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Sequeira JJ, Panda M, Dixit S, Kumawat R, Mustak MS, Sharma AN, Chaubey G, Shrivastava P. Forensic Characterization, Genomic Variability and Ancestry Analysis of Six Populations from Odisha Using mtDNA SNPs and Autosomal STRs. Biochem Genet 2024:10.1007/s10528-024-10887-2. [PMID: 39039324 DOI: 10.1007/s10528-024-10887-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 07/14/2024] [Indexed: 07/24/2024]
Abstract
Located on India's eastern coast, Odisha is known for its diverse tribes and castes. In the early days of genome sequencing technology, researchers primarily studied the Austroasiatic communities inhabiting this region to reconstruct the ancient origins and dispersal of this broad linguistic group. However, current research has shifted towards identifying population and individual-specific genome variation for forensic applications. This study aims to analyze the forensic efficiency and ancestry of six populations from Odisha. We assessed the SF mtDNA-SNP60™ PCR Amplification Kit by comparing it with PowerPlex® Fusion 6C System, a widely used autosomal STR (aSTR) kit, in an Indian cohort. Although the mtDNA SNP kit showed low discriminating power for individuals of a diverse population, it could identify deep lineage divergence. Also, we utilized mitochondrial and autosomal variation information to analyze the ancestry of six endogamous ethnic groups in Odisha. We observe two extremities-populations with higher West Asian affinity and those with East Asian affinity. This observation is in congruence with the existing information of their tribal and non-tribal affiliation. When compared with neighbouring populations from Central and Eastern India, multivariate analysis showed that the Brahmins clustered separately or with the Gopala, Kaibarta appeared as an intermediate, Pana and Kandha clustered with the Gonds, and Savara with the Munda tribes. Our findings indicate significant deep lineage stratification in the ethnic populations of Odisha and a gene flow from West and East Asia. The artefacts of unique deep lineage in such a diverse population will help in improving forensic identification. In addition, we conclude that the SF mtDNA-SNP60 PCR Amplification Kit may be used only as a supplementary tool for forensic analysis.
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Affiliation(s)
- Jaison Jeevan Sequeira
- Department of Applied Zoology, Mangalore University, Mangalagangothri, Mangalore, 574199, India
| | - Muktikanta Panda
- Department of Anthropology, Model Degree College, Malkangiri, Odisha, 764045, India
- Department of Anthropology, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar, Madhya Pradesh, 470003, India
| | - Shivani Dixit
- DNA Division, Central Forensic Science Laboratory, Chandigarh, 160036, India
| | - Ramkishan Kumawat
- DNA Division, State Forensic Science Laboratory, Jaipur, Rajasthan, India
| | - Mohammed S Mustak
- Department of Applied Zoology, Mangalore University, Mangalagangothri, Mangalore, 574199, India
| | - Awdhesh Narayan Sharma
- Department of Anthropology, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar, Madhya Pradesh, 470003, India
| | - Gyaneshwer Chaubey
- DNA Division, Central Forensic Science Laboratory, Chandigarh, 160036, India
- Department of Zoology, Banaras Hindu University (BHU), Varanasi, India
| | - Pankaj Shrivastava
- Department of Anthropology, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar, Madhya Pradesh, 470003, India.
- Regional Forensic Science Laboratory, Government of MP, Gwalior, Madhya Pradesh, India.
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Liu Y, Ye Y, Yi XQ, Zhang JH, Fan GY, Hao DY. Phylogenetic analyses of the 19 STR loci in X chromosome revealed discriminant forensic characteristics for Chinese Daur and Oroqen minorities. Int J Legal Med 2021; 136:551-553. [PMID: 34510269 DOI: 10.1007/s00414-021-02697-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/27/2021] [Indexed: 10/20/2022]
Abstract
In respect of forensic genetics, X-STRs are widely applied for deficiency paternity cases. Given the popularization of AGCU-X19 STR Kit in China, there has been investigation conducted into the genetic data and forensic parameters of 19 X-STR loci in many of the Chinese ethnic groups, which makes it possible to perform nationwide phylogenetic comparation. To evaluate the allele and haplotype diversity of 19 X-STR loci and to explore their forensic efficiency in the Daur and Oroqen minorities, unrelated healthy Daur (n = 86) and Oroqen (n = 165) individuals were recruited from Heilongjiang province, so as to reveal the phylogenetic relationship between the two minorities and other Chinese ethnic groups. Of the Daur and Oroqen minorities, 172 and 183 alleles at the 19 X-STR loci were observed, respectively. Haplotype diversity exceeded 0.9 among all the linkage clusters. High cumulative value was observed for the power of discrimination, the probability of exclusion, and the mean exclusion chance for deficiency cases (normal trios and duo cases). As revealed by this study, the panel of 19 X-STR loci is an effective supplementary tool for the kinship test of the studied nationalities.
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Affiliation(s)
- Yang Liu
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, 150025, Heilongjiang, China.,Forensic Center, College of Medicine, Shaoxing University, No. 508 Huancheng West Road, Shaoxing, 312000, Zhejiang, China
| | - Yi Ye
- Department of Forensic Toxicological Analysis, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xiao-Qin Yi
- Department of Forensic Toxicological Analysis, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jia-Hui Zhang
- College of Medicine, Shaoxing University, No. 508 Huancheng West Road, Shaoxing, 312000, Zhejiang, China
| | - Guang-Yao Fan
- Forensic Center, College of Medicine, Shaoxing University, No. 508 Huancheng West Road, Shaoxing, 312000, Zhejiang, China.
| | - Dong-Yun Hao
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, 150025, Heilongjiang, China.
