• Users Online: 634
  • Home
  • Print this page
  • Email this page
Home About us Editorial board Ahead of print Current issue Search Archives Submit article Instructions Subscribe Contacts Login 


 
 Table of Contents  
ORIGINAL ARTICLE
Year : 2019  |  Volume : 5  |  Issue : 2  |  Page : 65-79

Genetic distributions of 22 short tandem repeat loci in 760 unrelated tibet, Uygur, and mongolia individuals from China


1 CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
2 Beijing Fengtai District People's Court, Beijing, China
3 Public Security Bureau of Jiangsu, Huai'an, China
4 Public Security Department of Inner Mongolia, Huhehaote, China
5 Microread Genetics Incorporation, Beijing, China
6 Key Laboratory of Evidence Science, China University of Political Science and Law, Ministry of Education, Beijing, China

Date of Web Publication26-Jun-2019

Correspondence Address:
Di Lu
Key Laboratory of Evidence Science, China University of Political Science and Law, Ministry of Education, Beijing 100188
China
Login to access the Email id

Source of Support: None, Conflict of Interest: None


DOI: 10.4103/jfsm.jfsm_17_19

Rights and Permissions
  Abstract 


In recent years, paternity testing in ethnic minority areas in China increases rapidly. However, the number of existing genetic markers does not meet the needs. The objective is to study the information of 22 genetic markers in Mongolian, Tibetan, and Uygur Nationality. The genetic polymorphism of 22 short tandem repeat (STR) loci (D10S1435, D11S2368, D12S391, D13S325, D14S608, D15S659, D16S539, D17S1290, D18S535, D19S253, D1S1656, D20S470, D21S1270, D22GATA198B05, D2S1338, D3S3045, D4S2366, D5S2500, D6S477, D7S3048, D8S1132, and D9S925) was estimated in 259 Uyghur, 251 Tibetan, and 250 Inner Mongolian individuals from China who were all unrelated. Allele frequencies and forensic parameters were evaluated. The Hardy–Weinberg equilibrium (HWE) of each locus and the linkage disequilibrium (LD) for all pairwise STR loci were tested. Additionally, the Nei's genetic distance was used to estimate the genetic heterogeneity between Tibetan, Uyghur, Mongolian, Chinese Northern Han and Chinese Li population. The 22 loci showed high genetic polymorphism in the three ethnic groups. An exact test for the genotype distribution of the markers showed no significant deviation from HWE. These 22 STR loci could be treated as independent loci at the population level in these three ethnic groups. Relatively short genetic distances were found between the Mongolian and Han and Uygur populations. The 22 loci had no LD in the three ethnic groups and showed high heterozygosity, providing genetic information and forensic statistics for the Uyghur, Tibetan, and Inner Mongolian groups. These 22 STR loci will be useful for identification and kinship analysis in these three populations in China.

Keywords: Forensic genetics, genetic polymorphism, inner Mongolian, short tandem repeat, Tibetan, Uyghur


How to cite this article:
Yang YR, Yang J, Li F, Wang YZ, Yu ZL, Yan JW, Lu D. Genetic distributions of 22 short tandem repeat loci in 760 unrelated tibet, Uygur, and mongolia individuals from China. J Forensic Sci Med 2019;5:65-79

How to cite this URL:
Yang YR, Yang J, Li F, Wang YZ, Yu ZL, Yan JW, Lu D. Genetic distributions of 22 short tandem repeat loci in 760 unrelated tibet, Uygur, and mongolia individuals from China. J Forensic Sci Med [serial online] 2019 [cited 2019 Jul 16];5:65-79. Available from: http://www.jfsmonline.com/text.asp?2019/5/2/65/261526

