1
|
He Y, Lei C, Wan C, Zeng S, Zhang T, Luo F, Li R, Li X, Zhao A, Xiao D, Luo Y, Shan K, Qi X, Jin X. A comprehensive whole genome database of ethnic minority populations. Sci Rep 2024; 14:13954. [PMID: 38886537 PMCID: PMC11183174 DOI: 10.1038/s41598-024-63892-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 06/03/2024] [Indexed: 06/20/2024] Open
Abstract
China, is characterized by its remarkable ethnical diversity, which necessitates whole genome variation data from multiple populations as crucial tools for advancing population genetics and precision medical research. However, there has been a scarcity of research concentrating on the whole genome of ethnic minority groups. To fill this gap, we developed the Guizhou Multi-ethnic Genome Database (GMGD). It comprises whole genome sequencing data from 476 healthy unrelated individuals spanning 11 ethnic minorities groups in Guizhou Province, Southwest China, including Bouyei, Dong, Miao, Yi, Bai, Gelo, Zhuang, Tujia, Yao, Hui, and Sui. The GMGD database comprises more than 16.33 million variants in GRCh38 and 16.20 million variants in GRCh37. Among these, approximately 11.9% (1,956,322) of the variants in GRCh38 and 18.5% (3,009,431) of the variants in GRCh37 are entirely new and do not exist in the dbSNP database. These novel variants shed light on the genetic diversity landscape across these populations, providing valuable insights with an average coverage of 5.5 ×. This makes GMGD the largest genome-wide database encompassing the most diverse ethnic groups to date. The GMGD interactive interface facilitates researchers with multi-dimensional mutation search methods and displays population frequency differences among global populations. Furthermore, GMGD is equipped with a genotype-imputation function, enabling enhanced capabilities for low-depth genomic research or targeted region capture studies. GMGD offers unique insights into the genomic variation landscape of different ethnic groups, which are freely accessible at https://db.cngb.org/pop/gmgd/ .
Collapse
Affiliation(s)
- Yan He
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology of Guizhou Province, Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Changgui Lei
- BGI Research, Shenzhen, 518083, China
- BGI Research, Guiyang, 550000, China
- BGI Research, Wuhan, 430074, China
| | - Chanjuan Wan
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology of Guizhou Province, Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Shuang Zeng
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology of Guizhou Province, Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, 550004, Guizhou, China
- BGI Research, Shenzhen, 518083, China
- BGI Research, Guiyang, 550000, China
- BGI Research, Wuhan, 430074, China
| | - Ting Zhang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology of Guizhou Province, Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Fei Luo
- BGI Research, Shenzhen, 518083, China
- BGI Research, Guiyang, 550000, China
- BGI Research, Wuhan, 430074, China
| | - Ruichao Li
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology of Guizhou Province, Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Xiaokun Li
- BGI Research, Shenzhen, 518083, China
- BGI Research, Guiyang, 550000, China
| | - Anshu Zhao
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology of Guizhou Province, Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Defu Xiao
- BGI Research, Shenzhen, 518083, China
- BGI Research, Guiyang, 550000, China
| | - Yunyan Luo
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology of Guizhou Province, Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, 550004, Guizhou, China
- BGI Research, Guiyang, 550000, China
| | - Keren Shan
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology of Guizhou Province, Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Xiaolan Qi
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology of Guizhou Province, Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, 550004, Guizhou, China.
| | - Xin Jin
- BGI Research, Shenzhen, 518083, China.
- BGI Research, Guiyang, 550000, China.
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI Research, Shenzhen, China.
- School of Medicine, South China University of Technology, Guangzhou, China.
| |
Collapse
|
2
|
Jia L, Wang M, Duan S, Chen J, Zhao M, Ji S, Lv B, Jiang X, He G, Yang J. Genetic history of esophageal cancer group in southwestern China revealed by Y-chromosome STRs and genomic evolutionary connection analysis. Heliyon 2024; 10:e29867. [PMID: 38720733 PMCID: PMC11076658 DOI: 10.1016/j.heliyon.2024.e29867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/09/2024] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
Genetic and environmental factors play crucial roles in the development of esophageal cancer (EC) and contribute uniquely or cooperatively to human cancer susceptibility. Sichuan is located in the interior of southwestern China, and the northern part of Sichuan is one of the regions with a high occurrence of EC. However, the factors influencing the high incidence rate of EC in the Sichuan Han Chinese population and its corresponding genetic background and origins are still poorly understood. Here, we utilized genome-wide single nucleotide polymorphisms (SNPs) and Y-chromosome short tandem repeats (Y-STRs) to characterize the genetic structure, connection, and origin of cancer groups and general populations. We generated Y-STR-based haplotype data from 214 Sichuan individuals, including the Han Chinese EC population and a control group of Han Chinese individuals. Our results, obtained from Y-STR-based population statistical methods (analysis of molecular variance (AMOVA), principal component analysis (PCA), and phylogenetic analysis), demonstrated that there was a genetic substructure difference between the EC population in the high-incidence area of northern Sichuan Province and the control population. Additionally, there was a strong genetic relationship between the EC population in the northern Sichuan high-incidence area and those at high risk in both the Fujian and Chaoshan areas. In addition, we obtained high-density SNP data from saliva samples of 60 healthy Han Chinese individuals from three high-prevalence areas of EC in China: Sichuan Nanchong, Fujian Quanzhou, and Henan Xinxiang. As inferred from the allele frequency of SNPs and sharing patterns of haplotype segments, the evolutionary history and admixture events suggested that the Han population from Nanchong in northern Sichuan Province shared a close genetic relationship with the Han populations from Xinxiang in Henan Province and Quanzhou in Fujian Province, both of which are regions with a high prevalence of EC. Our study illuminated the genetic profile and connection of the Northern Sichuan Han population and enriched the genomic resources and features of the Han Chinese populations in China, especially for the Y-STR genetic data of the Han Chinese EC population. Populations living in different regions with high incidences of EC may share similar genetic backgrounds, which offers new insights for further exploring the genetic mechanisms underlying EC.
