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Analysis of 19 STR loci reveals genetic characteristic of eastern Chinese Han population
Forensic Science International: Genetics 14 (2015) 108–109
Contents lists available at ScienceDirect
Forensic Science International: Genetics journal homepage: www.elsevier.com/locate/fsig
Letter to the Editor Analysis of 19 STR loci reveals genetic characteristic of eastern Chinese Han population Dear Editor, Jiangsu province is located in East China coastal areas with Shanghai, Anhui, Shandong and Zhejiang neighbored. Jiangsu ranks the fifth large province of China, numbering 78,659,903 in 2010. Han population accounts for 99.67% of the total population in Jiangsu and the proportion in Anhui is 99.37% [1]. As shown in Fig. S1, Huai’an, Taizhou and Yangzhou, are located in the center of Jiangsu province, and Suzhou in Anhui province. In the present study, we examined the genetic polymorphisms of 19 STR loci (D8S1179, D21S11, D7S820, CSF1P0, D3S1358, THOl, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, FGA, D16S1043, PentaD, PentaE, D21S391) from Han population living in the four cities. Blood samples were collected from 636 unrelated Han individuals (475 males and 161 females) from Huai’an (n = 137), Yangzhou (n = 184), Taizhou (n = 115) and Suzhou (n = 200) cities, following informed consent. Genomic DNA was extracted by Chelex-100. STR loci were co-amplified using the GoldenEyeTM DNA ID system 20A kit (Golden Eye Ltd., Beijing, China) in the GeneAmp PCR system 9700 with a gold-plate silver or silver block (Applied Biosystems, Foster City, CA, USA). The amplified products were separated on ABI3130XL DNA Genetic Analyzer (Applied Biosystems, USA) and genotyped with the GeneMapper ID-X software (Applied Biosystems, Foster City, CA, USA). Genetic parameters of interest and the exact chi-square test for the Hardy– Weinberg equilibrium (HWE) were calculated by the modified PowerStates ver 1.2 spread-sheet. The software Phylip and Mega 4.0 [2] were used to calculate the Nei’s distance and draw a UPGMA (Unweighted Pair-Group Method Using Arithmetic averages) tree on the basis of shared STR loci allele frequencies data of the 19 populations [3–16]. The principal component analysis of the studied populations based on allele frequency was performed by using SPSS 11.0 software. The locus-by-locus comparison of the allelic frequencies was carried out between the studied populations and other previously published population data using analysis of molecular variance method (AMOVA, based on Fstatistics), which was performed with ARLEQUIN version 3.0 software [17]. Allelic frequencies, forensic parameters and genotype data of the four populations are presented in Tables S1–S8. Except D7S820 (p = 0.0084), D16S539 (p = 0.0078), PentaD (p = 0.0073) of Yangzhou population and D6S1043 (p = 0.0206) of Suzhou population, rest of the STR loci in the study showed no deviations from HWE tests. There would be no deviations at all the 19 loci of the four populations when the Bonferroni correction was employed using the number of loci analyzed, the signification was reduced to 0.0026. The genetic relevance between the four studied http://dx.doi.org/10.1016/j.fsigen.2014.09.015 1872-4973/ß 2014 Elsevier Ireland Ltd. All rights reserved.
populations and other ethnic groups were delineated by phylogenetic reconstruction. Based on the 19 STR dataset, Nei’s distance and Fst genetic values revealed the relationships of 19 populations were calculated as shown in Tables S9 and S10. As well, a phylogenetic tree was built in Fig. 1. Two main clusters exist in this phylogenetic tree. The first cluster was consisted of Manchu population from Liaoning province and Han population of Taizhou, Huai’an, Suzhou, Henan, Yangzhou and Shandong; another cluster was composed of the other 11 populations. The results showed that Suzhou Han had the shortest genetic distance with Henan Han (d = 0.007808), then followed the genetic distances between Yangzhou Han and Shandong Han (d = 0.008553), Shandong Han and Henan Han (d = 0.008557), Yangzhou Han and Henan Han (d = 0.008899). The genetic relationship of the four populations we studied was very close to each other, with the Nei’s distance ranges from 0.010633 to 0.017663. Our data also showed that Han population from the lower reaches of Yangtze River has a different origin compared to Han population from the south and the northwest of China such as Shanghai City, Zhejiang Province and Xi’an City in Shaanxi Province. To confirm the result, we next performed principal component analysis based on allele frequency (Fig. 2). The PC map represents the first three principal components. The first PC incorporated about 61.97% of the total original variation, the second and third accounted for 27.27% and
Fig. 1. Phylogenetic tree of nineteen populations based on Neis distance given in Table S9.
