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Dong B, Li Q, Zhang T, Liang X, Jia M, Fu Y, Bai J, Fu S. Population Genetic Polymorphism of Skeletal Muscle Strength Related Genes in Five Ethnic Minorities in North China. Front Genet 2021; 12:756802. [PMID: 34745225 PMCID: PMC8564566 DOI: 10.3389/fgene.2021.756802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Abstract
Musculoskeletal performance is a complex trait influenced by environmental and genetic factors, and it has different manifestations in different populations. Heilongjiang province, located in northern China, is a multi-ethnic region with human cultures dating back to the Paleolithic Age. The Daur, Hezhen, Ewenki, Mongolian and Manchu ethnic groups in Heilongjiang province may have strong physical fitness to a certain extent. Based on the genetic characteristics of significant correlation between some important genes and skeletal muscle function, this study selected 23 SNPs of skeletal muscle strength-related genes and analyzed the distribution of these loci and genetic diversity in the five ethnic groups. Use Haploview (version 4.1) software to calculate the chi-square and the Hardy-Weinberg equilibrium to assess the difference between the two ethnic groups. Use R (version 4.0.2) software to perform principal component analysis of different ethnic groups. Use MEGA (version 7.0) software to construct the phylogenetic tree of different ethnic groups. Use POPGENE (version 1.32) software to calculate the heterozygosity and the FST values of 23 SNPs. Use Arlequin (version 3.5.2.2) software to analyze molecular variance (AMOVA) among 31 populations. The results showed that there was haplotype diversity of VDR, angiotensin-converting enzyme, ACTN3, EPO and IGF1 genes in the five ethnic groups, and there were genetic differences in the distribution of these genes in the five ethnic groups. Among them, the average gene heterozygosity (AVE_HET) of the 23 SNPs in the five populations was 0.398. The FST values of the 23 SNPs among the five ethnic groups varied from 0.0011 to 0.0137. According to the principal component analysis, the genetic distance of Daur, Mongolian and Ewenki is relatively close. According to the phylogenetic tree, the five ethnic groups are clustered together with the Asian population. These data will enrich existing genetic information of ethnic minorities.
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Affiliation(s)
- Bonan Dong
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
| | - Qiuyan Li
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China.,Editorial Department of International Journal of Genetics, Harbin Medical University, Harbin, China
| | - Tingting Zhang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
| | - Xiao Liang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
| | - Mansha Jia
- Scientific Research Centre, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yansong Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
| | - Jing Bai
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
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Next generation sequencing of a set of ancestry-informative SNPs: ancestry assignment of three continental populations and estimating ancestry composition for Mongolians. Mol Genet Genomics 2020; 295:1027-1038. [PMID: 32206883 DOI: 10.1007/s00438-020-01660-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 02/27/2020] [Indexed: 12/31/2022]
Abstract
When traditional short tandem repeat profiling fails to provide valuable information to arrest the criminal, forensic ancestry inference of the biological samples left at the crime scene will probably offer investigative leads and facilitate the investigation process of the case. That is why there are consistent efforts in developing panels for ancestry inference in forensic science. Presently, a 30-plex next generation sequencing-based assay was exploited in this study by assembling well-differentiated single nucleotide polymorphisms for ancestry assignment of unknown individuals from three continental populations (African, European and East Asian). And meanwhile, relatively balanced population-specific differentiation values were maintained to avoid the over-estimation or under-estimation of co-ancestry proportions in individuals with admixed ancestry. The principal component analysis and STRUCTURE analysis of reference populations, test populations and the studied Mongolian group indicated that the novel assay was efficient enough to determine the ancestry origin of an unknown individual from the three continental populations. Besides, ancestry membership proportion estimations for the Mongolian group revealed that a large fraction of the ancestry was contributed by East Asian genetic component (approximately 83.9%), followed by European (approximately 12.6%) and African genetic components (approximately 3.5%), respectively. And next generation sequencing technology applied in this study offers possibility to incorporate more single nucleotide polymorphisms for individual identification and phenotype prediction into the same assay to provide as many as possible investigative clues in the future.
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Wei YY, Jin XY, Lan Q, Cui W, Chen C, Kong TT, Guo YX, Chen JG, Zhu BF. Genetic distribution and forensic evaluation of multiplex autosomal short tandem repeats in the Chinese Xinjiang Mongolian group. J Zhejiang Univ Sci B 2019; 20:287-290. [PMID: 30829016 DOI: 10.1631/jzus.b1800279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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.
