Genetic distribution analyses and population background explorations of Gansu Yugur and Guizhou Miao groups via InDel markers

Article metrics

  • 97 Accesses

Abstract

Insertion and deletion markers (InDels) have gained considerable attentions in population genetics and forensic research. In this study, we investigated genetic distributions of 30 InDels in Gansu Yugur and Guizhou Miao groups and evaluated their forensic application values. Genetic relationship analyses between Gansu Yugur, Guizhou Miao groups and other published populations were conducted based on these 30 InDels. Power of discrimination and power of exclusion in trio and duo cases of 30 InDels ranged from 0.3528 to 0.6247, 0.0937 to 0.1873, and 0.0219 to 0.1247 in Gansu Yugur group; and they ranged from 0.2579 to 0.6247, 0.0671 to 0.1874, and 0.0105 to 0.1247 in Guizhou Miao group. Obtained cumulative power of discrimination values indicated these InDels could be used for forensic individual identifications in both ethnic groups. Principal component analysis and phylogenetic reconstruction revealed that Gansu Yugur and Guizhou Miao groups had close affinities with their neighboring populations. Genetic structure analyses among these populations also indicated that studied Gansu Yugur and Guizhou Miao groups showed similar genetic structure with their neighboring populations. Further analyses of Y-STR, mtDNA, and ancestry informative markers should be conducted to better understand genetic backgrounds of Gansu Yugur and Guizhou Miao groups in the future.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

References

  1. 1.

    Edwards A, Civitello A, Hammond HA, Caskey CT. DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am J Hum Genet. 1991;49:746–56.

  2. 2.

    LaRue BL, Ge J, King JL, Budowle B. A validation study of the Qiagen Investigator DIPplex(R) kit; an INDEL-based assay for human identification. Int J Leg Med. 2012;126:533–40.

  3. 3.

    Brinkmann B, Klintschar M, Neuhuber F, Huhne J, Rolf B. Mutation rate in human microsatellites: influence of the structure and length of the tandem repeat. Am J Hum Genet. 1998;62:1408–15.

  4. 4.

    Nachman MW, Crowell SL. Estimate of the mutation rate per nucleotide in humans. Genetics. 2000;156:297–304.

  5. 5.

    Romanini C, Catelli ML, Borosky A, Pereira R, Romero M, Salado Puerto M, et al. Typing short amplicon binary polymorphisms: supplementary SNP and Indel genetic information in the analysis of highly degraded skeletal remains. Forensic Sci Int Genet. 2012;6:469–76.

  6. 6.

    Zaumsegel D, Rothschild MA, Schneider PM. A 21 marker insertion deletion polymorphism panel to study biogeographic ancestry. Forensic Sci Int Genet. 2013;7:305–12.

  7. 7.

    Santos NPC, Ribeiro-Rodrigues EM, Ribeiro-dos-Santos AKC, Pereira R, Gusmao L, Amorim A, et al. Assessing individual interethnic admixture and population substructure using a 48-insertion-deletion (INSEL) ancestry-informative marker (AIM) panel. Hum Mutat. 2010;31:184–90.

  8. 8.

    Lan Q, Shen C, Jin X, Guo Y, Xie T, Chen C, et al. Distinguishing three distinct biogeographic regions with an in-house developed 39-AIM-InDel panel and further admixture proportion estimation for Uyghurs. Electrophoresis. 2019. https://doi.org/10.1002/elps.201800448.

  9. 9.

    Li CT, Zhao SM, Zhang SH, Li L, Liu Y, Chen JZ, et al. Genetic polymorphism of 29 highly informative InDel markers for forensic use in the Chinese Han population. Forensic Sci Int-Gen. 2011;5:E27–E30.

  10. 10.

    Larue BL, Lagace R, Chang CW, Holt A, Hennessy L, Ge J, et al. Characterization of 114 insertion/deletion (INDEL) polymorphisms, and selection for a global INDEL panel for human identification. Leg Med-Tokyo. 2014;16:26–32.

  11. 11.

    Zhu B, Lan Q, Guo Y, Xie T, Fang Y, Jin X, et al. Population genetic diversity and clustering analysis for chinese dongxiang group with 30 autosomal indel loci simultaneously analyzed. Front Genet. 2018;9:279.