Letter to the Editor / Forensic Science International: Genetics 14 (2015) 108–109
Fig. 2. Principal component map of the studied populations based on STR allele frequency.
9.30% respectively. The cluster pattern in the PC map was in good agreement with the results of the phylogenetic tree, which displayed a close genetic relationship among four studied populations, Henan, Shandong and Manchu. The genetics distances between the four studied populations were far from the other Chinese Han populations, including Shanghai Han and Zhejiang Han, even though they are geographically close to each other (Fig. S1). The genetic characteristics of the four studied populations can be explained by recorded population migration in Chinese history (shown in Fig. S1) [18,19]. This study is performed follows the guidelines for publication of population genetics data in the journal [20,21].
109
[8] M. Ozeki, K. Tamaki, Allele frequencies of 37 short tandem repeat loci in a Japanese population, Leg. Med. (Tokyo) 15 (2013) 342–346. [9] Z. Wang, P. Huang, L. Chen, Y. Xu, K. He, X. Zhu, Genetic polymorphisms of 15 STR loci in Chinese Hui population, J. Forensic Sci. 50 (2005) 1508–1509. [10] A.A. Westen, T. Kraaijenbrink, E.A. Robles de Medina, J. Harteveld, P. Willemse, S.B. Zuniga, K.J. van der Gaag, N.E. Weiler, J. Warnaar, M. Kayser, T. Sijen, P. de Knijff, Comparing six commercial autosomal STR kits in a large Dutch population sample, Forensic Sci. Int. Genet. 10 (2014) 55–63. [11] Y.M. Wu, X.N. Zhang, Y. Zhou, Z.Y. Chen, X.B. Wang, Genetic polymorphisms of 15 STR loci in Chinese Han population living in Xi’an city of Shaanxi Province, Forensic Sci. Int. Genet. 2 (2008) e15–18. [12] C. Yan, Z. Yu-ning, L. Shi-ming, Y. Jian-fei, M. Yu, Establishment application of 18STR database in Han population from Zhejiang Province, J. Sun Yat-Sen Univ. (Med. Sci.) 01 (2010) 0107–0122. [13] B.F. Zhu, C.M. Shen, Q.J. Wu, Y.J. Deng, Population data of 15 STR loci of Chinese Yi ethnic minority group, Leg. Med. (Tokyo) 10 (2008) 220–224. [14] B.F. Zhu, G. Yang, C.M. Shen, H.X. Qin, S.L. Fan, L.B. Deng, F. Chen, L.P. Chen, H.D. Wang, Z.Y. Wang, R. Lucas, Z.M. Lian, Population genetic analysis of 15 autosomal STR loci in the Russian population of northeastern Inner-Mongolia, China, Mol. Biol. Rep. 37 (2010) 3889–3895. [15] J. Zhu, J. Li, Y. Guo, K. Liu, B. Zhu, Y. Liu, Population data of 15 STR in Chinese Han population from north of Guangdong, J. Forensic Sci. 50 (2005) 1510–1511. [16] J. Zhu, C. Shen, Y. Ma, Y. He, J. Zhao, X. Li, Y. Liu, Genetic polymorphisms of 15 STR in Chinese Salar ethnic minority group, Forensic Sci. Int. 173 (2007) 210–213. [17] L. Excoffier, G. Laval, S. Schneider, Arlequin (version 3.0): an integrated software package for population genetics data analysis, Evol. Bioinform. Online 1 (2005) 47–50. [18] Jiangsu, Encyclopaedia Britannica. Encyclopaedia Britannica Online, Encyclopædia Britannica Inc., 2014 (web accessed: 22.7.14). [19] J. Ge, Chinese Population Development History, Fujian People Publisher, 1991. [20] A. Carracedo, J.M. Butler, L. Gusmao, A. Linacre, W. Parson, L. Roewer, P.M. Schneider, New guidelines for the publication of genetic population data, Forensic Sci. Int. Genet. 7 (2013) 217–220. [21] A. Carracedo, J.M. Butler, L. Gusmao, A. Linacre, W. Parson, L. Roewer, P.M. Schneider, Update of the guidelines for the publication of genetic population data, Forensic Sci. Int. Genet. 10 (2014) A1–2.
