常染色体19个STR位点在新疆蒙古族中的遗传多态性和法医学价值研究

Genetic distribution and forensic evaluation of multiplex autosomal short tandem repeats in the Chinese Xinjiang Mongolian group # # 常染色体19个STR位点在新疆蒙古族中的遗传多态性和法医学价值研究 1 2 first-author 1 2 3 4 1 2 3 1 2 3 1 2 1 2 3 5 corresp ‡Corresponding Author ‡Corresponding Author †E-mail:chenjiangang@cifs.gov.cnzhubofeng7372@126.com †E-mail:chenjiangang@cifs.gov.cnzhubofeng7372@126.com chenjiangang@cifs.gov.cn 1 2 4 corresp ‡Corresponding Author ‡Corresponding Author †E-mail:chenjiangang@cifs.gov.cnzhubofeng7372@126.com †E-mail:chenjiangang@cifs.gov.cnzhubofeng7372@126.com chenjiangang@cifs.gov.cn Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China College of Medicine and Forensics, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China College of Medicine and Forensics, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China To further enrich the genetic data of the Chinese xinjiang Mongolian group, the genetic distribution and forensic parameters of 19 autosomal short tandem repeats (STRs) were investigated. Altogether, 249 alleles were observed in these 19 STRs. The mean values of the polymorphism information content (PIC), match probability (MP), discrimination power (DP), and probability of exclusion (PE) for these 19 STRs were 0.7775, 0.0699, 0.9301, and 0.6085, respectively. Additionally, the cumulative DP and PE values obtained in the Mongolian group were 0.999 999 999 999 999 999 999 995 67 and 0.999 999 992 163, respectively. Furthermore, population genetic analysis of the Mongolian group and 20 published populations was conducted based on the population data of 15 overlapping STRs. Genetic distances indicated that the Mongolian group had closer genetic similarities with the Uyghur, Xibe, and other Chinese populations rather than the other continental populations. Multidimensional scaling analysis further revealed that the Mongolian group possessed similar genetic distributions as most Chinese populations. To sum it all up, these STRs could be used as an extremely efficient tool for forensic applications in the xinjiang Mongolian group. 目的 2 分析常染色体19个短串联重复序列(STR)位点在新疆蒙古族群体中的遗传多态性分布,为其法医学应用提供数据支持. 创新点 2 丰富了新疆蒙古族群体的常染色体STR遗传数据. 方法 2 从新疆地区采集1133个无血缘关系的蒙古族健康个体,应用一个包含常染色体19个STR位点的复合扩增体系对这些样本进行基因分型检测.同时,基于15个共有的STR位点,采用多维尺度分析、遗传距离( D A )和遗传分化系数( F ST )的方法探讨了新疆蒙古族群体和既往报道的20个群体间的群体遗传关系. 结论 2 研究的19个STR位点在新疆蒙古族群体中表现出高度的多态性,获得的累积非父排除概率和累计个体识别率分别为0.999 999 992 163和0.999 999 999 999 999 999 999 995 67,表明这19个STR位点可很好地应用于新疆蒙古族群体的个体识别和亲缘关系鉴识研究.群体遗传分析的结果显示:相比其他洲际群体,新疆蒙古族群体和维吾尔族、锡伯族以及其他中国群体具有更近的遗传距离. Xinjiang Mongolian group Short tandem repeats (STRs) Forensic applications 新疆蒙古族 短串联重复序列(STR) 法医学 To further enrich the genetic data of the Chinese Xinjiang Mongolian group, the genetic distribution and forensic parameters of 19 autosomal short tandem repeats (STRs) were investigated. Altogether, 249 alleles were observed in these 19 STRs. The mean values of the polymorphism information content (PIC), match probability (MP), discrimination power (DP), and probability of exclusion (PE) for these 19 STRs were 0.7775, 0.0699, 0.9301, and 0.6085, respectively. Additionally, the cumulative DP and PE values obtained in the Mongolian group were 0.999 999 999 999 999 999 999 995 67 and 0.999 999 992 163, respectively. Furthermore, population genetic analysis of the Mongolian group and 20 published populations was conducted based on the population data of 15 overlapping STRs. Genetic distances indicated that the Mongolian group had closer genetic similarities with the Uyghur, Xibe, and other Chinese populations rather than the other continental populations. Multidimensional scaling analysis further revealed that the Mongolian group possessed similar genetic distributions as most Chinese populations. To sum it all up, these STRs could be used as an extremely efficient tool for forensic applications in the Xinjiang Mongolian group. STRs, with repeat units of 2–6 bp, are abundant in the human genome. The high polymorphism of STRs makes them potential genetic markers for forensic applications (Ruitberg et al., 2001 2001 ). Since genetic differences existed in different populations (Rosenberg et al., 2003 2003 ; Xin et al., 2008 2008 ), it was imperative to obtain the population genetic data of the STR loci before these markers were used for forensic applications in certain populations. Mongolian, the ninth minority group in China, mainly lives in the Inner Mongolia and the Xinjiang Uygur Autonomous Regions, the Gansu and Qinghai Provinces, China. Most Mongolians believe in Lama Buddhism and still maintain a semi-nomadic lifestyle ( http://www.paulnoll.com/China/Minorities/min-Mongolian.html http://www.paulnoll.com/China/Minorities/min-Mongolian.html ). To date, genetic polymorphism analyses of 21 non-CODIS STR (Zha et al., 2014 2014 ), X-STR (Hou et al., 2007 2007 ), and Y-STR (Guo, 2015 2015 ) loci have been reported in the Mongolian group from the Inner Mongolia autonomous region; however, few genetic analyses have been conducted for autosomal STRs in the Xinjiang Mongolian group. Twenty genetic markers, i.e., D3S1358, D13S317, D7S820, D16S539, Penta E, TPOX, TH01, D2S1338, CSF1PO, Penta D, D19S433, vWA, D21S11, D18S51, D6S1043, D8S1179, D5S818, D12S391, FGA, and Amelogenin loci, were simultaneously amplified using the 5-dye fluorescence system based on the AGCU EX20 kit (AGCU ScienTech, Jiangsu, China), which could be used to establish the forensic DNA database in China. In the current study, we investigated allele distributions of these markers and evaluated their forensic values in the Xinjiang Mongolian group based on the aforementioned STR panel. Moreover, the genetic distances ( D A ), fixation indexes ( F ST ), and multidimensional scaling (MDS) analyses were conducted among the 21 populations using the genetic data of 15 available STR loci (excluding Penta D, D12S391, D6S1043, and Penta E). Compared populations and their corresponding references were given in Table S1 S1 . Materials and methods involved in this study were given in Data S1 S1 . Results of the Hardy-Weinberg equilibrium (HWE) tests for 19 STR loci are shown in Table S2 S2 . No deviations from the HWE were observed at these 19 STRs since their P -values for the HWE tests were greater than the significant level (0.05), implying that these loci conformed to the HWE in the studied Mongolian group. As shown in Fig. S1, the coefficients of linkage disequilibrium (Lewontin’s D ') of the pairwise loci were observed to be less than 0.2, which demonstrated the relatively weak correlations of these pairwise loci. Consequently, these STRs could be viewed as independent loci in the Xinjiang Mongolian group. Allele frequencies of the 19 STR loci are given in Table S2. Out of the 19 STR loci, 7 to 22 alleles could be observed. The lowest number of alleles was observed at the TH01 and TPOX loci, whereas the highest number of alleles was found at the Penta E locus. Furthermore, the minimum frequency value (0.0004) was observed in several alleles of different STR loci e.g., alleles 7 and 9 at the D8S1179 locus, whereas the maximum frequency value (0.4797) was observed at allele 8 of the TPOX locus. Forensic parameters of the 19 STRs in the Mongolian group showed that the obtained MP, DP, PE, PIC, observed heterozygosity ( H o ), and expected heterozygosity ( H e ) values ranged from 0.0115 to 0.1751, 0.8249 to 0.9885, 0.3820 to 0.8412, 0.5996 to 0.9191, 0.6690 to 0.9223, and 0.6562 to 0.9251, respectively. Among these STRs, the TPOX locus possessed the least DP, PIC, PE, H o , and H e values, while the Penta E locus had the highest DP, PIC, PE, H o , and H e values. A previous study suggested that a locus with a PIC value more than 0.5 was highly informative (Botstein et al., 1980 1980 ). Therefore, these 19 STRs could be treated as highly informative markers for the Mongolian group. Based on the results shown in Fig. S1 S1 , the multiplication law was used to calculate the cumulative DP and PE values in the Mongolian group, which were 0.999 999 999 999 999 999 999 995 67 and 0.999 999 992 163, respectively, indicating that these 