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Genetic analysis of 17 Y-chromosomal STR loci of Chinese Tujia ethnic group residing in Youyang Region of Southern China
Legal Medicine 16 (2014) 173–175
Contents lists available at ScienceDirect
Legal Medicine journal homepage: www.elsevier.com/locate/legalmed
Announcement of Population Data
Genetic analysis of 17 Y-chromosomal STR loci of Chinese Tujia ethnic group residing in Youyang Region of Southern China Ya-Ran Yang a,1, Yu-Ting Jing b,1, Guo-Dong Zhang b, Xiang-Dong Fang a, Jiang-Wei Yan a,⇑ a b
Key Laboratory of Genome Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China Institute of Forensic Science, Chongqing Public Security Bureau, Chongqing 400021, PR China
a r t i c l e
i n f o
Article history: Received 23 July 2013 Received in revised form 28 January 2014 Accepted 28 January 2014 Available online 5 February 2014 Keywords: Y-chromosome Yfiler Haplotype Tujia ethnic Genetic distance
a b s t r a c t Y-STR haplotype data were obtained in a population sample of 197 unrelated healthy male individuals of Chinese Tujia ethnic minority group residing in an autonomous county of Southern China using 17 Y-chromosome STR markers. A total of 197 haplotypes were identified in the set of Y-STR loci. The overall haplotype diversity for the Tujia population at 17 Y-STR loci was 1.0000 ± 0.0005. Genetic distance was estimated between this population and other 14 Chinese populations including Paiwan and Atayal populations of Taiwan, and Southern Han, Dong, Jing, Miao, Yao, Zhuang, Yi, Maonan, She, Hui, Sala, and Tibetan ethnic groups. The results demonstrated that the 17 Y-STR loci analyzed were highly polymorphic in Tujia ethnic group examined and hence useful for forensic cases, paternity testing, and population genetic studies. Ó 2014 Elsevier Ireland Ltd. All rights reserved.
Studied population: The Tujia ethnic group, with a population of 8,353,900 (according to the sixth population survey of China in 2010), mostly lived in the Chongqing municipality and Hunan, Hubei and Guizhou provinces. The Tujia language belongs to the Tujia sub-branch of the Tibetan–Burman language branch of the Chinese–Tibetan language family (Supplementary Figs. 1 and 2). The haplotype and frequency data based on 11 Y-STRs on Tujia ethnic group living in Shizhu autonomous county has been reported [1]. In this study, 197 unrelated healthy male individuals living in Youyang which is another autonomous county of Chongqing municipality were analyzed by 17 Y-STRs. All samples were collected with informed consent of the donors. DNA extraction and PCR: Genomic DNA was extracted using the Chelex-100 protocol as described by Walsh et al. [2]. PCR for 17 Ychromosomal STRs was performed in fluorescence-based multiplex reaction using the AmpFlSTRÒ Yfiler™ PCR Amplification Kit (Applied Biosystems, Foster City, CA, USA) (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4). Typing: The amplified products were separated and detected using an ABI Prism 3130XL Genetic analyzer (Applied Biosystems) following the manufacturer’s recommended protocol. GeneScan 500 LIZ was used as the internal lane standard. Fragment sizes ⇑ Corresponding author. Tel.: +86 01084097386. 1
E-mail address: [email protected] (J.-W. Yan). These authors have contributed equally to this work.
http://dx.doi.org/10.1016/j.legalmed.2014.01.010 1344-6223/Ó 2014 Elsevier Ireland Ltd. All rights reserved.
