Skip to main content

Genetic polymorphism analysis of mitochondrial DNA from Chinese Xinjiang Kazak ethnic group by a novel mitochondrial DNA genotyping panel

Molecular Biology Reports volume 46, pages 17–25 (2019)Cite this article

Abstract

Genetic polymorphism analysis of 60 mitochondrial DNA (mtDNA) loci in Chinese Xinjiang Kazak group was conducted in this study. Blood samples from 141 unrelated healthy volunteers were randomly collected from Chinese Kazak ethnic group in Ili, Xinjiang Uygur Autonomous region. Among these mtDNA loci, single nucleotide transition was the most commonly observed variant (87.93%). A total of 25 haplogroups and 79 haplotypes were found in Kazak group, and Haplogroup D4 was the most common haplogroup (21.28%). Among the entire 79 haplotypes, 53 of them were observed for only once, 14 for twice. The haplotype diversity was 0.978 ± 0.005, and the nucleotide diversity was 0.17449. The detection of (CA)n and 9-bp deletion polymorphisms could improve the discrimination power of the mtDNA genetic marker. Moreover, Xinjiang Kazak group was compared with other previously reported groups to infer its genetic background. The present results revealed that Xinjiang Kazak ethnic group was genetically closer related to Xinjiang Uygur, Xinjiang Uzbek and Xinjiang Han populations. Meanwhile, our results also indicated the potential closer genetic relationships among Xinjiang Kazak group with Altaian Kazak as well as Xinjiang Xibe group. In conclusion, this novel mtDNA panel could be effectively utilized for forensic applications. Additionally, to further reveal the genetic background of Chinese Kazak group, more relevant populations and genetic markers should be incorporated in our future study.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

43,34 €

Price includes VAT (Finland)
Tax calculation will be finalised during checkout.

Fig. 1
Fig. 2
Fig. 3

References

  1. Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F (1981) Sequence and organization of the human mitochondrial genome. Nature 290(5806):457–465

    Article  CAS  PubMed  Google Scholar 

  2. Ginther C, Issel-Tarver L, King MC (1992) Identifying individuals by sequencing mitochondrial DNA from teeth. Nat Genet 2(2):135–138. https://doi.org/10.1038/ng1092-135

    Article  CAS  PubMed  Google Scholar 

  3. Holland MM, Parsons TJ (1999) Mitochondrial DNA sequence analysis—validation and use for forensic casework. Forensic Sci Rev 11(1):21–50

    CAS  PubMed  Google Scholar 

  4. Wittig H, Augustin C, Baasner A, Bulnheim U, Dimo-Simonin N, Edelmann J, Hering S, Jung S, Lutz S, Michael M, Parson W, Poetsch M, Schneider PM, Weichhold G, Krause D (2000) Mitochondrial DNA in the Central European population. Human identification with the help of the forensic mt-DNA D-loop-base database. Forensic Sci Int 113(1–3):113–118

    Article  CAS  PubMed  Google Scholar 

  5. Holland MM, Cave CA, Holland CA, Bille TW (2003) Development of a quality, high throughput DNA analysis procedure for skeletal samples to assist with the identification of victims from the World Trade Center attacks. Croatian Med J 44(3):264–272

    Google Scholar 

  6. Macaulay V, Hill C, Achilli A, Rengo C, Clarke D, Meehan W, Blackburn J, Semino O, Scozzari R, Cruciani F, Taha A, Shaari NK, Raja JM, Ismail P, Zainuddin Z, Goodwin W, Bulbeck D, Bandelt HJ, Oppenheimer S, Torroni A, Richards M (2005) Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science 308(5724):1034–1036. https://doi.org/10.1126/science.1109792

    Article  CAS  PubMed  Google Scholar 

  7. Gilbert MT, Djurhuus D, Melchior L, Lynnerup N, Worobey M, Wilson AS, Andreasen C, Dissing J (2007) mtDNA from hair and nail clarifies the genetic relationship of the 15th century Qilakitsoq Inuit mummies. Am J Phys Anthropol 133(2):847–853. https://doi.org/10.1002/ajpa.20602

    Article  PubMed  Google Scholar 

  8. Boattini A, Castri L, Sarno S, Useli A, Cioffi M, Sazzini M, Garagnani P, De Fanti S, Pettener D, Luiselli D (2013) mtDNA variation in East Africa unravels the history of Afro-Asiatic groups. Am J Phys Anthropol 150(3):375–385. https://doi.org/10.1002/ajpa.22212

    Article  PubMed  Google Scholar 

  9. Kohnemann S, Pfeiffer H (2011) Application of mtDNA SNP analysis in forensic casework. Forensic Sci Int Genet 5(3):216–221. https://doi.org/10.1016/j.fsigen.2010.01.015

