Genes & Genomics

, Volume 36, Issue 5, pp 583–590 | Cite as

Mitochondrial DNA haplogroups and homogeneity in the Korean population

  • Seung Beom Hong
  • Ki Cheol Kim
  • Wook KimEmail author
Research Article


Mitochondrial DNA (mtDNA) haplogroup data provide valuable information for inferring patterns of variation and population structure of maternal lineages. In this study, we analyzed the distribution of mtDNA haplogroup variation using a 20-plex SNaPshot assay for determination of the major East Asian haplogroups to evaluate the possible genetic structure and differentiation from 708 unrelated individuals residing in six major provinces in Korea. The most common mtDNA haplogroups were found to be D4 and B4, followed by A, D4a, and M7, which are prevalent in East Asian populations. All provinces exhibited high haplogroup diversities, ranging from 0.8957 in Jeju Island to 0.9284 in Gyeongsang. Pair-wise F ST distances and AMOVA of the studied Korean provinces reflected no maternal subpopulation heterogeneity present within the population group, except for Jeju Island, showing small, but statistically significant differences between the populations (p < 0.01). This result indicates that the Jeju Island may point to the need for creating a local mtDNA database, to avoid bias in forensic parameters estimates caused by genetic heterogeneity of the population. However, since there is no geographic pattern to suggest this result represents any population heterogeneity on a peninsular level in Korea, the present data could be useful in serving as a basis for comprehensive Korean population and forensic mtDNA database.


mtDNA haplogroups Population genetics Population structure Forensic DNA database Koreans 



The authors would like to thank all the volunteers for providing DNA samples. They also thank S.S. Hong and S.G. Lee for technical assistance to this survey. The present research was supported by the research fund of Dankook University in 2012.

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

13258_2014_194_MOESM1_ESM.pdf (96 kb)
Supplementary material 1 (PDF 95 kb)
13258_2014_194_MOESM2_ESM.pdf (76 kb)
Supplementary material 2 (PDF 76 kb)