Caiyong Yin Qiang Ji* Kai Li Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
Acknowledgements This project was supported by the funding for Science and Technology of Jiangsu Province China (No. BK20140902 to FC), National Natural Science Foundation of China (No. 81400033 to FC) and an established investigator start funding from Nanjing Medical University (No. KY101RC041307 to FC). Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at doi:10.1016/j.fsigen.2014.09.015.
Haofang Mu Center of Forensic Sciences, Beijing Genomics Institute, Beijing 101300, China Bofeng Zhu School of Medicine, Xi’an Jiaotong University, Xi’an 710061, China Jiangwei Yan Key Laboratory of Genome Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China Yanfang Yu Jianwen Wang Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
References [1] G. Zhu, D. Zhong, J. Cao, H. Zhou, J. Li, Y. Liu, L. Bai, S. Xu, M.H. Wang, G. Zhou, X. Chang, Q. Gao, G. Yan, Transcriptome profiling of pyrethroid resistant and susceptible mosquitoes in the malaria vector, Anopheles sinensis, BMC Genomics 15 (2014) 448. [2] K. Tamura, J. Dudley, M. Nei, S. Kumar, MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0, Mol. Biol. Evol. 24 (2007) 1596–1599. [3] A. Hedjazi, A. Nilcbalcht, M. Hosseini, A. Hoseinzadeh, S.M.V. Hosseini, Allele frequencies for 15 autosomal STR loci in Fars province population, southwest of Iran, Leg. Med. 15 (2013) 226–228. [4] Hong-Dan Wang, Dong Wu, Zhan-Qi Feng, Zhi-An Jing, Tao Li, Qian-Nan Guo, Xian-Ping Zhang, Qiao-Fang Hou, Liang-Jie Guo, Bing Kang, Hui Zhang, Bo-Feng Zhu, S.-X. Liao, Genetic polymorphisms of 20 short tandem repeat loci from the Han population in Henan, China, Electrophoresis 35 (2014) 1509–1514. [5] Q. Huang, J.C. Escrina Lopez, C. Baeza, E. Arroyo-Pardo, A.M. Lopez-Parra, Genetic polymorphism of 15 STR loci in Chinese Han population from Shanghai municipality in East China, Forensic Sci. Int. Genet. 7 (2013) e31–e34. [6] J. Liu, L. Guo, R. Qi, S.-y. Li, J.-y. Yin, W. Zhang, Z. Sun, X. Tian, B. Gao, Allele frequencies of 19 autosomal STR loci in Manchu population of China with phylogenetic structure among worldwide populations, Gene 529 (2013) 282–287. [7] Z. Mao-xiu, H. Shu-yi, G. Hong-mei, S. Shan-hui, X. Dong-jie, L. Yang, W. Yun-shan, Genetic polymorphisms of 19 STR loci in Shandong Han population, J. Forensic Med. 06 (2013) 440–443, 446.