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Affiliation(s)
- Yuan-Yuan Wei
- 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
| | - Xiao-Ye Jin
- 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.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Qiong Lan
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Wei Cui
- 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.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Chong Chen
- 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.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Ting-Ting Kong
- 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
| | - Yu-Xin Guo
- 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.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Jian-Gang Chen
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
| | - Bo-Feng Zhu
- 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.,Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
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Chen L, Guo Y, Xiao C, Wu W, Lan Q, Fang Y, Chen J, Zhu B. Genetic polymorphisms and forensic efficiency of 19 X-chromosomal STR loci for Xinjiang Mongolian population. PeerJ 2018; 6:e5117. [PMID: 30002965 PMCID: PMC6034600 DOI: 10.7717/peerj.5117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 06/05/2018] [Indexed: 01/10/2023] Open
Abstract
Aim X-chromosomal short tandem repeat (X-STR) loci are playing an increasingly important role in some complex kinship cases in recent years. To investigate the forensic efficiency of X-STRs of Mongolian minority group from Xinjiang Uygur Autonomous Region, China, and further depict the genetic relationship among Xinjiang Mongolians and other populations, 267 blood samples from unrelated healthy Xinjiang Mongolians were amplified by an AGCU X-19 STR kit. Results No deviations for all 19 X-STR loci were observed from the Hardy-Weinberg equilibrium after Bonferroni correction (p > 0.0026) in female samples. The most frequent allele was allele 10 at locus DXS10164 with the frequency 0.5663. The polymorphism information content values of the 19 X-STR loci were more than 0.5 with the highest polymorphism at the locus DXS10135. The cumulative power of discrimination were 0.99999999999999999999988761005481 in females and 0.999999999999903 in males, respectively; and the cumulative mean exclusion chances were 0.9999999969738068321121 in duos and 0.999999999998952 in trios, respectively. The seven linkage groups were extremely informative, with all the haplotype diversities greater than 0.9487. No linkage disequilibrium was observed for a significance level of 0.00029 (p = 0.05/171) after Bonferroni correction. The DA distances, multidimensional scaling plot and phylogenetic tree based on the 11 overlapping X-STR loci all presented that the Xinjiang Mongolian population was genetically different from other Asian populations, including the Mongolian population from Inner Mongolia Autonomous Region, China. Conclusion This study indicated that the 19 X-STR multiplex PCR system was of high utility value for both forensic practices and population genetic research in Xinjiang Mongolian group.
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Affiliation(s)
- Ling Chen
- Department of Forensic Biology, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Cheng Xiao
- Department of Forensic Biology, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Weibin Wu
- Department of Forensic Biology, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Qiong Lan
- Department of Forensic Biology, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Yating Fang
- Department of Forensic Biology, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Jiangang Chen
- Institute of Forensic Science, Ministry of Public Security, Beijing, China
| | - Bofeng Zhu
- Department of Forensic Biology, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China.,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
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Meng HT, Han JT, Zhang YD, Liu WJ, Wang TJ, Yan JW, Huang JF, Du WA, Guo JX, Wang HD, Zhang YH, Zhou RH, Zhu BF, Wei X. Diversity study of 12 X-chromosomal STR loci in Hui ethnic from China. Electrophoresis 2014; 35:2001-7. [PMID: 24723364 DOI: 10.1002/elps.201400045] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 02/27/2014] [Accepted: 04/01/2014] [Indexed: 11/05/2022]
Affiliation(s)
- Hao-Tian Meng
- Xi'an Jiaotong University; Health Science Center; Xi'an P. R. China***
| | - Jun-Tao Han
- Department of Burns and Cutaneous Surgery; Xijing Hospital, Fourth Military Medical University; Xi'an P. R. China
| | - Yu-Dang Zhang
- Xi'an Jiaotong University; Health Science Center; Xi'an P. R. China***
| | - Wen-Juan Liu
- Xi'an Jiaotong University; Health Science Center; Xi'an P. R. China***
| | - Tian-Ju Wang
- Blood Center of Shaanxi Province; Xi'an P. R. China
| | - Jiang-Wei Yan
- Beijing Institute of Genomics; Chinese Academy of Science; Beijing P. R. China