19 STRs could be used for individual identification and paternity analysis in the Xinjiang Mongolian group. The D A heatmap of pairwise populations is shown in Fig. 1 1 , and their corresponding values are shown in Table S3 S3 . Different colors denote different D A value levels: cyan for low values, pink for intermediate values, and green for large values. Compared to 20 reference populations, the studied Mongolian group showed the lowest genetic distance to the Uyghur group (0.0074), followed by the Xibe (0.0097), Henan Han (0.0101), Tibetan (0.0105), Sichuan Han (0.0106), and other Chinese populations; whereas larger genetic distances were observed when compared to the African American (0.0539), Caucasian American (0.0329), Portuguese (0.0305), Mexican (0.0296), and Hispanic American (0.0231) populations. The pairwise F ST values of these 21 populations (Table S4 S4 ) also showed that the Mongolian group had lower F ST values when paired with the Uyghur, Xibe, and Uzbek groups. The present results revealed close genetic relationships between the Mongolian group and the Uyghur, Xibe, and other Chinese populations. Different colors indicate different levels of D A values: cyan for low values, pink for intermediate values, and green for large values MDS was plotted using SPSS software v18.0 based on the pairwise F ST values of the 21 populations (Fig. 2 2 ). In Dimension 1, most Chinese populations were distinguishable from other populations, and two Central Asian groups (Uyghur and Uzbek) were located between the Chinese and other continental populations. In Dimension 2, the Mexican and African American populations, located in the upper right and lower right parts of the graph, respectively, were distinguishable from the other populations. The studied Mongolian group was located closer to the Chinese populations and farther from the other continental populations, highlighting the similar genetic distributions between Mongolian and other Chinese populations. Based on the 15 shared STR data, we found that close relationships existed between the Mongolian group and the Uyghur, Xibe, and other Chinese populations. According to Chinese historical records, the Donghu, a nomadic group living in eastern Mongolian and northeast Chinese regions, might be proto-Mongols of the present Mongolian group. In the 13th century, Genghis Khan unified an army of Mongolian tribes, and he along with his Mongolian soldiers expanded westward and soon occupied almost all Eurasiatic regions. After the fall of the Mongolian empire, these dispersed Mongolian individuals were gradually assimilated by the surrounding people and became a part of the Uyghur, Xibe, and other tribes (https://en.wikipedia.org/wiki/Mongols). Findley ( 2005 2005 ) suggested that the modern Uyghurs probably possessed admixture genetic information of Mongolian and Caucasian people, resulting in close genetic relationships between the Mongolian and Uyghur groups. Another study also revealed that the Xibe had an intimate relationship with the Mongolian group. For instance, the phylogenetic tree constructed using 17 Y-STR loci haplotypes showed the Xibe forming a branch with the Mongolian group firstly, followed by other populations (Zheng et al., 2009 2009 ). More importantly, the Xibe people are descendants of the ancient Xianbei tribes, who are a branch of the ancient Donghu group (Wu, 2002 2002 ). Thus, the common ancestral origins of the Mongolian and Xibe groups likely contributed to their close ties. In brief, allele frequencies and forensic statistical parameters were obtained for 19 autosomal STRs in the Xinjiang Mongolian group, and these results laid the foundation for the STR database spanning different Chinese ethnic groups. The cumulative DP and PE values indicated that the multiplex STR system exhibited exceedingly high values for forensic applications in the Xinjiang Mongolian group. Moreover, the results of genetic distances and MDS analysis between the studied Mongolian group and other reference populations revealed that the Mongolian group had close genetic relationships with the Uyghur, Xibe, and other Chinese populations. References D Botstein , RL White , M Skolnick , 等 . Construction of a genetic linkage map in man using restriction fragment length polymorphisms . Am J Hum Genet , 1980 . 