a
Feng Chena,b,* Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China b Vascular Biology Center, Georgia Regents University, Augusta, GA 30912, United States
*Corresponding authors at: Department of Forensic Medicine, Nanjing Medical University, 140 Hanzhong Road, Nanjing, Jiangsu 210029, China. Tel.: +86 25 86662896; fax: +86 25 86662896 E-mail addresses: [email protected] (Q. Ji). [email protected], [email protected] (F. Chen). 30 August 2014 Available online
Contents lists available at ScienceDirect
Forensic Science International: Genetics journal homepage: www.elsevier.com/locate/fsig
Letter to the Editor Analysis of 19 STR loci reveals genetic characteristic of eastern Chinese Han population Dear Editor, Jiangsu province is located in East China coastal areas with Shanghai, Anhui, Shandong and Zhejiang neighbored. Jiangsu ranks the fifth large province of China, numbering 78,659,903 in 2010. Han population accounts for 99.67% of the total population in Jiangsu and the proportion in Anhui is 99.37% [1]. As shown in Fig. S1, Huai’an, Taizhou and Yangzhou, are located in the center of Jiangsu province, and Suzhou in Anhui province. In the present study, we examined the genetic polymorphisms of 19 STR loci (D8S1179, D21S11, D7S820, CSF1P0, D3S1358, THOl, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, FGA, D16S1043, PentaD, PentaE, D21S391) from Han population living in the four cities. Blood samples were collected from 636 unrelated Han individuals (475 males and 161 females) from Huai’an (n = 137), Yangzhou (n = 184), Taizhou (n = 115) and Suzhou (n = 200) cities, following informed consent. Genomic DNA was extracted by Chelex-100. STR loci were co-amplified using the GoldenEyeTM DNA ID system 20A kit (Golden Eye Ltd., Beijing, China) in the GeneAmp PCR system 9700 with a gold-plate silver or silver block (Applied Biosystems, Foster City, CA, USA). The amplified products were separated on ABI3130XL DNA Genetic Analyzer (Applied Biosystems, USA) and genotyped with the GeneMapper ID-X software (Applied Biosystems, Foster City, CA, USA). Genetic parameters of interest and the exact chi-square test for the Hardy– Weinberg equilibrium (HWE) were calculated by the modified PowerStates ver 1.2 spread-sheet. The software Phylip and Mega 4.0 [2] were used to calculate the Nei’s distance and draw a UPGMA (Unweighted Pair-Group Method Using Arithmetic averages) tree on the basis of shared STR loci allele frequencies data of the 19 populations [3–16]. The principal component analysis of the studied populations based on allele frequency was performed by using SPSS 11.0 software. The locus-by-locus comparison of the allelic frequencies was carried out between the studied populations and other previously published population data using analysis of molecular variance method (AMOVA, based on Fstatistics), which was performed with ARLEQUIN version 3.0 software [17]. Allelic frequencies, forensic parameters and genotype data of the four populations are presented in Tables S1–S8. Except D7S820 (p = 0.0084), D16S539 (p = 0.0078), PentaD (p = 0.0073) of Yangzhou population and D6S1043 (p = 0.0206) of Suzhou population, rest of the STR loci in the study showed no deviations from HWE tests. There would be no deviations at all the 19 loci of the four populations when the Bonferroni correction was employed using the number of loci analyzed, the signification was reduced to 0.0026. The genetic relevance between the four studied http://dx.doi.org/10.1016/j.fsigen.2014.09.015 1872-4973/ß 2014 Elsevier Ireland Ltd. All rights reserved.
populations and other ethnic groups were delineated by phylogenetic reconstruction. Based on the 19 STR dataset, Nei’s distance and Fst genetic values revealed the relationships of 19 populations were calculated as shown in Tables S9 and S10. As well, a phylogenetic tree was built in Fig. 1. Two main clusters exist in this phylogenetic tree. The first cluster was consisted of Manchu population from Liaoning province and Han population of Taizhou, Huai’an, Suzhou, Henan, Yangzhou and Shandong; another cluster was composed of the other 11 populations. The results showed that Suzhou Han had the shortest genetic distance with Henan Han (d = 0.007808), then followed the genetic distances between Yangzhou Han and Shandong Han (d = 0.008553), Shandong Han and Henan Han (d = 0.008557), Yangzhou Han and Henan Han (d = 0.008899). The genetic relationship of the four populations we studied was very close to each other, with the Nei’s distance ranges from 0.010633 to 0.017663. Our data also showed that Han population from the lower reaches of Yangtze River has a different origin compared to Han population from the south and the northwest of China such as Shanghai City, Zhejiang Province and Xi’an City in Shaanxi Province. To confirm the result, we next performed principal component analysis based on allele frequency (Fig. 2). The PC map represents the first three principal components. The first PC incorporated about 61.97% of the total original variation, the second and third accounted for 27.27% and
Fig. 1. Phylogenetic tree of nineteen populations based on Neis distance given in Table S9.