Ya-Ran Yang, Jian Yang. These authors contributed equally to this work





  Introduction Top


There are 56 ethnic groups in China.[1] The Han population is the largest and most widely distributed ethnic group in China. The Mongolian ethnic group resides mostly in the northern parts of China and has a population size of 5,981,840 (0.45% of the Chinese population). The Uyghur and Tibetan ethnic groups are found in the western parts of China, with population sizes of 10,069,346 (0.76%) and 6,282,187 (0.47%), respectively [Figure 1].[2] In this study, population genetic data and forensic parameters of 22 autosomal short tandem repeats (STRs) were obtained from 760 unrelated individuals from among these three ethnic groups.
Figure 1: The geographical location and population proportion of the ethnic minorities

Click here to view



  Materials and Methods Top


Samples and DNA extraction

Bloodstain samples were collected from healthy and unrelated Inner Mongolian (n = 250; 165 male, 85 female), Tibetan (n = 251; 120 male, 131 female), and Uyghur (n = 259; 146 male, 113 female) individuals after obtaining their informed consent. DNA was extracted from the samples using the Chelex-100 protocol.[3] The quantity of recovered DNA was determined using the Qubit Quantitation System (Invitrogen, Hercules, CA, USA) according to the manufacturer's specifications.

DNA amplification and electrophoresis

The DNA samples were amplified using a Microreader™ 23 ID System (Microread Genetics Incorporation, China), which included amelogenin and 22 autosomal STR loci (D6S477, D18S535, D19S253, D15S659, D11S2368, D20S470, D1S1656, D22-GATA198B05, D8S1132, D4S2366, D21S1270, D13S325, D9S925, D3S3045, D14S608, D10S1435, D12S391, D7S3048, D17S1290, D5S2500, D2S1338, and D16S539).[4]

The polymerase chain reactions (PCRs) were conducted using a GeneAmp PCR 9700 Thermal Cycler System (Applied Biosystems, Foster City, CA, USA). The amplified products were separated by capillary electrophoresis on an ABI PRISM 3130XL Genetic Analyzer (Applied Biosystems, Foster City, CA, USA). Data were analyzed using GeneMapper ID 3.2 software (Applied Biosystems).

Statistical analysis

Allele frequencies and forensic parameters were evaluated using ARLEQUIN version 3.1 (University of Berne, Berne, Switzerland).[5] The Hardy-Weinberg equilibrium (HWE) of each locus and the linkage disequilibrium (LD) for all pairwise STR loci were tested using the Genepop version 4.0.10 software package (Bataillon, France).[6] To estimate Nei's genetic distances between the Tibetan, Uyghur, Mongolian, Chinese Northern Han,[7] and Chinese Li populations,[8] DISPAN software and MEGA version 6.0 were used to construct a dendrogram.

Quality control

All laboratory procedures have been accredited according to ISO17025.[9] Laboratory internalcontrol standards were employed according to the recommendations published by the Paternity Testing Commission of the International Society for Forensic Genetics.[10]


  Results and Discussion Top


Allele frequencies and forensic statistics of each locus from the Chinese Inner Mongolian population are shown in [Table 1]. All the 22 STR loci were found to be polymorphic. Among them, D7S3048 showed the highest observed heterozygosity (Ho), discrimination power (DP), and probability of paternity exclusion in trios (PE [T]), with values of 0.864, 0.968, and 0.723, respectively. D10S1435 showed the lowest Ho, DP, and PE (T) with values of 0.752, 0.894, and 0.513, respectively. The cumulative match probability was approximately 1.574 × 10−27, and the cumulative PE (T) was 0.9999991. Deviations from HWE were detected for D11S2368 (P = 0.007). However, after Bonferroni correction (i.e., P = 0.05/22 = 0.002),[11] none of the loci showed significant deviations from HWE. Thirty-one pairs of loci showed significant LD (P < 0.05) among 231 pairwise comparisons [Table 2]. After Bonferroni correction (P = 0.05/231 = 0.0002), only the D11S2368 versus D15S659 and D11S2368 versus D20S470 pairs still showed significant LD (P < 0.001), possibly due to a sampling artifact because these three loci are not on the same chromosome. Therefore, these 22 STR loci could be treated as independent loci at the population level in the Chinese Inner Mongolian group.
Table 1: The allele frequencies and forensic parameters of 22 STR in Chinese Mongolia population (n=250)