32 ( 3 ): 314 - 331 . 6247908 . Construction of a genetic linkage map in man using restriction fragment length polymorphisms CV Findley . The Turks in World History , 2005 . Oxford University Press, Oxford, UK , . The Turks in World History F Guo . Population genetics for 17 Y-STR loci in Mongolian ethnic minority from Liaoning Province, Northeast China . Forensic Sci Int Genet , 2015 . 17 153 - 154 . 26002546 DOI: 10.1016/j.fsigen.2015.05.008 http://doi.org/10.1016/j.fsigen.2015.05.008 . Population genetics for 17 Y-STR loci in Mongolian ethnic minority from Liaoning Province, Northeast China QF Hou , B Yu , SB Li . Genetic polymorphisms of nine X-STR loci in four population groups from Inner Mongolia, China . Genom Proteom Bioinform , 2007 . 5 ( 1 ): 59 - 65 . DOI: 10.1016/S1672-0229(07)60015-1 http://doi.org/10.1016/S1672-0229(07)60015-1 . Genetic polymorphisms of nine X-STR loci in four population groups from Inner Mongolia, China NA Rosenberg , LM Li , R Ward , 等 . Informativeness of genetic markers for inference of ancestry . Am J Hum Genet , 2003 . 73 ( 6 ): 1402 - 1422 . 14631557 DOI: 10.1086/380416 http://doi.org/10.1086/380416 . Informativeness of genetic markers for inference of ancestry CM Ruitberg , DJ Reeder , JM Butler . STRBase: a short tandem repeat DNA database for the human identity testing community . Nucleic Acids Res , 2001 . 29 ( 1 ): 320 - 322 . 11125125 DOI: 10.1093/nar/29.1.320 http://doi.org/10.1093/nar/29.1.320 . STRBase: a short tandem repeat DNA database for the human identity testing community KY Wu . Appearing the national origin and national name of he Sibo nationality from the successive dynasties ancient books . Heilongjiang Natl Ser , 2002 . ( 4 ): 64 - 66 . (in Chinese) DOI: 10.3969/j.issn.1004-4922.2002.04.015 http://doi.org/10.3969/j.issn.1004-4922.2002.04.015 . Appearing the national origin and national name of he Sibo nationality from the successive dynasties ancient books N Xin , T Chen , B Yu , 等 . 12 Y-STRs haplotypes in Chinese Naxi ethnic minority group . Forensic Sci Int , 2008 . 174 ( 2-3 ): 244 - 248 . 17532159 DOI: 10.1016/j.forsciint.2007.03.021 http://doi.org/10.1016/j.forsciint.2007.03.021 . 12 Y-STRs haplotypes in Chinese Naxi ethnic minority group L Zha , Y Liu , YD Guo , 等 . Genetic polymorphism of 21 non-CODIS STR loci in the Chinese Mongolian ethnic minority . Forensic Sci Int Genet , 2014 . 9 e32 - e33 . 24041912 DOI: 10.1016/j.fsigen.2013.08.010 http://doi.org/10.1016/j.fsigen.2013.08.010 . Genetic polymorphism of 21 non-CODIS STR loci in the Chinese Mongolian ethnic minority LH Zheng , HM Sun , JW Wang , 等 . Y chromosomal STR polymorphism in northern Chinese populations . Biol Res , 2009 . 42 ( 4 ): 497 - 504 . 20140305 DOI: 10.4067/S0716-97602009000400011 http://doi.org/10.4067/S0716-97602009000400011 . Y chromosomal STR polymorphism in northern Chinese populations Compliance with ethics guidelines Yuan-yuan WEI, Xiao-ye JIN, Qiong LAN, Wei CUI, Chong CHEN, Ting-ting KONG, Yu-xin GUO, Jian-gang CHEN, and Bo-feng ZHU declare that they have no conflicts of interest. All procedures followed were in accordance with the ethical standards of the responsible committee on human experimentation (institutional and national) and with the Helsinki Declaration of 1975, as revised in 2008 (5). Informed consent was obtained from all participants for being included in the study. 10.1631/jzus.B1800279 Project supported by the National Natural Science Foundation of China (No. 81460286) and the Guangdong Province Universities and Colleges Pearl River Scholar Funded Scheme (GDUPS) (2017), China 2018-05-11 2018-12-23 2022-01-05 Copyright © Zhejiang University and Springer-Verlag GmbH Germany, part of Springer Nature 2019 2019 Journal of Zhejiang University-SCIENCE B (Biomedicine and Biotechnology) 03 20