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Genetic profile of 23 Y chromosomal STR loci in Guizhou Shui population, southwest China
Accepted Manuscript Title: Genetic profile of 23 Y chromosomal STR loci in Guizhou Shui population, southwest China Authors: Jingyan Ji, Zheng Ren, Hongling Zhang, Qiyan Wang, Jie Wang PII: DOI: Reference:
S1872-4973(17)30019-4 http://dx.doi.org/doi:10.1016/j.fsigen.2017.01.010 FSIGEN 1647
To appear in:
Forensic Science International: Genetics
Authors: Zhiming Kong, Chunmei Xu, Mi Tian PII: DOI: Reference:
S1872-4973(17)30019-4 http://dx.doi.org/doi:10.1016/j.fsigen.2017.01.010 FSIGEN 1647
To appear in:
Forensic Science International: Genetics
Author: Jiang Huang PII: DOI: Reference:
S1872-4973(17)30019-4 http://dx.doi.org/doi:10.1016/j.fsigen.2017.01.010 FSIGEN 1647
To appear in:
Forensic Science International: Genetics
Received date:
15-11-2016
Please cite this article as: Jiang Huang, Genetic profile of 23 Y chromosomal STR loci in Guizhou Shui population, southwest China, Forensic Science International: Genetics http://dx.doi.org/10.1016/j.fsigen.2017.01.010 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Genetic profile of 23 Y chromosomal STR loci in Guizhou Shui population, southwest China Jingyan Jia,1, Zheng Rena,1, Hongling Zhanga, Qiyan Wanga, Jie Wanga, Zhiming Kongb, Chunmei Xub, Mi Tianb, Jiang Huanga,* aDepartment
of Forensic Genetics, Guizhou medical university, Guiyang 550004, Guizhou, China. Public Security Bureau, QIanNan Buyi and Miao Autonomous Prefecture, Duyun 558800, Guizhou, China. b
1The
two authors contributed equally to the work.
*Corresponding authors at: Department of Forensic Medicine, Guizhou Medical University, Beijing Road, 9th, Guiyang 550004, Guizhou Province, P.R. China. E-mail address: [email protected]
Dear Editor, China is a multi-ethnic country, while Guizhou is an ethnic-diverse province in China that has 49 ethnicities. There are approximately 407,000 people of Shui in total, and more than 90% of them live in Guizhou, accounting for one percent of the total population in Guizhou. Although the Shui population of Guizhou may involve in some gene exchanges with other ethnic groups, they may still have genetic differences compared to other minorities living in the same region. Unfortunately, no such population data concerning the Guizhou Shui have been reported. Due to lack of Y-chromosomal STR data for the Guizhou Shui population, it was our aim for this study to determine haplotype distribution of 23 Y-STRs in Guizhou Shui. Blood samples were obtained from 200 apparently unrelated blood donors from the Shui population living in Guizhou province, southwest China. All participants gave their informed consent in writing after we explained the aims and procedures of this study. DNA was extracted from blood samples collected on FTA cards (Changchun Bokun Biotech CO., Ltd, China) according to the Chelex-100 protocol. PCR was used to amplify 23 Y chromosomal STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a, DYS385b, DYS438, DYS439, DYS437, DYS448, DYS456, DYS458, DYS635, YGATAH4, DYS576, DYS481, DYS549, DYS533, DYS570, and DYS643) using the PowerPlex® Y23 System kit (Promega, USA) on a GeneAmp PCR System 9700 (Thermo Fisher, USA). The fragments were separated using a 3500 Series Genetic Analyzer (Thermo Fisher, USA) and genotyped according to Genemapper ID-X software. The nomenclature used was that of the International Society of Forensic Genetics [1]. Haplotype frequencies were calculated by direct counting. Haplotype