Click here to view
Table 2: The significant linkage disequilibrium P values of 22 short tandem repeats in Chinese Mongolia population

Click here to view


Allele frequencies and forensic statistics of each locus from the Chinese Tibetan population are shown in [Table 3]. All the 22 loci were found to be polymorphic. Among them, D7S3048 showed the highest Ho, DP, and PE (T), with values of 0.900, 0.957, and 0.795, respectively. D3S3045 showed the lowest Ho (0.720), D4S2366 showed the lowest DP (0.856), and D10S1435 and D9S925 showed the lowest PE (T) (0.5201) values. The cumulative match probability was approximately 5.463 × 10−26, and the cumulative PE (T) was 0.9999997. Deviations from HWE were detected for D15S659 (P = 0.007) and D4S2366 (P = 0.007). After Bonferroni correction, none of the loci showed significant deviations from HWE. Fifty pairs of loci showed significant LD (P < 0.05) among 231 pairwise comparisons [Table 4]. After Bonferroni correction, the D11S2368 versus D15S659, D11S2368 versus D19S253, D11S2368 versus D2S1338, D14S608 versus D20S470, D15S659 versus D17S1290, and D2S1338 versus D7S3048 pairs still showed significant LD (P < 0.001). This result may be due to a sampling artifact because these six loci are not on the same chromosome. Therefore, these 22 STR loci could be treated as independent loci at the population level in the Chinese Tibetan group.
Table 3: The allele frequencies and forensic parameters of 22 short tandem repeats in Chinese Tibet population (n=251)

Click here to view
Table 4: The significant linkage disequilibrium P values of 22 short tandem repeats in Chinese Tibet population

Click here to view


Allele frequencies and forensic statistics of each locus from the Chinese Uyghur population are shown in [Table 5]. All the 22 STR loci were found to be polymorphic. Among them, D20S470 showed the highest Ho and PE (T), with values of 0.892 and 0.779, respectively. D10S1435 showed the lowest Ho, DP, and PE (T) with values of 0.749, 0.894, and 0.508, respectively, similar to its values for the Inner Mongolian group. The cumulative match probability was approximately 1.122 × 10−27, and the cumulative PE (T) was 0.9999997. Deviations from HWE were detected for D8S1132 (P = 0.041). After Bonferroni correction, none of the loci showed significant deviations from HWE. Seven pairs of loci showed significant LD (P < 0.05) among 231 pairwise comparisons [Table 6]. After Bonferroni correction, none of the locus pairs showed statistically significant LD. Therefore, these 22 STR loci could be treated as independent loci at the population level in the Chinese Uyghur group.
Table 5: The allele frequencies and forensic parameters of 22 short tandem repeats in Chinese Uyghur population (n=259)


Click here to view
Table 6: The significant linkage disequilibrium P values of 22 short tandem repeats in Chinese Uygur population

Click here to view


Genetic distance can be measured using a variety of statistical parameters to determine the genetic divergence between populations.[12],[13],[14] Pairwise Nei's genetic distance values between the Inner Mongolian and four other populations are shown in [Table 7]. Relatively short genetic distances were found between the Mongolian and Han (0.0056) and Uygur (0.0175) populations, whereas longer distances were found between the Li and Tibetan (0.0365), Uyghur (0.0338), and Mongolian (0.0245) populations. The neighbor-joining tree [Figure 2] showed that the Tibetan group clustered with the Uyghur group first and then clustered with the Inner Mongolian and Han groups. The Li group showed the longest distances between the other four groups, which is consistent with their geographical location in southern China [Figure 1]. These results are consistent with those of previous studies using other genetic markers.[8]
Table 7: Nei's DA genetic distances from Mongolian and other 4 groups

Click here to view
Figure 2: The neighbor-joining tree built from Chinese Mongolian and other 4 groups

Click here to view



  Conclusions Top


The 22 STR loci showed high genetic polymorphism in the Tibetan, Uyghur, and Inner Mongolian populations in China. This study provides basic data for Chinese forensic DNA databases and population genetic databases[15] and has significance for forensic individual identification, paternity testing, and population genetic studies.