were assigned using GeneMapper ID v3.2.1 software (Applied Biosystems). Allele designations were determined by comparison of the sample fragments with those of allelic ladders provided with the kit. Quality control: The laboratory undergoes internal control standards and kit controls. It also participated in China National Accreditation Board for Laboratory (CNAL) blind trials for the aforementioned Y loci and is awarded with the respective proficiencies. The haplotypes used in this study have been submitted to YHRD (YRHD accession numbers is YA003845). Data analysis: Haplotype frequencies were estimated by haplotype counting. Haplotype diversity (HD) and standard error (SE) were calculated according to Nei’s formula [3]. Arlequin software (v 3.5.1.2) [4] was used to calculate population pairwise genetic distances (FST). FST values were ascertained at a significance level of 0.05 using 10,000 permutations [5]. A Bonferroni adjustment (a = 0.01/105 = 0.00009524) was applied to compensate for potential type I errors [6]. To illustrate the relationship between populations, a multidimensional scaling (MDS) plot was performed from pairwise FST values using SPSS software version 18 [7]. A reduced median-joining network for the recombination-free population data was constructed using the Network software v.4.610 (fluxus-engineering.com) [8]. Due to the complex repeat structure, DYS390, DYS389II and DYS385 were excluded from the analysis. Results: The haplotype distribution of Tujia population was shown in Supplementary Table 1. A total of 197 haplotypes were observed and the overall haplotype diversity for the Tujia popula-
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Y.-R. Yang et al. / Legal Medicine 16 (2014) 173–175
tion at 17 Y-STR loci was 1.0000 ± 0.0005. When query of the 197 haplotypes against 97,575 haplotypes in the YHRD database, 179 (90.86%) haplotypes did not occur in the YHRD (release 37 from June 21, 2011). 18 (9.14%) haplotypes were shared by East Asian Metapopulation. The search for the haplotype 15-13,13-12-29– 23-11–14-13–14-10–11-18–17-15–19-12 for DYS19-DYS385a/bDYS389I-DYS389II-DYS390-DYS391-DYS392-DYS393-DYS437-DY S438-DYS439-DYS448-DYS456-DYS458-DYS635-Y_GATA_H4 returned 19 matches, from Zhejiang, China [Han] (18) and Liaoning, China [Manchu] (1). The haplotype 15-13,14-12-29-23-10-14-1314-10-11-18-16-15-20-11 returned 7 matches from Zhejiang, China [Han] (6) and Kham, China [Tibetan](1) and the haplotype 16-12,20-12-28-24-9-13-12-14-10-11-19-14-17-22-12 returned 5 matches, all from Zhejiang, China [Han]. Supplementary Table 2 lists the allelic frequencies and gene diversity values for the 17 Y-STR loci analyzed in the Tujia population. Rare alleles were observed at loci DYS385a/b (10.2, 11) and (12, 12.3). A reduced median-joining network was presented in Supplementary Fig. 3. Based on pairwise FST comparisons, our present haplotype data were compared with the previously published data from other 14 Chinese populations including Paiwan and Atayal populations of Taiwan, and Southern Han, Dong, Jing, Miao, Yao, Zhuang, Yi, Maonan, She, Hui, Sala, and Tibetan ethnic groups [9–17]. The FST values and associated P-values between pairs of populations were given in Supplementary Table 3. Tujia was found to be significantly different (a = 0.01/105 = 0.00009524) from Paiwan, Atayal, Miao, She, Hui, Sala and Tibetan ethnic groups, while no significant difference from Southern Han, Dong, Jing, Yao, Zhuang, Yi and Maonan ethnic groups. The Tujia population in this study was also compared with another Tujia group in Shizhou [1] using 11 Y-STRs. The FST values and associated P-values are 0.00095 and 0.1621, respectively. This showed that the two tujia populations had no difference from each other. The MDS plot illustrated the genetic relationship between the studied populations (Fig. 1). This study demonstrates that the set of Y-STR loci was a
valuable and handy tool in forensic field for personal identification and paternity analysis in the region and in population genetics. Acknowledgement This study was supported by National Natural Science Foundation of China (81172909 and 81072511). Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/j.legalmed.2014. 01.010. References [1] Shi M, Bai R, Wan L, Yu X, Chang L. Population genetics for Y-chromosomal STRs haplotypes of Chinese Tujia ethnic group. Forensic Sci Int Genet 2008;2:e65–8. [2] Walsh PS, Metzger DA, Higushi R. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. BioTechniques 1991;10:506–13. [3] Nei M. Molecular evolutionary genetics. New York: Columbia University Press; 1987. p. 176–179. [4] 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. [5] Kayser M, Brauer S, Schädlich H, Prinz M, Batzer MA, Zimmerman PA, et al. Y chromosome STR haplotypes and the genetic structure of U.S. populations of African, European, and Hispanic ancestry. Genome Res 2003;13:624–34. [6] Yosef H. A charper Bonferroni procedure for multiple test of significance. Biometrika 1998;75:800–2. [7] SPSS for Windows, Version 18.0, Chicago, SPSS Inc. [8] Bandelt HJ, Forster P, Röhl A. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 1999;16:37–48. [9] Wu FC, Ho CW, Pu CE, Hu KY, Willuweit S, Roewer L, et al. Y-chromosomal STRs haplotypes in the Taiwanese Paiwan population. Int J Legal Med 2011;125:39–43. [10] Wu FC, Ho CW, Pu CE, Hu KY, Liu DH. Genetic polymorphisms of 17 Ychromosomal short tandem repeat loci in Atayal population of Taiwan. Croat Med J 2009;50:313–20.
