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Genetic investigation of Chinese she ethnic based on autosomal STRs and X-STRs

  • Jingyi Zhang
    Affiliations
    Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, PR China

    Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China
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  • Zihao Yang
    Affiliations
    Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China

    Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, 325035, PR China
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  • Ruiyang Tao
    Affiliations
    Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China

    Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, PR China
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  • Suhua Zhang
    Correspondence
    Corresponding author at: Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China.
    Affiliations
    Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China
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  • Chengtao Li
    Correspondence
    Corresponding author at: Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China.
    Affiliations
    Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, PR China

    Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China
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Published:October 04, 2019DOI:https://doi.org/10.1016/j.fsigss.2019.09.017

      Abstract

      The She ethnic is a large minority in China with approximately 700,000 individuals. For more than one thousand years, they mainly resided in Zhejiang and Fujian provinces. To obtain a better understanding of the genetic background of She, we investigate 21 autosomal STRs (A-STRs) and 16 X-STRs in 296 unrelated healthy individuals from Zhejiang She population. Allele frequencies and forensic parameters prove these markers are useful for forensic application. We also investigate the genetic background with the two types of markers. Nei genetic distances between She and Eastern Han population are always the lowest, regardless of the markers used for analysis. Although the tested STRs are located on different chromosomes with different inheritance laws, A-STRs and X-STRs provided in general congruent phylogenetic signal and similar cluster among compared groups. These results demonstrated that geographic isolation and interactions play significant roles in differentiation of genetic constitution of ethnic groups.

      Keywords

      1. Introduction

      Autosomal STR (A-STR) markers have been used to study genetic polymorphism for a long time. Over the past 30 years, a number of studies have been performed in different populations worldwide with A-STRs [
      • Xie B.
      • Chen L.
      • Yang Y.
      • et al.
      Genetic distribution of 39 STR loci in 1027 unrelated Han individuals from Northern China.
      ]. X-STRs are emerging popular genetic markers for genetic investigation in forensic community. In this study, we try to explore the genetic background of She ethnic minority with the two types of markers. She, an ancient population in China, mostly clustered in small, relatively isolated villages in mountainous regions. This isolation has helped preserve the integrity of their language and traditions.

      2. Materials and methods

      Blood samples were collected from 296 unrelated individuals (129 males and 167 females) from the Zhejiang She population with written informed consents. QIAamp DNA Blood Mini Kit (QIAGEN, Hilden, Germany) was used to extract Genomic DNA. All samples were amplified with Goldeneye™ DNA ID 22NC Kit and Goldeneye™ DNA ID 17X Kit in the GeneAmp PCR System 9700 (Thermo Fisher Scientific, USA). Goldeneye™ DNA ID 22NC Kit contains 17 non−CODIS loci (D19S253, D6S477, D22GATA198B05, D15S659, D8S1132, D3S3045, D14S608, D17S1290, D3S1744, D2S411, D18S535, D13S325, D7S1517, D10S1435, D11S2368, D4S2366, D7S3048) and 3 CODIS loci (D3S1358, D1S1656 and D10S1248), while Goldeneye™ DNA ID 17X Kit contains 16 X-STRs (DXS6795, DXS9902, DXS8378, HPRTB, GATA165B12, DXS7132, DXS7424, DXS6807, DXS6803, GATA172D05, DXS6800, DXS10134, GATA31E08, DXS6810, DXS6789, DXS10159). The PCR products were separated by capillary electrophoresis using POP-4 polymers on a Genetic Analyzer ABI 3130xl (Thermo Fisher Scientific, USA) and the data were analyzed with GeneMapper ID Analysis Software. The A-STRs dataset has successfully passed STRidER quality control (STRidER dataset reference STR000177) [
      • Bodner M.
      • Bastisch I.
      • Butler J.M.
      • et al.
      Recommendations of the DNA Commission of the International Society for Forensic Genetics (ISFG) on quality control of autosomal Short Tandem Repeat allele frequency databasing (STRidER).
      ].
      Arlequin v3.5 was utilized to calculate Hardy-Weinberg equilibrium (HWE) and to perform linkage disequilibrium (LD) test. The allele frequencies and forensic parameters of 21 A-STRs were calculated using PowerStat V1.2 (Promega, Madison, WI). Forensic parameters of 16 X-STRs, including polymorphism information content (PIC), heterozygosity (HET), power of discrimination in males (PDM) and females (PDF), and mean paternity exclusion chance in duos (MECD) and trios (MECT), were estimated based on an online tool provided by Forensic ChrX-STR database (http://www.chrx-str.org). The Fst pairwise genetic distances were explored by Arlequin V3.5. Multidimensional scaling (MDS) plots were generated based on Fst values using the SPSS Statistics 24 software (SPSS, Chicago, IL).