diversity was estimated based on the Nei formula [2]. Pairwise genetic distances (Rst) between the Guizhou Shui population and Beijing Han [3], Shanghai Han [4-5], Cangzhou Hui (from YHRD), Liaoning Manchu [6-7], Inner Mongolia Mongolian [8-10], Tibet Tibetan [9], Guangxi Zhuang [11], Tsukuba Japanese (from YHRD), Seoul Korean [12] submitted to Y-STR haplotype reference database (YHRD, http://www.yhrd.org) were estimated in YHRD, and a multidimensional scaling (MDS) plot was generated using IBM SPSS Statistics 23 software. A total of 173 haplotypes were observed among the 200 Shui individuals, with 154 being unique; there were twelve shared by two individuals, six shared among three individuals and one was shared among four individuals. The haplotype frequencies were shown in Table S1, and the haplotype diversity was calculated to be 0.9993. We found that some haplotype were shared among the samples, which was not surprising given that the Shui were concentrated in Guizhou province. So there may be some blood relation among these samples. The pairwise Rst values and associated P values calculated by 23 Y-STRs between the Guizhou Shui and other nine populations and associated P values were listed in Table S2 (Supplementary information). The genetic distances were statistically significant between Shui and other populations (p=0.0000). As demonstrated in the MDS plot (Figure S1, Supplementary information), the Guizhou Shui was relatively isolated from other populations. Guizhou Shui population lived mainly in the Sandu County which located in the southeast part of Guizhou. Due to their unique ethnic language and culture, they were not willing to intermarry with other ethnic groups, such as Han, settling in Sandu County as well. This might be the reason why Guizhou Shui showed far genetic distance from the other populations. In addition, Tibet Tibetan was also relatively isolated from other populations, which was consistent with the results of Ou et al. [9]. It can be seen from the MDS that the points pertaining to Beijing Han, Shanghai Han and
Liaoning Manchu were very close. This was consistent with the results of Bai et al. [6]. However, they were all far from Guizhou Shui, which suggested that the former three ethnic groups were genetically different from Guizhou Shui. In conclusion, the PowerPlex® Y23 System provided substantially strong discriminatory power in the Shui population in Guizhou. And our study reported the haplotype distributions and forensic parameters. This study strictly followed the International Society for Forensic Genetics (ISFG) recommendations [1] and guidelines for publication of population data, as requested by the journal [14]. Our data have been submitted to YHRD and were assigned the following accession number: YA004224.
Acknowledgments This study was supported by grants from the Guizhou University Engineering Technology Research Center Project (Qian Science KY NO. [2013]114), the Guizhou Education Department Industry University Research Base Project (Qian Education KY NO. [2013]114), the Guizhou Medical University Doctor Foundation (QianJ-2014-PHD-032), the Guizhou Education Department Young Scientific and Technical Talents Project (Qian Education KY NO. [2016]144) and National Natural Science Foundation (No. 81601650).