Acknowledgments

This study was supported by the Ministry of Education, Humanities and Social Science research projects (grant number 13YJA8200031).

Financial support and sponsorship

Nil.

Conflicts of interest

There are no conflicts of interest.



 
  References Top

1.
State Ethnic Affairs Commission. China's Ethnic Yearbook 2017. Editorial Department of China's Ethnic Yearbook. 2017:12.  Back to cited text no. 1
    
2.
National Bureau of Statistics of China. Communique of the National Bureau of Statistics of the People's Republic of China on Major Figures of the 2010 Population Census [1] (No.1). Beijing Review 2011;54.  Back to cited text no. 2
    
3.
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.  Back to cited text no. 3
    
4.
Li J, Luo H, Song F, Zhang L, Deng C, Yu Z, et al. Validation of the microreader™ 23sp ID system: A new STR 23-plex system for forensic application. Forensic Sci Int Genet 2017;27:67-73.  Back to cited text no. 4
    
5.
Excoffier L, Laval G, Schneider S. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinformatics Online 2007;1:47-50.  Back to cited text no. 5
    
6.
Hartl DL, Clark AG. Principles of population genetics. J Anim Breed Genet 2015;117:143-4.  Back to cited text no. 6
    
7.
Xie B, Chen L, Yang Y, Lv Y, Chen J, Shi Y, et al. Genetic distribution of 39 STR loci in 1027 unrelated Han individuals from Northern China. Forensic Sci Int Genet 2015;19:205-6.  Back to cited text no. 7
    
8.
Chen J, Xie B, Yang Y, Yang M, Liu C, Lv Y, et al. Genetic variability and forensic efficiency of 39 microsatellite loci in the li ethnic group from Hainan Island in the South China Sea. Ann Hum Biol 2017;44:467-74.  Back to cited text no. 8
    
9.
The International Organization for Standardization and the International Electrotechnical Commission. ISO/IEC 17025:2017 General requirements for the competence of testing and calibration laboratories. Available from: https://www.iso.org/obp/ui/#iso:std:iso-iec:17025:ed-3:v1:en. [Last accessed on 2019 Feb 01].  Back to cited text no. 9
    
10.
Morling N, Allen RW, Carracedo A, Geada H, Guidet F, Hallenberg C, et al. Paternity Testing Commission of the International Society of Forensic Genetics: Recommendations on genetic investigations in paternity cases. Forensic Sci Int 2002;129:148-57.  Back to cited text no. 10
    
11.
Armstrong RA. When to use the bonferroni correction. Ophthalmic Physiol Opt 2014;34:502-8.  Back to cited text no. 11
    
12.
Nei M. Genetic Distance between Populations. Am Nat 1972;106:283-92.  Back to cited text no. 12
    
13.
Rogers J. Measures of genetic similarity and genetic distance. Studies in Genetics VII. University of Texas Publication; 1972;7213:145-153.  Back to cited text no. 13
    
14.
Nei M. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 1978;89:583-90.  Back to cited text no. 14
    
15.
Ge J, Yan J, Budowle B, Ranajit C, Arthur E. Issues on China forensic DNA database. Chin J Forensic Med 2011;26:252-5.  Back to cited text no. 15
    


    Figures

  [Figure 1], [Figure 2]
 
 
    Tables

  [Table 1], [Table 2], [Table 3], [Table 4], [Table 5], [Table 6], [Table 7]



 

Top
 
 
  Search
 
Similar in PUBMED
   Search Pubmed for
   Search in Google Scholar for
 Related articles
Access Statistics
Email Alert *
Add to My List *
* Registration required (free)

 
  In this article
Abstract
Introduction
Materials and Me...
Results and Disc...
Conclusions
References
Article Figures
Article Tables

 Article Access Statistics
    Viewed163    
    Printed6    
    Emailed0    
    PDF Downloaded18    
    Comments [Add]    

Recommend this journal


[TAG2]
[TAG3]
[TAG4]