| | - Jing-Feng Huang
- Xi'an Jiaotong University; Health Science Center; Xi'an P. R. China***
| | - Wei-An Du
- Xi'an Jiaotong University; Health Science Center; Xi'an P. R. China***
| | - Jian-Xin Guo
- First Affiliated Hospital, School of Medicine; Xi'an Jiaotong University; Xi'an P. R. China
| | - Hong-Dan Wang
- Medical Genetic Institute of Henan Province; Henan Provincial People's Hospital, People's Hospital of Zhengzhou University; Zhengzhou P. R. China
| | - Yu-Hong Zhang
- Criminal Police Detachment of Nantong City Public Security Bureau; Nantong P. R. China
| | - Ru-Hua Zhou
- Criminal Police Detachment of Suzhou City Public Security Bureau; Suzhou P. R. China
| | - Bo-Feng Zhu
- Xi'an Jiaotong University; Health Science Center; Xi'an P. R. China***
| | - Xing Wei
- Department of Trauma Orthopedics; Xi'an Hong-hui Hospital; Xi'an P. R. China
- Department of Trauma Orthopedics; Hong-hui Hospital; Xi'an Jiaotong University College of Medicine; Xi'an P. R. China
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Silva F, Pereira R, Gusmão L, Santos C, Amorim A, Prata MJ, Bettencourt C, Lourenço P, Lima M. Genetic profiling of the Azores Islands (Portugal): data from 10 X-chromosome STRs. Am J Hum Biol 2009; 22:221-3. [PMID: 19593741 DOI: 10.1002/ajhb.20971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The populations from the Azores islands have been the target of several genetic studies, using data derived from monoparental and recombining genetic systems. These studies have provided a complex picture of the genetic landscape of the three groups of Azorean islands, and further data are required to assess its genetic profile. We present a study of the polymorphism in 10 X-chromosome STR loci (DSXS8378, DXS9898, DXS7133, GATA31E08, GATA172D05, DXS7423, DXS6809, DXS7132, DXS9902, DXS6789) conducted on a total of 304 chromosomes (97 females and 110 males) of unrelated individuals with Azorean ancestry. Average gene diversity was 74.47%, ranging from 66.21% (DXS7133) to 81.19% (GATA172D05). No shared haplotypes were found. Genotype frequencies among females displayed conformity with Hardy-Weinberg expectations for all loci. Pairwise linkage disequilibrium tests did not reveal evidences of association between the studied markers. Significant differences in allelic frequencies between the Western and the Eastern group of islands are in agreement with previous results from mitochondrial DNA and Y chromosome studies, providing further evidence that the Azores cannot be considered an homogeneous population. Moreover, differences between the Western group and the North of Portugal are also reported, supporting the pertinence of a specific database for the Azores populations, on what concerns the genetic markers analyzed.
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Affiliation(s)
- Francisca Silva
- Center for Research in Natural Resources, and Department of Biology, University of the Azores, Ponta Delgada, Portugal
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Chen YJ, Chen F, Xin N, Zhang HB, Zheng HB, Yu B, Li SB, Chen T. [Genetic polymorphisms of X-STR loci in Chinese Yugur ethnic group and its application]. YI CHUAN = HEREDITAS 2008; 30:1143-52. [PMID: 18779171 DOI: 10.3724/sp.j.1005.2008.01143] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
To study the genetic polymorphism of nine short tandem repeats (STRs) loci (DXS7130, DXS7132, DXS6804, DXS7423, DXS7424, DXS6789, DXS6799, DXS8378, and HPRTB) on X chromosome in Chinese Yugur ethnic group. The allele and genotype frequency of nine X-STR loci among 120 unrelated individuals (55 female, 65 male) from Yugur ethnic group were analyzed using PCR and followed by polyacrylamide gel electrophoresis and silver staining. The numbers of alleles in the nine X-STR loci were 8, 6, 6, 5, 6, 7, 6, 4, and 6, respectively; the numbers of genotypes in the nine loci were 16, 14, 13, 6, 13, 20, 11, 6, and 12, respectively. The genotype frequencies in females were in accordance with Hardy-Weinberg equilibrium (P>0.05). The nine X-STR loci were relatively abundant in polymorphic information for individual identification, paternity testing and population genetics. A total of 15 haplotypes were detected in DXS7130 and DXS8378 loci, and 55 haplotypes were detected in DXS6789, DXS6799, DXS7424, and DXS6804 loci. The haplotype diversity reached 0.8212 and 0.9947, respectively. Phylogeny tree and cluster analysis based on X-STR allele frequencies in genesis showed that Yugur ethnic group share a close relationship with Mongolian ethnic group and Chinese Han, Tibetan population and far from Hui and Uygur ethnic group, who dwell in the northwest of China.
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Affiliation(s)
- Yan-Jiong Chen
- Department of Immunology and Pathogenic Biology, Xi'an Jiaotong University School of Medicine, Xi'an 710061, China.
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