  1. Adachi N, Shinoda K, Umetsu K, Matsumura H (2009) Mitochondrial DNA analysis of Jomon skeletons from the Funadomari site, Hokkaido, and its implication for the origins of Native American. Am J Phys Anthropol 138:255–265CrossRefPubMedGoogle Scholar
  2. Bermisheva MA, Kutuev IA, Spitsyn VA, Villems R, Batyrova AZ, Korshunova TIu, Khusnutdinova EK (2005) Analysis of mitochondrial DNA variation in the population of Oroks. Genetika 41:78–84PubMedGoogle Scholar
  3. Brion M, Sobrino B, Blanco-Verea A, Lareu MV, Carracedo A (2005) Hierarchical analysis of 30 Y-chromosome SNPs in European populations. Int J Legal Med 119:10–15CrossRefPubMedGoogle Scholar
  4. Budowle B, Allard MW, Wilson MR, Chakraborty R (2003) Forensics and mitochondrial DNA: applications, debates, and foundations. Annu Rev Genomics Hum Genet 4:119–141CrossRefPubMedGoogle Scholar
  5. Chen F, Wang SY, Zhang RZ, Hu YH, Gao GF, Liu YH, Kong QP (2008) Analysis of mitochondrial DNA polymorphisms in Guangdong Han Chinese. Forensic Sci Int Genet 2:150–153CrossRefPubMedGoogle Scholar
  6. Choi ML, Rhee SN (2001) Korean archaeology for the 21st century: from prehistory to State formation. Seoul J Kor Stud 14:117–147Google Scholar
  7. Cockerton S, McManus K, Buckleton J (2012) Interpreting lineage markers in view of subpopulation effects. Forensic Sci Int Genet 6:393–397CrossRefPubMedGoogle Scholar
  8. Derenko MV, Lunkina AV, Maliarchuk BA, Zakharov IA, Tsedev T, Park KS, Cho YM, Lee NK, Chu CH (2004) Restriction polymorphism of mitochondrial DNA in Koreans and Mongolians. Genetika 40:1562–1570PubMedGoogle Scholar
  9. Excoffier L, Lischer HE (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567CrossRefPubMedGoogle Scholar
  10. Gill P, Ivanov PL, Kimpton C, Piercy R, Benson N, Tully G, Evett I, Hagelberg E, Sullivan K (1994) Identification of the remains of the Romanov family by DNA analysis. Nat Genet 6:130–135CrossRefPubMedGoogle Scholar
  11. Holland MM, Parson TJ (1999) Mitochondrial DNA sequence analysis—validation and use for forensic casework. Forensic Sci Rev 11:21–50PubMedGoogle Scholar
  12. Jin HJ, Kwak KD, Hammer MF, Nakahori Y, Shinka T, Lee JW, Jin F, Jia X, Tyler-Smith C, Kim W (2003) Y-chromosomal DNA haplogroups and their implications for the dual origins of the Koreans. Hum Genet 114:27–35CrossRefPubMedGoogle Scholar
  13. Jin HJ, Kwak KD, Hong SB, Shin DJ, Han MS, Tyler-Smith C, Kim W (2006) Forensic genetic analysis of mitochondrial DNA hypervariable region I/II sequences: an expanded Korean population database. Forensic Sci Int 158:125–130CrossRefPubMedGoogle Scholar
  14. Jin HJ, Tyler-Smith C, Kim W (2009) The peopling of Korea revealed by analyses of mitochondrial DNA and Y-chromosomal markers. PLoS ONE 4:e4210PubMedCentralCrossRefPubMedGoogle Scholar
  15. Kaderali L, Deshpande A, Nolan JP, White PS (2003) Primer-design for multiplexed genotyping. Nucleic Acids Res 31:1796–1802PubMedCentralCrossRefPubMedGoogle Scholar
  16. Kim SH, Han MS, Kim W, Kim W (2010) Y chromosome homogeneity in the Korean population. Int J Legal Med 124:653–657CrossRefPubMedGoogle Scholar
  17. Kivisild T, Tolk HV, Parik J, Wang Y, Papiha SS, Bandelt HJ, Villems R (2002) The emerging limbs and twigs of the East Asian mtDNA tree. Mol Biol Evol 19:1737–1751CrossRefPubMedGoogle Scholar
  18. Lee JW, Lee HS, Hwang JJ (2002) Statistical analysis for estimating heterogeneity of the Korean population in DNA typing using STR loci. Int J Legal Med 116:153–160CrossRefPubMedGoogle Scholar
  19. Lee HY, Yoo JE, Park MJ, Chung U, Kim CY, Shin KJ (2006a) East Asian mtDNA haplogroup determination in Koreans: haplogroup-level coding region SNP analysis and subhaplogroup-level control region sequence analysis. Electrophoresis 27:4408–4418CrossRefPubMedGoogle Scholar
  20. Lee HY, Yoo JE, Park MJ, Chung U, Shin KJ (2006b) Mitochondrial DNA control region sequences in Koreans: identification of useful variable sites and phylogenetic analysis for mtDNA data quality control. Int J Legal Med 120:5–14CrossRefPubMedGoogle Scholar
