Sequence polymorphisms of mtDNA HV1, HV2 and HV3 regions in eight population groups living in Taiwan

Analysis of human mitochondrial DNA (mtDNA) polymorphisms in the D-loop region has become a useful tool in forensic casework and matrilineal origin research. In this study, the mtDNA D-loop region including hypervariable region 1 (HV1), hypervariable region 2 (HV2), segment between HV1 and HV2 (7S DNA spanned region), and extended hypervariable region 3 (HV3ex) was sequenced in 539 unrelated individuals from eight population groups living in Taiwan. Combined analyses of the complete D-loop revealed a total of 383 haplotypes with 319 unique haplotypes. The probability of any two individuals sharing the same mtDNA haplotype decreased as the combination of control region segments extended and reached 0.48% with the combination of a complete D-loop region. Sequence variants in HV3ex can further discriminate the haplotypes in some population groups. Phylogenetic haplogroups of these subjects were analyzed. The multidimensional scaling plots of these population groups, constructed based on sequence of the complete D-loop, demonstrated a clear matrilineal genetic substructure in this area. In conclusion, this database of mtDNA complete D-loop sequence including HV3 can serve as a reference for forensic identification. Sequence polymorphisms of the D-loop located outside the HV1 and HV2 may be helpful in further haplogroup characterization.