Letter to the Editor / Forensic Science International: Genetics 14 (2015) 108–109
Fig. 2. Principal component map of the studied populations based on STR allele frequency.
9.30% respectively. The cluster pattern in the PC map was in good agreement with the results of the phylogenetic tree, which displayed a close genetic relationship among four studied populations, Henan, Shandong and Manchu. The genetics distances between the four studied populations were far from the other Chinese Han populations, including Shanghai Han and Zhejiang Han, even though they are geographically close to each other (Fig. S1). The genetic characteristics of the four studied populations can be explained by recorded population migration in Chinese history (shown in Fig. S1) [18,19]. This study is performed follows the guidelines for publication of population genetics data in the journal [20,21].
109
[8] M. Ozeki, K. Tamaki, Allele frequencies of 37 short tandem repeat loci in a Japanese population, Leg. Med. (Tokyo) 15 (2013) 342–346. [9] Z. Wang, P. Huang, L. Chen, Y. Xu, K. He, X. Zhu, Genetic polymorphisms of 15 STR loci in Chinese Hui population, J. Forensic Sci. 50 (2005) 1508–1509. [10] A.A. Westen, T. Kraaijenbrink, E.A. Robles de Medina, J. Harteveld, P. Willemse, S.B. Zuniga, K.J. van der Gaag, N.E. Weiler, J. Warnaar, M. Kayser, T. Sijen, P. de Knijff, Comparing six commercial autosomal STR kits in a large Dutch population sample, Forensic Sci. Int. Genet. 10 (2014) 55–63. [11] Y.M. Wu, X.N. Zhang, Y. Zhou, Z.Y. Chen, X.B. Wang, Genetic polymorphisms of 15 STR loci in Chinese Han population living in Xi’an city of Shaanxi Province, Forensic Sci. Int. Genet. 2 (2008) e15–18. [12] C. Yan, Z. Yu-ning, L. Shi-ming, Y. Jian-fei, M. Yu, Establishment application of 18STR database in Han population from Zhejiang Province, J. Sun Yat-Sen Univ. (Med. Sci.) 01 (2010) 0107–0122. [13] B.F. Zhu, C.M. Shen, Q.J. Wu, Y.J. Deng, Population data of 15 STR loci of Chinese Yi ethnic minority group, Leg. Med. (Tokyo) 10 (2008) 220–224. [14] B.F. Zhu, G. Yang, C.M. Shen, H.X. Qin, S.L. Fan, L.B. Deng, F. Chen, L.P. Chen, H.D. Wang, Z.Y. Wang, R. Lucas, Z.M. Lian, Population genetic analysis of 15 autosomal STR loci in the Russian population of northeastern Inner-Mongolia, China, Mol. Biol. Rep. 37 (2010) 3889–3895. [15] J. Zhu, J. Li, Y. Guo, K. Liu, B. Zhu, Y. Liu, Population data of 15 STR in Chinese Han population from north of Guangdong, J. Forensic Sci. 50 (2005) 1510–1511. [16] J. Zhu, C. Shen, Y. Ma, Y. He, J. Zhao, X. Li, Y. Liu, Genetic polymorphisms of 15 STR in Chinese Salar ethnic minority group, Forensic Sci. Int. 173 (2007) 210–213. [17] L. Excoffier, G. Laval, S. Schneider, Arlequin (version 3.0): an integrated software package for population genetics data analysis, Evol. Bioinform. Online 1 (2005) 47–50. [18] Jiangsu, Encyclopaedia Britannica. Encyclopaedia Britannica Online, Encyclopædia Britannica Inc., 2014 (web accessed: 22.7.14). [19] J. Ge, Chinese Population Development History, Fujian People Publisher, 1991. [20] A. Carracedo, J.M. Butler, L. Gusmao, A. Linacre, W. Parson, L. Roewer, P.M. Schneider, New guidelines for the publication of genetic population data, Forensic Sci. Int. Genet. 7 (2013) 217–220. [21] A. Carracedo, J.M. Butler, L. Gusmao, A. Linacre, W. Parson, L. Roewer, P.M. Schneider, Update of the guidelines for the publication of genetic population data, Forensic Sci. Int. Genet. 10 (2014) A1–2.