Fig. 1. Multidimensional scaling (MDS) plot based on pairwise FST values between Tujia and 14 previously published populations (stress value = 0.03419).
Y.-R. Yang et al. / Legal Medicine 16 (2014) 173–175 [11] Chen YK, Li Q, Li DC, et al. Study on the genetic polymorphism of 17 Ychromosome specific STR loci of non-related male individuals in southern Chinese Han population. Exp Lab Med 2008;26:351–6. [12] Liang ZR, Liu CH, Liu C. Polymorphism of 17 Y-STR loci in three minority populations in Guangxi of China. Basic Clin Med 2009;29:488–94. [13] Feng DL, Liu CH, Liang ZR, Liu C. Genetic polymorphism of 17 Y-STR loci in four minority populations in Guangxi of China. Hereditas (Beijing) 2009;31:921–35. [14] Bai RF, Yang LH, Yuan L, Liang QZ, Lu D, Yang X, Shi MS. Polymorphism of 17 YSTR loci in She ethnic population in Fujian and genetic relationship with 11 population. Hereditas (Beijing) 2012;34:1020–30.
175
[15] Guo H, Yan J, Jiao Z, Tang H, Zhang Q, Zhao L, et al. Genetic polymorphisms for 17 Y-chromosomal STRs haplotypes in Chinese Hui population. Leg Med (Tokyo). 2008;10:163–9. [16] Zhu B, Shen C, Xun X, Yan J, Deng Y, Zhu J, et al. Population genetic polymorphisms for 17 Y-chromosomal STRs haplotypes of Chinese Salar ethnic minority group. Leg Med (Tokyo) 2007;9:203–9. [17] Zhu B, Wu Y, Shen C, Yang T, Deng Y, Xun X, et al. Genetic analysis of 17 Ychromosomal STRs haplotypes of Chinese Tibetan ethnic group residing in Qinghai province of China. Forensic Sci Int 2008;175:238–43.
Contents lists available at ScienceDirect
Legal Medicine journal homepage: www.elsevier.com/locate/legalmed
Announcement of Population Data
Genetic analysis of 17 Y-chromosomal STR loci of Chinese Tujia ethnic group residing in Youyang Region of Southern China Ya-Ran Yang a,1, Yu-Ting Jing b,1, Guo-Dong Zhang b, Xiang-Dong Fang a, Jiang-Wei Yan a,⇑ a b
Key Laboratory of Genome Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China Institute of Forensic Science, Chongqing Public Security Bureau, Chongqing 400021, PR China
a r t i c l e
i n f o
Article history: Received 23 July 2013 Received in revised form 28 January 2014 Accepted 28 January 2014 Available online 5 February 2014 Keywords: Y-chromosome Yfiler Haplotype Tujia ethnic Genetic distance
a b s t r a c t Y-STR haplotype data were obtained in a population sample of 197 unrelated healthy male individuals of Chinese Tujia ethnic minority group residing in an autonomous county of Southern China using 17 Y-chromosome STR markers. A total of 197 haplotypes were identified in the set of Y-STR loci. The overall haplotype diversity for the Tujia population at 17 Y-STR loci was 1.0000 ± 0.0005. Genetic distance was estimated between this population and other 14 Chinese populations including Paiwan and Atayal populations of Taiwan, and Southern Han, Dong, Jing, Miao, Yao, Zhuang, Yi, Maonan, She, Hui, Sala, and Tibetan ethnic groups. The results demonstrated that the 17 Y-STR loci analyzed were highly polymorphic in Tujia ethnic group examined and hence useful for forensic cases, paternity testing, and population genetic studies. Ó 2014 Elsevier Ireland Ltd. All rights reserved.