References [1] L. Gusmao, J.M. Butler, A. Carracedo, P. Gill, M. Kayser, W.R. Mayr, N. Morling, M. Prinz, L.Roewer, C. Tyler-Smith, P.M. Schneider, DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis, Int. J. Legal Med. 120 (2006) 191-200. [2] M. Nei, Molecular Evolutionary Genetics, Columbia University Press, New York, 1987, pp. 176-179. [3] K.D. Kwak, H.J. Jin, D.J. Shin, J.M. Kim, L. Roewer, M. Krawczak, C. Tyler Smith, W. Kim, Y-chromosomal STR haplotypes and their applications to forensic and population studies in east Asia, Int. J. Legal Med. 119(4) (2005) 195-201. [4] L. Li, G. Yu, S. Li, L. Jin., S. Yan, Genetic analysis of 17 Y-STR loci from 1019 individuals of six Han populations in East China, Forensic Sci. Int. Genet. 20 (2016) 101-102. [5] S. Zhang, H. Tian, Z. Wang, S. Zhao, A.Z Hu, C. Li, C. Ji, Development of a new 26plex Y-STRs typing system for forensic application, Forensic Sci. Int. Genet. 13 (2014) 112-120. [6] R. Bai, Y. Liu, X. Lv, M. Shi, S. Ma, Genetic polymorphisms of 17 Y chromosomal STRs in She and Manchu ethnic populations from China, Forensic Sci. Int. Genet. 22 (2016) e12-e14. [7] J. He, F. Guo, Population genetics of 17 Y-STR loci in Chinese Manchu population from Liaoning Province, Northeast China, Forensic Sci. Int. Genet. 7 (3) e84-e85. [8] X. Fu, Y. Fu, Y. Liu, J. Guo, Y. Liu, Y. Guo, J. Yan, J. Cai, J. Liu, L. Zha, Genetic polymorphisms of 26 Y-STR loci in the Mongolian minority from Horqin district, China, International Journal of Legal Medicine 130 (4) (2016) 941-946. [9] X. Ou, Y. Wang, C. Liu, D. Yan, C. Zhang, S. Deng, H. Sun, Haplotype analysis of the polymorphic 40 Y-STR markers in Chinese populations, Forensic Sci. Int. Genet. 19 (2015) 255-262. [10] B. Zhu, X. Li, Z. Wang, H. Wu, Y. He, J. Zhao, Y. Liu, Y-STRs haplotypes of Chinese Mongol ethnic group using Y-PLEX 12, Forensic Sci. Int. 153 (2-3) (2005) 260-263. [11] H. Luo, F. Song, L. Zhang, Y. Hou, Genetic polymorphism of 23 Y-STR loci in the Zhuang minority population in Guangxi of China, International Journal of Legal Medicine 4 (2015) 737-738. [12] M.J. Park, H.Y. Lee, J.E. Yoo, U. Chung, S.Y. Lee, K.J. Shin, Forensic evaluation and haplotypes of 19 Y-chromosomal STR loci in Koreans, Forensic Sci. Int. 152 (2-3) (2005) 133-147. [13] H. Zhou, Z. Ren, H. Zhang, J. Wang, J. Huang, Genetic profile of 17 Y chromosome STRs in the Guizhou Han population of southwestern China, Forensic Sci. Int. Genet. 25 (2016) e6-e7. [14] 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.
S1872-4973(17)30019-4 http://dx.doi.org/doi:10.1016/j.fsigen.2017.01.010 FSIGEN 1647
To appear in:
Forensic Science International: Genetics
Authors: Zhiming Kong, Chunmei Xu, Mi Tian PII: DOI: Reference:
S1872-4973(17)30019-4 http://dx.doi.org/doi:10.1016/j.fsigen.2017.01.010 FSIGEN 1647
To appear in:
Forensic Science International: Genetics
Author: Jiang Huang PII: DOI: Reference:
S1872-4973(17)30019-4 http://dx.doi.org/doi:10.1016/j.fsigen.2017.01.010 FSIGEN 1647
To appear in:
Forensic Science International: Genetics
Received date:
15-11-2016
Please cite this article as: Jiang Huang, Genetic profile of 23 Y chromosomal STR loci in Guizhou Shui population, southwest China, Forensic Science International: Genetics http://dx.doi.org/10.1016/j.fsigen.2017.01.010 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Genetic profile of 23 Y chromosomal STR loci in Guizhou Shui population, southwest China Jingyan Jia,1, Zheng Rena,1, Hongling Zhanga, Qiyan Wanga, Jie Wanga, Zhiming Kongb, Chunmei Xub, Mi Tianb, Jiang Huanga,* aDepartment
of Forensic Genetics, Guizhou medical university, Guiyang 550004, Guizhou, China. Public Security Bureau, QIanNan Buyi and Miao Autonomous Prefecture, Duyun 558800, Guizhou, China. b
1The
two authors contributed equally to the work.
