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Haplogroups determination from RNR1 and RNR2 regions of mitochondrial DNA

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.