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Cui W, Jin X, Guo Y, Chen C, Zhang W, Kong T, Wang Y, Huang J, Zhu B. Forensic applicability of autosomal insertion/deletion loci in Chinese Daur ethnic group and genetic affinity evaluations between Daur group and reference populations. Leg Med (Tokyo) 2020; 47:101741. [PMID: 32682294 DOI: 10.1016/j.legalmed.2020.101741] [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: 06/27/2019] [Revised: 04/01/2020] [Accepted: 06/26/2020] [Indexed: 12/25/2022]
Abstract
In present study, we evaluated the genetic diversities of 30 insertion/deletion (InDel) loci and analyzed the genetic relationships between Daur and other comparison populations. In the studied Daur group, any two InDel loci showed no linkage disequilibrium, and all loci showed no deviations from exact tests of Hardy-Weinberg equilibrium. Insertion allele frequencies at 30 InDel loci ranged from 0.1459 (HLD39) to 0.8774 (HLD118). The observed heterozygosity and expected heterozygosity values were ranged from 0.1984 (HLD118) to 0.5564 (HLD6) and 0.2155 (HLD118) to 0.5000 (HLD92 and HLD6), respectively. The combined power of discrimination and power of exclusion values were 0.999999999993428 and 0.9878, respectively, which indicated that this panel of 30 InDels could be used for individual identifications in Daur group. Population genetic analyses including pairwise fixation index, STRUCTURE analysis, principal component analysis, genetic distance, multidimensional scaling analysis and phylogenetic analysis demonstrated that the Daur group had the closer genetic relationships with the groups from western China in comparison with other continental populations.
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Affiliation(s)
- 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
| | - Xiaoye 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
| | - Yuxin 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
| | - 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
| | - Wenqing Zhang
- 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
| | - Tingting 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
| | - Yijie Wang
- 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
| | - Jingfeng Huang
- College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Bofeng 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; Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics; School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China.
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Joint Genetic Analyses of Mitochondrial and Y-Chromosome Molecular Markers for a Population from Northwest China. Genes (Basel) 2020; 11:genes11050564. [PMID: 32443545 PMCID: PMC7290686 DOI: 10.3390/genes11050564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 12/27/2022] Open
Abstract
The genetic markers on mitochondria DNA (mtDNA) and Y-chromosome can be applied as a powerful tool in population genetics. We present a study to reveal the genetic background of Kyrgyz group, a Chinese ethnic group living in northwest China, and genetic polymorphisms of 60 loci on maternal inherited mtDNA and 24 loci on paternal inherited Y-chromosome short tandem repeats (Y-STRs) were investigated. The relationship between the two systems was tested, and the result indicated that they were statistically independent from each other. The genetic distances between Kyrgyz group and 11 reference populations for mtDNA, and 13 reference populations for Y-STRs were also calculated, respectively. The present results demonstrated that the Kyrgyz group was genetically closer to East Asian populations than European populations based on the mtDNA loci but the other way around for the Y-STRs. The genetic analyses could largely strengthen the understanding for the genetic background of the Kyrgyz group.
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Wei YY, Ren ZP, Jin XY, Cui W, Chen C, Guo YX, Meng HT, Zhu BF. Haplogroup Structure and Genetic Variation Analyses of 60 Mitochondrial DNA Markers in Southern Shaanxi Han Population. Biochem Genet 2019; 58:279-293. [PMID: 31696339 DOI: 10.1007/s10528-019-09942-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 10/24/2019] [Indexed: 12/30/2022]
Abstract
Mitochondrial DNA (mtDNA) has been widely employed as one tool for the studies of human migration and phylogenetic evolution owing to the characteristics of its lack of recombination and matrilineal inheritance. In this study, we analyze genetic distributions of 60 mtDNA markers in 126 unrelated individuals of Southern Shaanxi Han population and classify their haplogroups. Genetic distribution comparisons between Southern Shaanxi Han and other populations from different continents are conducted based on the same mtDNA markers. The majority of 60 mtDNA markers are polymorphic in Southern Shaanxi Han population. The most common haplogroups observed in Southern Shaanxi Han population are B5, followed by D5, A, D4e, and N9a1'3. Obtained matching probability for these 60 mtDNA markers indicates that the panel could be used as a valuable tool in forensic caseworks. Results of genetic distances (Fst) and multidimensional scaling analysis show that Southern Shaanxi Han population has relatively close genetic relationships with other Han populations in different regions. In conclusion, the panel comprising 60 mtDNA markers could be utilized for forensic applications in Southern Shaanxi Han population.
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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, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Zhan-Ping Ren
- Department of Cranio-Maxillofacial Trauma Plastic Surgery, Stomatology Hospital of Xi'an Jiaotong University College of Medicine, Xi'an, China
| | - Xiao-Ye Jin
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Wei Cui
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Chong Chen
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Yu-Xin Guo
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Hao-Tian Meng
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Bo-Feng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China. .,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China. .,Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China.
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Xie T, Hu L, Guo YX, Li YC, Chen F, Zhu BF. Genetic polymorphism analysis of mitochondrial DNA from Chinese Xinjiang Kazak ethnic group by a novel mitochondrial DNA genotyping panel. Mol Biol Rep 2018; 46:17-25. [DOI: 10.1007/s11033-018-4375-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/10/2018] [Indexed: 11/24/2022]
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