Journal of Forensic Science and Medicine

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


Ya-Ran Yang1, Jian Yang2, Feng Li3, Yong-Zai Wang4, Zai-Liang Yu5, Jiang-Wei Yan1, Di Lu6,  
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

Correspondence Address:
Di Lu
Key Laboratory of Evidence Science, China University of Political Science and Law, Ministry of Education, Beijing 100188
China

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.



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 Aug 22 ];5:65-79
Available from: http://www.jfsmonline.com/text.asp?2019/5/2/65/261526


Full Text



 Introduction



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}

 Materials and Methods



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



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}{Table 2}

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}{Table 4}

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}{Table 6}

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}{Figure 2}

 Conclusions



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

1State Ethnic Affairs Commission. China's Ethnic Yearbook 2017. Editorial Department of China's Ethnic Yearbook. 2017:12.
2National 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.
3Walsh 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.
4Li 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.
5Excoffier 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.
6Hartl DL, Clark AG. Principles of population genetics. J Anim Breed Genet 2015;117:143-4.
7Xie 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.
8Chen 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.
9The 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].
10Morling 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.
11Armstrong RA. When to use the bonferroni correction. Ophthalmic Physiol Opt 2014;34:502-8.
12Nei M. Genetic Distance between Populations. Am Nat 1972;106:283-92.
13Rogers J. Measures of genetic similarity and genetic distance. Studies in Genetics VII. University of Texas Publication; 1972;7213:145-153.
14Nei M. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 1978;89:583-90.
15Ge J, Yan J, Budowle B, Ranajit C, Arthur E. Issues on China forensic DNA database. Chin J Forensic Med 2011;26:252-5.