Caiyong Yin Qiang Ji* Kai Li Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
Acknowledgements This project was supported by the funding for Science and Technology of Jiangsu Province China (No. BK20140902 to FC), National Natural Science Foundation of China (No. 81400033 to FC) and an established investigator start funding from Nanjing Medical University (No. KY101RC041307 to FC). Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at doi:10.1016/j.fsigen.2014.09.015.
Haofang Mu Center of Forensic Sciences, Beijing Genomics Institute, Beijing 101300, China Bofeng Zhu School of Medicine, Xi’an Jiaotong University, Xi’an 710061, China Jiangwei Yan Key Laboratory of Genome Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China Yanfang Yu Jianwen Wang Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
References [1] G. Zhu, D. Zhong, J. Cao, H. Zhou, J. Li, Y. Liu, L. Bai, S. Xu, M.H. Wang, G. Zhou, X. Chang, Q. Gao, G. Yan, Transcriptome profiling of pyrethroid resistant and susceptible mosquitoes in the malaria vector, Anopheles sinensis, BMC Genomics 15 (2014) 448. [2] K. Tamura, J. Dudley, M. Nei, S. Kumar, MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0, Mol. Biol. Evol. 24 (2007) 1596–1599. [3] A. Hedjazi, A. Nilcbalcht, M. Hosseini, A. Hoseinzadeh, S.M.V. Hosseini, Allele frequencies for 15 autosomal STR loci in Fars province population, southwest of Iran, Leg. Med. 15 (2013) 226–228. [4] Hong-Dan Wang, Dong Wu, Zhan-Qi Feng, Zhi-An Jing, Tao Li, Qian-Nan Guo, Xian-Ping Zhang, Qiao-Fang Hou, Liang-Jie Guo, Bing Kang, Hui Zhang, Bo-Feng Zhu, S.-X. Liao, Genetic polymorphisms of 20 short tandem repeat loci from the Han population in Henan, China, Electrophoresis 35 (2014) 1509–1514. [5] Q. Huang, J.C. Escrina Lopez, C. Baeza, E. Arroyo-Pardo, A.M. Lopez-Parra, Genetic polymorphism of 15 STR loci in Chinese Han population from Shanghai municipality in East China, Forensic Sci. Int. Genet. 7 (2013) e31–e34. [6] J. Liu, L. Guo, R. Qi, S.-y. Li, J.-y. Yin, W. Zhang, Z. Sun, X. Tian, B. Gao, Allele frequencies of 19 autosomal STR loci in Manchu population of China with phylogenetic structure among worldwide populations, Gene 529 (2013) 282–287. [7] Z. Mao-xiu, H. Shu-yi, G. Hong-mei, S. Shan-hui, X. Dong-jie, L. Yang, W. Yun-shan, Genetic polymorphisms of 19 STR loci in Shandong Han population, J. Forensic Med. 06 (2013) 440–443, 446.
a
Feng Chena,b,* Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China b Vascular Biology Center, Georgia Regents University, Augusta, GA 30912, United States
*Corresponding authors at: Department of Forensic Medicine, Nanjing Medical University, 140 Hanzhong Road, Nanjing, Jiangsu 210029, China. Tel.: +86 25 86662896; fax: +86 25 86662896 E-mail addresses: [email protected] (Q. Ji). [email protected], [email protected] (F. Chen). 30 August 2014 Available online