Studied population: The Tujia ethnic group, with a population of 8,353,900 (according to the sixth population survey of China in 2010), mostly lived in the Chongqing municipality and Hunan, Hubei and Guizhou provinces. The Tujia language belongs to the Tujia sub-branch of the Tibetan–Burman language branch of the Chinese–Tibetan language family (Supplementary Figs. 1 and 2). The haplotype and frequency data based on 11 Y-STRs on Tujia ethnic group living in Shizhu autonomous county has been reported [1]. In this study, 197 unrelated healthy male individuals living in Youyang which is another autonomous county of Chongqing municipality were analyzed by 17 Y-STRs. All samples were collected with informed consent of the donors. DNA extraction and PCR: Genomic DNA was extracted using the Chelex-100 protocol as described by Walsh et al. [2]. PCR for 17 Ychromosomal STRs was performed in fluorescence-based multiplex reaction using the AmpFlSTRÒ Yfiler™ PCR Amplification Kit (Applied Biosystems, Foster City, CA, USA) (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4). Typing: The amplified products were separated and detected using an ABI Prism 3130XL Genetic analyzer (Applied Biosystems) following the manufacturer’s recommended protocol. GeneScan 500 LIZ was used as the internal lane standard. Fragment sizes ⇑ Corresponding author. Tel.: +86 01084097386. 1
E-mail address: [email protected] (J.-W. Yan). These authors have contributed equally to this work.
http://dx.doi.org/10.1016/j.legalmed.2014.01.010 1344-6223/Ó 2014 Elsevier Ireland Ltd. All rights reserved.
were assigned using GeneMapper ID v3.2.1 software (Applied Biosystems). Allele designations were determined by comparison of the sample fragments with those of allelic ladders provided with the kit. Quality control: The laboratory undergoes internal control standards and kit controls. It also participated in China National Accreditation Board for Laboratory (CNAL) blind trials for the aforementioned Y loci and is awarded with the respective proficiencies. The haplotypes used in this study have been submitted to YHRD (YRHD accession numbers is YA003845). Data analysis: Haplotype frequencies were estimated by haplotype counting. Haplotype diversity (HD) and standard error (SE) were calculated according to Nei’s formula [3]. Arlequin software (v 3.5.1.2) [4] was used to calculate population pairwise genetic distances (FST). FST values were ascertained at a significance level of 0.05 using 10,000 permutations [5]. A Bonferroni adjustment (a = 0.01/105 = 0.00009524) was applied to compensate for potential type I errors [6]. To illustrate the relationship between populations, a multidimensional scaling (MDS) plot was performed from pairwise FST values using SPSS software version 18 [7]. A reduced median-joining network for the recombination-free population data was constructed using the Network software v.4.610 (fluxus-engineering.com) [8]. Due to the complex repeat structure, DYS390, DYS389II and DYS385 were excluded from the analysis. Results: The haplotype distribution of Tujia population was shown in Supplementary Table 1. A total of 197 haplotypes were observed and the overall haplotype diversity for the Tujia popula-
174
Y.-R. Yang et al. / Legal Medicine 16 (2014) 173–175
tion at 17 Y-STR loci was 1.0000 ± 0.0005. When query of the 197 haplotypes against 97,575 haplotypes in the YHRD database, 179 (90.86%) haplotypes did not occur in the YHRD (release 37 from June 21, 2011). 18 (9.14%) haplotypes were shared by East Asian Metapopulation. The search for the haplotype 15-13,13-12-29– 23-11–14-13–14-10–11-18–17-15–19-12 for DYS19-DYS385a/bDYS389I-DYS389II-DYS390-DYS391-DYS392-DYS393-DYS437-DY S438-DYS439-DYS448-DYS456-DYS458-DYS635-Y_GATA_H4 returned 19 matches, from Zhejiang, China [Han] (18) and Liaoning, China [Manchu] (1). The haplotype 15-13,14-12-29-23-10-14-1314-10-11-18-16-15-20-11 returned 7 matches from Zhejiang, China [Han] (6) and Kham, China [Tibetan](1) and the haplotype 16-12,20-12-28-24-9-13-12-14-10-11-19-14-17-22-12 returned 5 matches, all from Zhejiang, China [Han]. Supplementary Table 2 lists the allelic frequencies and gene diversity values for the 17 Y-STR loci analyzed in the Tujia population. Rare alleles were observed at loci