    Article  CAS  PubMed  Google Scholar 

  10. Kohnemann S, Pennekamp P, Schmidt PF, Pfeiffer H (2010) qPCR and mtDNA SNP analysis of experimentally degraded hair samples and its application in forensic casework. Int J Legal Med 124(4):337–342. https://doi.org/10.1007/s00414-010-0466-0

    Article  PubMed  Google Scholar 

  11. Zerjal T, Wells RS, Yuldasheva N, Ruzibakiev R, Tyler-Smith C (2002) A genetic landscape reshaped by recent events: Y-chromosomal insights into Central Asia. Am J Hum Genet 71(3):466–482. https://doi.org/10.1086/342096

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Yao YG, Kong QP, Wang CY, Zhu CL, Zhang YP (2004) Different matrilineal contributions to genetic structure of ethnic groups in the silk road region in china. Mol Biol Evol 21(12):2265–2280. https://doi.org/10.1093/molbev/msh238msh238

    Article  CAS  PubMed  Google Scholar 

  13. Gokcumen O, Dulik MC, Pai AA, Zhadanov SI, Rubinstein S, Osipova LP, Andreenkov OV, Tabikhanova LE, Gubina MA, Labuda D, Schurr TG (2008) Genetic variation in the enigmatic Altaian Kazakhs of south-central russia: insights into turkic population history. Am J Phys Anthropol 136(3):278–293. https://doi.org/10.1002/ajpa.20802

    Article  PubMed  Google Scholar 

  14. Walsh PS, Metzger DA, Higuchi R (2013) Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 54(3):134–139

    Article  CAS  PubMed  Google Scholar 

  15. Andrews R, Kubacka I, Chinnery P, Lightowlers R, Turnbull D, Howell N (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23:147

    Article  CAS  PubMed  Google Scholar 

  16. van Oven M, Kayser M (2009) Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30:E386–E394

    Article  PubMed  Google Scholar 

  17. Nei M, Tajima F (1981) DNA polymorphism detectable by restriction endonucleases. Genetics 97(1):145–163

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76(10):5269–5273

    Article  CAS  PubMed  Google Scholar 

  19. Shen CM, Hu L, Yang CH, Yin CY, Li ZD, Meng HT, Guo YX, Mei T, Chen F, Zhu BF (2017) Genetic polymorphisms of 54 mitochondrial DNA SNP loci in Chinese Xibe ethnic minority group. Sci Rep 7:44407. https://doi.org/10.1038/srep44407

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Kivisild T, Tolk HV, Parik J, Wang YM, Papiha SS, Bandelt HJ, Villems R (2002) The emerging limbs and twigs of the East Asian mtDNA tree. Mol Biol Evol 19(10):1737–1751

    Article  CAS  PubMed  Google Scholar 

  21. Yao YG, Kong QP, Bandelt HJ, Kivisild T, Zhang YP (2002) Phylogeographic differentiation of mitochondrial DNA in Han Chinese. Am J Hum Genet 70(3):635–651. https://doi.org/10.1086/338999

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. King JL, Larue BL, Novroski NM, Stoljarova M, Seo SB, Zeng XP, Warshauer DH, Davis CP, Parson W, Sajantila A, Budowle B (2014) High-quality and high-throughput massively parallel sequencing of the human mitochondrial genome using the Illumina MiSEq. Forensic Sci Int 12:128–135. https://doi.org/10.1016/j.fsigen.2014.06.001

    Article  CAS  Google Scholar 

  23. Bodner M, Iuvaro A, Strobl C, Nagl S, Huber G, Pelotti S, Pettener D, Luiselli D, Parson W (2015) Helena, the hidden beauty: resolving the most common West Eurasian mtDNA control region haplotype by massively parallel sequencing an Italian population sample. Forensic Sci Int 15:21–26. https://doi.org/10.1016/j.fsigen.2014.09.012

    Article  Google Scholar 

  24. Stoljarova M, King JL, Takahashi M, Aaspollu A, Budowle B (2016) Whole mitochondrial genome genetic diversity in an Estonian population sample. Int J Legal Med 130(1):67–71. https://doi.org/10.1007/s00414-015-1249-4

    Article  PubMed  Google Scholar 

  25. Nie Y, Zhang C, Jiao H, Zhao Z, Zhou H (2014) Development of a multiplex PCR system of 59 mitochondrial SNPs and genetic analysis in Chinese population. Electrophoresis 35(12–13):1903–1911. https://doi.org/10.1002/elps.201400047