  21. Marrero AR, Bravi C, Stuart S, Long JC, Pereira das Neves Leite F, Kommers T, Carvalho CM, Pena SD, Ruiz-Linares A, Salzano FM, Cátira Bortolini M (2007) Pre- and post-Columbian gene and cultural continuity: the case of the Gaucho from southern Brazil. Hum Hered 64:160–171Google Scholar
  22. Maruyama S, Komuro T, Izawa H, Tsutsumi H (2013) Analysis of human mitochondrial DNA polymorphisms in the Japanese population. Biochem Genet 51:33–70CrossRefPubMedGoogle Scholar
  23. Melton T, Clifford S, Kayser M, Nasidze I, Batzer M, Stoneking M (2001) Diversity and heterogeneity in mitochondrial DNA of North American populations. J Forensic Sci 46:46–52CrossRefPubMedGoogle Scholar
  24. Pakendorf B, Stoneking M (2005) Mitochondrial DNA and human evolution. Annu Rev Genomics Hum Genet 6:165–183CrossRefPubMedGoogle Scholar
  25. Quintana-Murci L, Quach H, Harmant C, Luca F, Massonnet B, Patin E, Sica L, Mouguiama-Daouda P, Comas D, Tzur S, Balanovsky O, Kidd KK, Kidd JR, van der Veen L, Hombert JM, Gessain A, Verdu P, Froment A, Bahuchet S, Heyer E, Dausset J, Salas A, Behar DM (2008) Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter-gatherers and Bantu-speaking farmers. Proc Natl Acad Sci USA 105:1596–1601PubMedCentralCrossRefPubMedGoogle Scholar
  26. Scholes C, Siddle K, Ducourneau A, Crivellaro F, Järve M, Rootsi S, Bellatti M, Tabbada K, Mormina M, Reidla M, Villems R, Kivisild T, Lahr MM, Migliano AB (2011) Genetic diversity and evidence for population admixture in Batak Negritos from Palawan. Am J Phys Anthropol 146:62–72CrossRefPubMedGoogle Scholar
  27. Tajima A, Hayami M, Tokunaga K, Juji T, Matsuo M, Marzuki S, Omoto K, Horai S (2004) Genetic origins of the Ainu inferred from combined DNA analyses of maternal and paternal lineages. J Hum Genet 49:187–193CrossRefPubMedGoogle Scholar
  28. Tanaka M, Cabrera VM, González AM, Larruga JM, Takeyasu T, Fuku N, Guo LJ, Hirose R, Fujita Y, Kurata M, Shinoda K, Umetsu K, Yamada Y, Oshida Y, Sato Y, Hattori N, Mizuno Y, Arai Y, Hirose N, Ohta S, Ogawa O, Tanaka Y, Kawamori R, Shamoto-Nagai M, Maruyama W, Shimokata H, Suzuki R, Shimodaira H (2004) Mitochondrial genome variation in eastern Asia and the peopling of Japan. Genome Res 14:1832–1850PubMedCentralCrossRefPubMedGoogle Scholar
  29. Umetsu K, Tanaka M, Yuasa I, Adachi N, Miyoshi A, Kashimura S, Park KS, Wei YH, Watanabe G, Osawa M (2005) Multiplex amplified product-length polymorphism analysis of 36 mitochondrial single-nucleotide polymorphisms for haplogrouping of East Asian populations. Electrophoresis 26:91–98CrossRefPubMedGoogle Scholar
  30. Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, Leunissen JA (2007) Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res 35:71–74CrossRefGoogle Scholar
  31. van Oven M, Kayser M (2009) Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30:E386–E394CrossRefPubMedGoogle Scholar
  32. van Oven M, Hämmerle JM, van Schoor M, Kushnick G, Pennekamp P, Zega I, Lao O, Brown L, Kennerknecht I, Kayser M (2011) Unexpected island effects at an extreme: reduced Y chromosome and mitochondrial DNA diversity in Nias. Mol Biol Evol 28:1349–1361CrossRefPubMedGoogle Scholar
  33. Wen B, Li H, Lu D, Song X, Zhang F, He Y, Li F, Gao Y, Mao X, Zhang L, Qian J, Tan J, Jin J, Huang W, Deka R, Su B, Chakraborty R, Jin L (2004) Genetic evidence supports demic diffusion of Han culture. Nature 431:302–305CrossRefPubMedGoogle Scholar
  34. Yao YG, Kong QP, Bandelt HJ, Kivisild T, Zhang YP (2002) Phylogeographic differentiation of mitochondrial DNA in Han Chinese. Am J Hum Genet 70:635–651PubMedCentralCrossRefPubMedGoogle Scholar

Copyright information

© The Genetics Society of Korea and Springer-Science and Media 2014

Authors and Affiliations

  1. 1.Department of Biological SciencesDankook UniversityCheonanKorea
  2. 2.Forensic DNA DivisionNational Forensic ServiceWonjuKorea

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