DYS385a/b (10.2, 11) and (12, 12.3). A reduced median-joining network was presented in Supplementary Fig. 3. Based on pairwise FST comparisons, our present haplotype data were compared with the previously published data from other 14 Chinese populations including Paiwan and Atayal populations of Taiwan, and Southern Han, Dong, Jing, Miao, Yao, Zhuang, Yi, Maonan, She, Hui, Sala, and Tibetan ethnic groups [9–17]. The FST values and associated P-values between pairs of populations were given in Supplementary Table 3. Tujia was found to be significantly different (a = 0.01/105 = 0.00009524) from Paiwan, Atayal, Miao, She, Hui, Sala and Tibetan ethnic groups, while no significant difference from Southern Han, Dong, Jing, Yao, Zhuang, Yi and Maonan ethnic groups. The Tujia population in this study was also compared with another Tujia group in Shizhou [1] using 11 Y-STRs. The FST values and associated P-values are 0.00095 and 0.1621, respectively. This showed that the two tujia populations had no difference from each other. The MDS plot illustrated the genetic relationship between the studied populations (Fig. 1). This study demonstrates that the set of Y-STR loci was a
valuable and handy tool in forensic field for personal identification and paternity analysis in the region and in population genetics. Acknowledgement This study was supported by National Natural Science Foundation of China (81172909 and 81072511). Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/j.legalmed.2014. 01.010. References [1] Shi M, Bai R, Wan L, Yu X, Chang L. Population genetics for Y-chromosomal STRs haplotypes of Chinese Tujia ethnic group. Forensic Sci Int Genet 2008;2:e65–8. [2] Walsh PS, Metzger DA, Higushi R. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. BioTechniques 1991;10:506–13. [3] Nei M. Molecular evolutionary genetics. New York: Columbia University Press; 1987. p. 176–179. [4] 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. [5] Kayser M, Brauer S, Schädlich H, Prinz M, Batzer MA, Zimmerman PA, et al. Y chromosome STR haplotypes and the genetic structure of U.S. populations of African, European, and Hispanic ancestry. Genome Res 2003;13:624–34. [6] Yosef H. A charper Bonferroni procedure for multiple test of significance. Biometrika 1998;75:800–2. [7] SPSS for Windows, Version 18.0, Chicago, SPSS Inc. [8] Bandelt HJ, Forster P, Röhl A. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 1999;16:37–48. [9] Wu FC, Ho CW, Pu CE, Hu KY, Willuweit S, Roewer L, et al. Y-chromosomal STRs haplotypes in the Taiwanese Paiwan population. Int J Legal Med 2011;125:39–43. [10] Wu FC, Ho CW, Pu CE, Hu KY, Liu DH. Genetic polymorphisms of 17 Ychromosomal short tandem repeat loci in Atayal population of Taiwan. Croat Med J 2009;50:313–20.
Fig. 1. Multidimensional scaling (MDS) plot based on pairwise FST values between Tujia and 14 previously published populations (stress value = 0.03419).
Y.-R. Yang et al. / Legal Medicine 16 (2014) 173–175 [11] Chen YK, Li Q, Li DC, et al. Study on the genetic polymorphism of 17 Ychromosome specific STR loci of non-related male individuals in southern Chinese Han population. Exp Lab Med 2008;26:351–6. [12] Liang ZR, Liu CH, Liu C. Polymorphism of 17 Y-STR loci in three minority populations in Guangxi of China. Basic Clin Med 2009;29:488–94. [13] Feng DL, Liu CH, Liang ZR, Liu C. Genetic polymorphism of 17 Y-STR loci in four minority populations in Guangxi of China. Hereditas (Beijing) 2009;31:921–35. [14] Bai RF, Yang LH, Yuan L, Liang QZ, Lu D, Yang X, Shi MS. Polymorphism of 17 YSTR loci in She ethnic population in Fujian and genetic relationship with 11 population. Hereditas (Beijing) 2012;34:1020–30.
175
[15] Guo H, Yan J, Jiao Z, Tang H, Zhang Q, Zhao L, et al. Genetic polymorphisms for 17 Y-chromosomal STRs haplotypes in Chinese Hui population. Leg Med (Tokyo). 2008;10:163–9. [16] Zhu B, Shen C, Xun X, Yan J, Deng Y, Zhu J, et al. Population genetic polymorphisms for 17 Y-chromosomal STRs haplotypes of Chinese Salar ethnic minority group. Leg Med (Tokyo) 2007;9:203–9. [17] Zhu B, Wu Y, Shen C, Yang T, Deng Y, Xun X, et al. Genetic analysis of 17 Ychromosomal STRs haplotypes of Chinese Tibetan ethnic group residing in Qinghai province of China. Forensic Sci Int 2008;175:238–43.