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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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Jia M, Li Q, Zhang T, Dong B, Liang X, Fu S, Yu J. Genetic Diversity Analysis of the Chinese Daur Ethnic Group in Heilongjiang Province by Complete Mitochondrial Genome Sequencing. Front Genet 2022; 13:919063. [PMID: 35801081 PMCID: PMC9253502 DOI: 10.3389/fgene.2022.919063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/12/2022] [Indexed: 11/30/2022] Open
Abstract
Mitochondrial DNA (mtDNA) has the characteristics of maternal inheritance, high mutation rate, high copy number, and no recombination. As the most powerful tool for studying the origin and evolution of modern humans, mtDNA has great significance in the research of population genetics and evolutionary genetics. Here, we provide new insights into the maternal genetic history of the Daur ethnic group by generating complete mitochondrial genomes from a total of 146 Daur individuals in China. We also collected the published complete mitochondrial genome sequences of 5,094 individuals from 56 worldwide populations as reference data to further explore the matrilineal genetic landscape of the Daur ethnic group. First, the haplotype diversity was 0.9943 ± 0.0019 and nucleotide diversity was 0.0428 ± 0.0210. The neutrality tests of the Daur group showed significant negative values and the mismatch distribution curve was obviously distributed in a unimodal pattern. The results showed that the Daur ethnic group has high genetic diversity and may have experienced recent population expansion. In addition, the main haplogroups of the Daur population were haplogroup D (31.51%), M* (20.55%), C (10.28%), F (7.53%), and B (6.85%), all of which were prevalent in northern China. It probably implies the northern Chinese origin of the Daur population. The PCA, FST, and phylogenetic analysis results indicated that the Daur group formed a cluster with East Asian populations, and had few genetic differences with the populations in northern China. More importantly, we found that disease-related mutation sites of the mitochondrial genome may be related to ethnic groups, which may have important implications for the prevention and occurrence of specific diseases. Overall, this study revealed the complexity and diversity of the matrilineal genetic background of the Daur ethnic group. Meanwhile, it provided meaningful data for the research on the diversity of the human genome.
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Affiliation(s)
- Mansha Jia
- Scientific Research Centre, The Second Affiliated Hospital of Harbin Medical University, 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
| | - 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
| | - 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
| | - 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
- *Correspondence: Songbin Fu, ; Jingcui Yu,
| | - Jingcui Yu
- Scientific Research Centre, The Second Affiliated Hospital of 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
- *Correspondence: Songbin Fu, ; Jingcui Yu,
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Xu H, Zhao C, Lan Q, Li S, Liu Y, Mei S, Fang Y, Zhu B. Forensic features and genetic structure revealed by 47 Individual Identification InDels in the Shaanxi Han population. Leg Med (Tokyo) 2022; 56:102030. [DOI: 10.1016/j.legalmed.2022.102030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 12/21/2021] [Accepted: 01/25/2022] [Indexed: 10/19/2022]
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Liu Y, Jin X, Lan Q, Zhao C, Xu H, Xie T, Lan J, Tai Y, Zhu B. Forensic characteristic and population structure dissection of Shaanxi Han population in the light of diallelic deletion/insertion polymorphism data. Genomics 2020; 112:3837-3845. [PMID: 32574833 DOI: 10.1016/j.ygeno.2020.06.028] [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: 05/11/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 12/08/2022]
Abstract
The genetic polymorphisms of diallelic deletion/insertion polymorphic (DIP) loci in the Shaanxi Han population are still not clearly characterized. Herein, allele frequencies and forensic application efficiencies for 30 diallelic DIP loci were investigated in 506 unrelated healthy Han individuals from Chinese Shaanxi province. Based on population data of the same 30 diallelic DIP loci, the genetic differentiations, hierarchical clustering relationships and population architectures among Shaanxi Han and other 50 populations were further dissected through genetic and bioinformatics analyses. Results indicated that most of the 30 diallelic DIP loci were relatively high polymorphisms in the Shaanxi Han population; and there were the genetically intimate relationships between Shaanxi Han and the East Asian populations. In summary, this study provided significant insights into genetic background of Shaanxi Han population, and the multiplex amplification of these 30 diallelic DIP loci was appropriate for forensic individual identification and population genetic research in Shaanxi Han population.
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Affiliation(s)
- Yanfang Liu
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 710004 Xi'an, China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, 710004, Xi'an, China; College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China
| | - Qiong Lan
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Congying Zhao
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Hui Xu
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Tong Xie
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Jiangwei Lan
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Yunchun Tai
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Bofeng Zhu
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 710004 Xi'an, China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, 710004, Xi'an, China.
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