  12. 12.

    Wang L, Lv ML, Zaumsegel D, Zhang LS, Liu FJ, Xiang JH, et al. A comparative study of insertion/deletion polymorphisms applied among Southwest, South and Northwest Chinese populations using Investigator (R) DIPplex. Forensic Sci Int-Gen. 2016;21:10–14.

  13. 13.

    Guo Y, Shen C, Meng H, Dong Q, Kong T, Yang C, et al. Population differentiations and phylogenetic analysis of tibet and Qinghai Tibetan Groups based on 30 indel loci. DNA Cell Biol. 2016;35:787–94.

  14. 14.

    Kong T, Chen Y, Guo Y, Wei Y, Jin X, Xie T, et al. Autosomal InDel polymorphisms for population genetic structure and differentiation analysis of Chinese Kazak ethnic group. Oncotarget. 2017;8:56651–58.

  15. 15.

    Hong L, Wang XG, Liu SJ, Zhang YM, Xue-Ling OU, Chen Y, et al. Genetic polymorphisms of 30 indel loci in guangdong han population. J Sun Yat-Sen Univ (Med Sci). 2013;34:299–304.

  16. 16.

    Guo Y, Chen C, Jin X, Cui W, Wei Y, Wang H, et al. Autosomal DIPs for population genetic structure and differentiation analyses of Chinese Xinjiang Kyrgyz ethnic group. Sci Rep. 2018;8:11054.

  17. 17.

    Zhang YD, Shen CM, Jin R, Li YN, Wang B, Ma LX, et al. Forensic evaluation and population genetic study of 30 insertion/deletion polymorphisms in a Chinese Yi group. Electrophoresis. 2015;36:1196–201.

  18. 18.

    Wang Z, Zhang S, Zhao S, Hu Z, Sun K, Li C. Population genetics of 30 insertion-deletion polymorphisms in two Chinese populations using Qiagen Investigator(R) DIPplex kit. Forensic Sci Int Genet. 2014;11:e12–4.

  19. 19.

    Shi M, Liu Y, Bai R, Jiang L, Lv X, Ma S. Population data of 30 insertion-deletion markers in four Chinese populations. Int J Leg Med. 2015;129:53–6.

  20. 20.

    Shen C, Zhu B, Yao T, Li Z, Zhang Y, Yan J, et al. A 30-InDel assay for genetic variation and population structure analysis of Chinese Tujia Group. Sci Rep. 2016;6:36842.

  21. 21.

    Mei T, Shen CM, Liu YS, Meng HT, Zhang YD, Guo YX, et al. Population genetic structure analysis and forensic evaluation of Xinjiang Uigur ethnic group on genomic deletion and insertion polymorphisms. Springerplus.2016;5:1087.

  22. 22.

    Ma R, Shen C, Wei Y, Jin X, Guo Y, Mu Y, et al. Genetic differentiation and forensic efficiency evaluation for Chinese Salar ethnic minority based on a 5-dye multiplex insertion and deletion panel. Gene. 2018;660:41–50.

  23. 23.

    Meng HT, Zhang YD, Shen CM, Yuan GL, Yang CH, Jin R, et al. Genetic polymorphism analyses of 30 InDels in Chinese Xibe ethnic group and its population genetic differentiations with other groups. Sci Rep. 2015;5:8260.

  24. 24.

    Wei YL, Qin CJ, Dong H, Jia J, Li CX. A validation study of a multiplex INDEL assay for forensic use in four Chinese populations. Forensic Sci Int Genet. 2014;9:e22–5.

  25. 25.

    Chen YJ, Chen F, Xin N, Zhang HB, Zheng HB, Yu B, et al. [Genetic polymorphisms of X-STR loci in Chinese Yugur ethnic group and its application]. Yi Chuan. 2008;30:1143–52.

  26. 26.

    Yang F, An Y. Elements of Tibetan, Mongolian, the Tus and Formation of the Yugurs. Natl Res Qinghai. 2016;2:107–10.

  27. 27.