    Article  CAS  PubMed  Google Scholar 

  26. Lum JK, Cann RL (1998) mtDNA and language support a common origin of Micronesians and Polynesians in Island Southeast Asia. Am J Phys Anthropol 105 (2):109–119

    Article  CAS  PubMed  Google Scholar 

  27. Merriwether DA, Friedlaender JS, Mediavilla J, Mgone C, Gentz F, Ferrell RE (1999) Mitochondrial DNA variation is an indicator of austronesian influence in Island Melanesia. Am J Phys Anthropol 110 (3):243–270

    Article  CAS  PubMed  Google Scholar 

  28. Alves-Silva J, Santos MS, Pena SD, Prado VF (1999) Multiple geographic sources of region V 9-bp deletion haplotypes in Brazilians. Hum Biol 71(2):245–259

    CAS  PubMed  Google Scholar 

  29. Barthold VV (1962) Four studies on the history of Central Asia, vol 3. Brill Publishers, Leiden

    Google Scholar 

  30. Millward JA (2007) Eurasian crossroads: a history of Xinjiang. Columbia University Press, New York

    Google Scholar 

  31. Perdue PC (2005) China marches west: the qing conquest of Central Eurasia. Harvard University Press, Cambridge

  32. Lattimore O (1950) Pivot of Asia; Sinkiang and the inner Asian frontiers of China and Russia. Little, Brown and Company, Boston

    Google Scholar 

  33. Comas (1999) Trading genes along the silk road: mtDNA sequences and the origin of central Asian populations (vol 63, pg 1824, 1998). Am J Hum Genet 65(1):277–277

    Article  Google Scholar 

  34. Conquest R (1987) The harvest of sorrow: soviet collectivization and the terror-famine. Oxford University Press, Oxford

    Google Scholar 

  35. The Annals of the American Academy of Political and Social Science, vol 277 (2010). vol 276–278. American Academy of Political and Social Science

  36. The Annals of the American Academy of Political and Social Science, Volume 277 (2012) A group of Kazakhs, originally numbering over 20000 people when expelled from Sinkiang by Sheng Shih-ts’ai in 1936, was reduced, after repeated massacres by their Chinese coreligionists under Ma Pu-fang, to a scattered 135 people. American Academy of Political and Social Science

Download references

Acknowledgements

This project was supported by the National Natural Science Foundation of China (NSFC, No. 81772031), GDUPS (2017). The authors sincerely thank all the volunteers for providing blood samples and Southern Medical University for providing the research platform.

Author information

Author notes

  1. Tong Xie and Li Hu have contributed equally to this work as first author.

  2. Feng Chen and Bo-Feng Zhu have contributed equally to this work as the corresponding author.

Affiliations

  1. School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, People’s Republic of China

    Tong Xie & Bo-Feng Zhu

  2. Department of Forensic Medicine, Nanjing Medical University, Nanjing, 210029, Jiangsu, China

    Li Hu & Feng Chen

  3. Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, Shaanxi, People’s Republic of China

    Yu-Xin Guo & Bo-Feng Zhu

  4. Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, Shaanxi, People’s Republic of China

    Yu-Xin Guo & Bo-Feng Zhu

  5. College of Medicine & Forensics, Xi’an Jiaotong University Health Science Center, Xi’an, 710061, Shaanxi, People’s Republic of China

    Yu-Xin Guo & Bo-Feng Zhu

  6. State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, People’s Republic of China

    Yu-Chun Li

  7. Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China

    Yu-Chun Li

  8. Kunming Key Laboratory of Healthy Aging Molecular Mechanism Study, Kunming, 650223, China

    Yu-Chun Li

  9. KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, 650223, China

    Yu-Chun Li

Authors
  1. Tong Xie
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Li Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yu-Xin Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yu-Chun Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Feng Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Bo-Feng Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Feng Chen or Bo-Feng Zhu.

Ethics declarations

Conflict of interest

The authors have declared no conflicts of interest.

Ethical approval

Blood samples were obtained respectively according to standard procedures. The study was conducted in accordance with the human and ethical research principles of Southern Medical University and Xi’an Jiaotong University, China.

Informed consent

All volunteers gave their written informed consents before inclusion.

Research involving human and animals participants

This study involved the 141 healthy volunteers of Kazak ethnic group in Ili, Xinjiang Uygur Autonomous region.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Xie, T., Hu, L., Guo, YX. et al. Genetic polymorphism analysis of mitochondrial DNA from Chinese Xinjiang Kazak ethnic group by a novel mitochondrial DNA genotyping panel. Mol Biol Rep 46, 17–25 (2019). https://doi.org/10.1007/s11033-018-4375-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-018-4375-5

Keywords

  • mtDNA
  • SNP
  • Haplogroup
  • Kazak