*Corresponding authors at: Department of Forensic Medicine, Guizhou Medical University, Beijing Road, 9th, Guiyang 550004, Guizhou Province, P.R. China. E-mail address: [email protected]
Dear Editor, China is a multi-ethnic country, while Guizhou is an ethnic-diverse province in China that has 49 ethnicities. There are approximately 407,000 people of Shui in total, and more than 90% of them live in Guizhou, accounting for one percent of the total population in Guizhou. Although the Shui population of Guizhou may involve in some gene exchanges with other ethnic groups, they may still have genetic differences compared to other minorities living in the same region. Unfortunately, no such population data concerning the Guizhou Shui have been reported. Due to lack of Y-chromosomal STR data for the Guizhou Shui population, it was our aim for this study to determine haplotype distribution of 23 Y-STRs in Guizhou Shui. Blood samples were obtained from 200 apparently unrelated blood donors from the Shui population living in Guizhou province, southwest China. All participants gave their informed consent in writing after we explained the aims and procedures of this study. DNA was extracted from blood samples collected on FTA cards (Changchun Bokun Biotech CO., Ltd, China) according to the Chelex-100 protocol. PCR was used to amplify 23 Y chromosomal STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a, DYS385b, DYS438, DYS439, DYS437, DYS448, DYS456, DYS458, DYS635, YGATAH4, DYS576, DYS481, DYS549, DYS533, DYS570, and DYS643) using the PowerPlex® Y23 System kit (Promega, USA) on a GeneAmp PCR System 9700 (Thermo Fisher, USA). The fragments were separated using a 3500 Series Genetic Analyzer (Thermo Fisher, USA) and genotyped according to Genemapper ID-X software. The nomenclature used was that of the International Society of Forensic Genetics [1]. Haplotype frequencies were calculated by direct counting. Haplotype diversity was estimated based on the Nei formula [2]. Pairwise genetic distances (Rst) between the Guizhou Shui population and Beijing Han [3], Shanghai Han [4-5], Cangzhou Hui (from YHRD), Liaoning Manchu [6-7], Inner Mongolia Mongolian [8-10], Tibet Tibetan [9], Guangxi Zhuang [11], Tsukuba Japanese (from YHRD), Seoul Korean [12] submitted to Y-STR haplotype reference database (YHRD, http://www.yhrd.org) were estimated in YHRD, and a multidimensional scaling (MDS) plot was generated using IBM SPSS Statistics 23 software. A total of 173 haplotypes were observed among the 200 Shui individuals, with 154 being unique; there were twelve shared by two individuals, six shared among three individuals and one was shared among four individuals. The haplotype frequencies were shown in Table S1, and the haplotype diversity was calculated to be 0.9993. We found that some haplotype were shared among the samples, which was not surprising given that the Shui were concentrated in Guizhou province. So there may be some blood relation among these samples. The pairwise Rst values and associated P values calculated by 23 Y-STRs between the Guizhou Shui and other nine populations and associated P values were listed in Table S2 (Supplementary information). The genetic distances were statistically significant between Shui and other populations (p=0.0000). As demonstrated in the MDS plot (Figure S1, Supplementary information), the Guizhou Shui was relatively isolated from other populations. Guizhou Shui population lived mainly in the Sandu County which located in the southeast part of Guizhou. Due to their unique ethnic language and culture, they were not willing to intermarry with other ethnic groups, such as Han, settling in Sandu County as well. This might be the reason why Guizhou Shui showed far genetic distance from the other populations. In addition, Tibet Tibetan was also relatively isolated from other populations, which was consistent with the results of Ou et al. [9]. It can be seen from the MDS that the points pertaining to Beijing Han, Shanghai Han and
Liaoning Manchu were very close. This was consistent with the results of Bai et al. [6]. However, they were all far from Guizhou Shui, which suggested that the former three ethnic groups were genetically different from Guizhou Shui. In conclusion, the PowerPlex® Y23 System provided substantially strong discriminatory power in the Shui population in Guizhou. And our study reported the haplotype distributions and forensic parameters. This study strictly followed the International Society for Forensic Genetics (ISFG) recommendations [1] and guidelines for publication of population data, as requested by the journal [14]. Our data have been submitted to YHRD and were assigned the following accession number: YA004224.