    Chen T, Jin TB, Xin N, Lai JH, Li SB. [Genetic polymorphisms and application of 9 STR loci of 5 ethnic groups in Gansu and Qinghai]. Zhong Nan Da Xue Xue Bao Yi Xue Ban. 2006;31:877–82.

  28. 28.

    Yao Y, Shi L, Tao Y, Kulski JK, Lin K, Huang X, et al. Distinct HLA allele and haplotype distributions in four ethnic groups of China. Tissue Antigens. 2012;80:452–61.

  29. 29.

    Martin P, Garcia O, Heinrichs B, Yurrebaso I, Aguirre A, Alonso A. Population genetic data of 30 autosomal indels in Central Spain and the Basque Country populations. Forensic Sci Int-Gen. 2013;7:E27–E30.

  30. 30.

    Friis SL, Borsting C, Rockenbauer E, Poulsen L, Fredslund SF, Tomas C, et al. Typing of 30 insertion/deletions in Danes using the first commercial indel kit–Mentype(R) DIPplex. Forensic Sci Int Genet. 2012;6:e72–4.

  31. 31.

    Kis Z, Zalan A, Volgyi A, Kozma Z, Domjan L, Pamjav H. Genome deletion and insertion polymorphisms (DIPs) in the Hungarian population. Forensic Sci Int Genet. 2012;6:e125–6.

  32. 32.

    Walsh PS, Metzger DA, Higuchi R. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. BioTechniques. 1991;10:506–13.

  33. 33.

    Hill CR, Duewer DL, Kline MC, Sprecher CJ, McLaren RS, Rabbach DR, et al. Concordance and population studies along with stutter and peak height ratio analysis for the PowerPlex (R) ESX 17 and ESI 17 Systems. Forensic Sci Int Genet. 2011;5:269–75.

  34. 34.

    Excoffier L, Lischer HE. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour. 2010;10:564–7.

  35. 35.

    Shi YY, He L. SHEsis, a powerful software platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphism loci. Cell Res. 2005;15:97–8.

  36. 36.

    Team RDC. R: A language and environment for statistical computing. R Foundation for Statistical Computing. Computing. 2009;14:12–21.

  37. 37.

    Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30:2725–9.

  38. 38.

    Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;155:945–59.

  39. 39.

    Rosenberg NA. DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes. 2004;4:137–8.

  40. 40.

    Yoo J, Lee Y, Kim Y, Rha SY, Kim Y. SNPAnalyzer 2.0: a web-based integrated workbench for linkage disequilibrium analysis and association analysis. BMC Bioinform. 2008;9:290.

  41. 41.

    Botstein D, White RL, Skolnick M, Davis RW. Construction of a genetic-linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet. 1980;32:314–31.

  42. 42.

    Liu C, Liu C, Wang H. STR data for the 15 loci from three minority populations in Guangxi municipality in South China. Forensic Sci Int. 2006;162:49–52.

  43. 43.

    Zhang L, Zhao Y, Guo F, Liu Y, Wang B. Population data for 15 autosomal STR loci in the Miao ethnic minority from Guizhou Province, Southwest China. Forensic Sci Int Genet. 2015;16:e3–e4.

  44. 44.

    An Y. A Study in The Formation History of Yugurs. Lanzhou University; 2016.

  45. 45.

    Deng Q, Xu L, Gong J, Zhou L, Li S, Deng X, et al. Genetic relationships among four minorities in Guangxi revealed by analysis of 15 STRs. J Genet Genom. 2007;34:1072–9.

  46. 46.

    Zhang X, Hu L, Du L, Nie A, Rao M, Pang JB, et al. Genetic analysis of 20 autosomal STR loci in the Miao ethnic group from Yunnan Province, Southwest China. Forensic Sci Int Genet. 2017;28:e28–e29.

Download references

Acknowledgements

This study was supported by Guangdong Province Universities and Colleges Pearl River Scholar Funded Scheme (GDUPS, 2017).

Author information

Correspondence to Bo-Feng Zhu.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Figure 1

Supplementary Figure 2

Supplementary Figure 3

Supplementary Figure 4

Supplementary Table 1

Suppmentary Table 2

Suppmentary Table 3

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark