. Recent advances in detecting mitochondrial DNA heteroplasmic variations. Molecules 23(2): 1–18.

Ghezzi, D., Marelli, C., Achilli, A., Goldwurm, S., Pezzoli, G., Barone, P., Pellecchia, M.T., Stanzione, P., Brusa, L., Bentivoglio, A.R., Bonuccelli, U., Petrozzi, L., Abbruzzese, G., Marchese, R., Cortelli, P., Grimaldi, D., Martinelli, P., Ferrarese, C., Garavaglia, B., Sangiorgi, S., Carelli, V., Torroni, A., Albanese, A. & Zeviani, M. 2005. Mitochondrial DNA haplogroup K is associated with a lower risk of parkinson’s disease in Italians. European Journal of Human Genetics 13(6): 748–752.

Gonder, M.K., Mortensen, H.M., Reed, F.A., De Sousa, A. & Tishkoff, S.A. 2007. Whole-mtDNA genome sequence analysis of ancient african lineages. Molecular Biology and Evolution 24(3): 757–768.

James T. Case & D.C.W. 1981. Maternal Inheritance of Mitochondrial DNA Polymorphisms in Cultured Human Fibroblasts. Somatic Cell Genetics 7(1): 103–108.

Karki, R., Pandya, D., Elston, R.C. & Ferlini, C. 2015. Defining “mutation” and “polymorphism” in the era of personal genomics. BMC Medical Genomics 8(1): 1–7.

Kong, Q.P., Sun, C., Wang, H.W., Zhao, M., Wang, W.Z., Zhong, L., Hao, X.D., Pan, H., Wang, S.Y., Cheng, Y.T., Zhu, C.L., Wu, S.F., Liu, L.N., Jin, J.Q., Yao, Y.G. & Zhang, Y.P. 2011. Large-Scale mtDNA screening reveals a surprising matrilineal complexity in East Asia and Its implications to the peopling of the region. Molecular Biology and Evolution 28(1): 513–522.

Liu, X., Wang, J.-C., Wang, S., Li, S., Zhu, Y., Ding, W., Xu, C.-Y., Duan, L., Xu, B. & Guo, Y. 2020. The mutation frequencies of GJB2, GJB3, SLC26A4 and MT-RNR1 of patients with severe to profound sensorineural hearing loss in northwest China. International Journal of Pediatric Otorhinolaryngology 136: 110143.

Pakendorf, B. & Stoneking, M. 2005. Mitochondrial DNA And Human Evolution. Annual Review of Genomics and Human Genetics 6(1): 165–183.

Sahidan, S., Shahrul Hisham, Z.A., Rus Dina, R.D., Rohaya, M.A.W., Intan Zarina, Z.A. & Zaidah, Z.A. 2014. Haplogroup Determination Using Hypervariable Region 1 and 2 of Human Mitochondrial DNA. Journal of Applied Sciences 14(2):197-200.

Shahrul Hisham, Z.A., Zulkeflie, Z., Sahidan, S., Rohaya, M.A.W., Mohd Fauzi, A.R. & Samsol, S. 2007. Molecular Archeology of Ancient Bone from 400 Year Old Shipwreck. Asia Pacific Journal of Molecular Biology and Biotechnology 15(1): 27-31.

Willerslev, E. & Cooper, A. 2005. Ancient DNA. Proceedings of the Royal Society B: Biological Sciences, 272 (1558): 3–16