Acknowledgments This study was supported by grants from the Guizhou University Engineering Technology Research Center Project (Qian Science KY NO. [2013]114), the Guizhou Education Department Industry University Research Base Project (Qian Education KY NO. [2013]114), the Guizhou Medical University Doctor Foundation (QianJ-2014-PHD-032), the Guizhou Education Department Young Scientific and Technical Talents Project (Qian Education KY NO. [2016]144) and National Natural Science Foundation (No. 81601650).
References [1] L. Gusmao, J.M. Butler, A. Carracedo, P. Gill, M. Kayser, W.R. Mayr, N. Morling, M. Prinz, L.Roewer, C. Tyler-Smith, P.M. Schneider, DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis, Int. J. Legal Med. 120 (2006) 191-200. [2] M. Nei, Molecular Evolutionary Genetics, Columbia University Press, New York, 1987, pp. 176-179. [3] K.D. Kwak, H.J. Jin, D.J. Shin, J.M. Kim, L. Roewer, M. Krawczak, C. Tyler Smith, W. Kim, Y-chromosomal STR haplotypes and their applications to forensic and population studies in east Asia, Int. J. Legal Med. 119(4) (2005) 195-201. [4] L. Li, G. Yu, S. Li, L. Jin., S. Yan, Genetic analysis of 17 Y-STR loci from 1019 individuals of six Han populations in East China, Forensic Sci. Int. Genet. 20 (2016) 101-102. [5] S. Zhang, H. Tian, Z. Wang, S. Zhao, A.Z Hu, C. Li, C. Ji, Development of a new 26plex Y-STRs typing system for forensic application, Forensic Sci. Int. Genet. 13 (2014) 112-120. [6] R. Bai, Y. Liu, X. Lv, M. Shi, S. Ma, Genetic polymorphisms of 17 Y chromosomal STRs in She and Manchu ethnic populations from China, Forensic Sci. Int. Genet. 22 (2016) e12-e14. [7] J. He, F. Guo, Population genetics of 17 Y-STR loci in Chinese Manchu population from Liaoning Province, Northeast China, Forensic Sci. Int. Genet. 7 (3) e84-e85. [8] X. Fu, Y. Fu, Y. Liu, J. Guo, Y. Liu, Y. Guo, J. Yan, J. Cai, J. Liu, L. Zha, Genetic polymorphisms of 26 Y-STR loci in the Mongolian minority from Horqin district, China, International Journal of Legal Medicine 130 (4) (2016) 941-946. [9] X. Ou, Y. Wang, C. Liu, D. Yan, C. Zhang, S. Deng, H. Sun, Haplotype analysis of the polymorphic 40 Y-STR markers in Chinese populations, Forensic Sci. Int. Genet. 19 (2015) 255-262. [10] B. Zhu, X. Li, Z. Wang, H. Wu, Y. He, J. Zhao, Y. Liu, Y-STRs haplotypes of Chinese Mongol ethnic group using Y-PLEX 12, Forensic Sci. Int. 153 (2-3) (2005) 260-263. [11] H. Luo, F. Song, L. Zhang, Y. Hou, Genetic polymorphism of 23 Y-STR loci in the Zhuang minority population in Guangxi of China, International Journal of Legal Medicine 4 (2015) 737-738. [12] M.J. Park, H.Y. Lee, J.E. Yoo, U. Chung, S.Y. Lee, K.J. Shin, Forensic evaluation and haplotypes of 19 Y-chromosomal STR loci in Koreans, Forensic Sci. Int. 152 (2-3) (2005) 133-147. [13] H. Zhou, Z. Ren, H. Zhang, J. Wang, J. Huang, Genetic profile of 17 Y chromosome STRs in the Guizhou Han population of southwestern China, Forensic Sci. Int. Genet. 25 (2016) e6-e7. [14] 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.