      3. Results and discussion

      For the 21 A-STRs, all loci follow the HWE after Bonferroni's correction; the 21 loci are highly informative with HET ranging from 0.699 (D2S441) to 0.892 (D11S2368), PD from 0.871 (D3S1358) to 0.968 (D7S1517) and PIC from 0.67 (D3S1358) to 0.86 (D7S3048). Since the 21 loci are independent from each other after LD testing, the combined power of discrimination (CPD) and combined power of exclusion (CPE) are 1–6.4E-25 and 0.999999996, respectively. The allele frequencies of 16 X-STRs in males and females show no significant difference at any locus (p >  0.05), therefore, pooled frequencies of males and females were used to calculate forensic parameters. The 16 X-STRs follow HWE in females. The HET range from 0.3244 (DXS6800) to 0.8680 (DXS10134). The discrimination power in females (PDF) and males (PDM) are 0.999999997 and 0.999999999999993, respectively. The mean exclusion chance in duos (MECD) and trios (MECT) are 0.9999931 and 0.99999997, respectively. Above results demonstrate that both the 21 A-STRs and 16 X-STRs can provide highly polymorphic information for forensic identification and paternity testing.
      To further explore the genetic relationship among populations, we compared A-STRs and X-STRs data of She with previously published data from Eastern Han [
      • Lin Y.
      • Que T.
      • Zhao Z.
      • et al.
      Forensic investigation of GoldeneyeTM DNA ID 22NC kit.
      ,
      • Song Y.
      • Liu J.
      • Zhu R.
      • et al.
      Genetic data on 16 X-chromosomal STR loci in three population samples from China.
      ], Northern Han [
      • Xie B.
      • Chen L.
      • Yang Y.
      • et al.
      Genetic distribution of 39 STR loci in 1027 unrelated Han individuals from Northern China.
      ,
      • Liu Y.
      • Guo L.
      • Yue J.
      • et al.
      Forensic application of 16 X-STR loci in Henan Han Population.
      ], Tibetan [
      • Gou H.
      • Zhou J.
      • Zhang Y.
      Allele frequency distribution of 21 forensic autosomal STR loci of GoldeneyeTM DNA ID 22NC Kit in Chinese Tibetan group.
      ] and Uygur [
      • Song F.
      • Li J.
      • Zhang L.
      • et al.
      Population data for 22 autosomal STR loci in the Uygur ethnic minority.
      ] on the same 21 A-STRs and 11 overlapping X-STRs. The Fst value between She and Eastern Han are always the lowest, regardless of the A-STRs or X-STRs were used (Fst = 0.0249 with A-STRs and Fst = 0.0054 with X-STRs). Based on the Fst genetic distance, the MDS plots generated by A-STRs and X-STRs are listed as Fig.1A and Fig.1B, respectively. In Fig.1, the She population is closely related to Eastern Han and distantly related to Tibetan, which is consistent with the historical and geographical background of the compared populations. Similar results were obtained in the previous studied based on 12 X-STRs [
      • Tao R.
      • Zhang J.
      • Bian Y.
      • et al.
      Investigation of 12 X-STR loci in Mongolian and Eastern Han populations of China with comparison to other populations.
      ] or 30 InDels [
      • Liu X.
      • Chen F.
      • Niu Y.
      • et al.
      Population genetics of 30 insertion/deletion polymorphisms in Han Chinese population from Zhejiang Province.
      ]. However, the observed genetic relationships could be complicated by many factors including the origins of samples, the choice of genetic markers and coverage of reference populations. Thus, great care must be taken when relating one ethnic group to another, as there may have been intermixture with now formally extinct populations that contributes to current population genetic structure.
      Fig. 1
      Fig. 1MDS plots based on Fst values between She population (marked with red triangle) and other four different Chinese populations (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article).

      4. Conclusion

      The forensic parameters indicate that the investigated 21 A-STRs and the 16 X-STRs are highly polymorphic and informative in the She population. These non−CODIS STRs can be useful in paternity cases with mutations or complex cases, while the X-STRs show higher efficiency in special kinship investigations involving mainly female offspring [
      • Szibor R.
      • Krawczak M.
      • Hering S.
      • et al.
      Use of X-linked markers for forensic purposes.
      ]. Although X-STRs tell a different story from A-STRs, they provided in general congruent phylogenetic signal and similar cluster among the five ethnic groups, which demonstrated that geographic isolation and interactions play significant roles in differentiation of genetic constitution of ethnic groups.

      Declaration of Competing Interest

      None.

      Acknowledgments

      This study was supported by grants from the National Natural Science Foundation of China ( 81625013 and 81772028 ), the Shanghai Outstanding Academic Leaders Plan ( 2017485 ), and the Shanghai Talent Development Funding ( 2017115 ). The funders had no role in study design, data analysis, publishing decisions, or manuscript preparation.

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