Collapse
Affiliation(s)
- Lihua Jia
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
| | - Mengge Wang
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Shuhan Duan
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Jianghua Chen
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
| | - Mei Zhao
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
| | - Simeng Ji
- School of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, 637000, China
| | - Bingbing Lv
- School of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, 637000, China
| | - Xiucheng Jiang
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Guanglin He
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Junbao Yang
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
- School of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, 637000, China
| |
Collapse
|
3
|
Sun Q, Wang M, Lu T, Duan S, Liu Y, Chen J, Wang Z, Sun Y, Li X, Wang S, Lu L, Hu L, Yun L, Yang J, Yan J, Nie S, Zhu Y, Chen G, Wang CC, Liu C, He G, Tang R. Differentiated adaptative genetic architecture and language-related demographical history in South China inferred from 619 genomes from 56 populations. BMC Biol 2024; 22:55. [PMID: 38448908 PMCID: PMC10918984 DOI: 10.1186/s12915-024-01854-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 02/26/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND The underrepresentation of human genomic resources from Southern Chinese populations limited their health equality in the precision medicine era and complete understanding of their genetic formation, admixture, and adaptive features. Besides, linguistical and genetic evidence supported the controversial hypothesis of their origin processes. One hotspot case was from the Chinese Guangxi Pinghua Han people (GPH), whose language was significantly similar to Southern Chinese dialects but whose uniparental gene pool was phylogenetically associated with the indigenous Tai-Kadai (TK) people. Here, we analyzed genome-wide SNP data in 619 people from four language families and 56 geographically different populations, in which 261 people from 21 geographically distinct populations were first reported here. RESULTS We identified significant population stratification among ethnolinguistically diverse Guangxi populations, suggesting their differentiated genetic origin and admixture processes. GPH shared more alleles related to Zhuang than Southern Han Chinese but received more northern ancestry relative to Zhuang. Admixture models and estimates of genetic distances showed that GPH had a close genetic relationship with geographically close TK compared to Northern Han Chinese, supporting their admixture origin hypothesis. Further admixture time and demographic history reconstruction supported GPH was formed via admixture between Northern Han Chinese and Southern TK people. We identified robust signatures associated with lipid metabolisms, such as fatty acid desaturases (FADS) and medically relevant loci associated with Mendelian disorder (GJB2) and complex diseases. We also explored the shared and unique selection signatures of ethnically different but linguistically related Guangxi lineages and found some shared signals related to immune and malaria resistance. CONCLUSIONS Our genetic analysis illuminated the language-related fine-scale genetic structure and provided robust genetic evidence to support the admixture hypothesis that can explain the pattern of observed genetic diversity and formation of GPH. This work presented one comprehensive analysis focused on the population history and demographical adaptative process, which provided genetic evidence for personal health management and disease risk prediction models from Guangxi people. Further large-scale whole-genome sequencing projects would provide the entire landscape of southern Chinese genomic diversity and their contributions to human health and disease traits.
Collapse
Affiliation(s)
- Qiuxia Sun
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
| | - Tao Lu
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Shuhan Duan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637100, China
| | - Yan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637100, China
| | - Jing Chen
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030001, China
| | - Zhiyong Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Yuntao Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Xiangping Li
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Shaomei Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Department of Public Health, Chengdu Medical College, Chengdu, 610500, China
| | - Liuyi Lu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Clinical Medical Sciences, North Sichuan Medical College, Nanchong, 637100, China
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Libing Yun
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Junbao Yang
- School of Clinical Medical Sciences, North Sichuan Medical College, Nanchong, 637100, China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030001, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Yanfeng Zhu
- Department of Public Health, Chengdu Medical College, Chengdu, 610500, China
| | - Gang Chen
- Hunan Key Lab of Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410075, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, Fujian, China
| | - Chao Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China
- Guangzhou Forensic Science Institute, Guangzhou, 510055, China
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China.
| |
Collapse
|
4
|
Wang X, Zhang H, Wang Q, Yang M, Liu Y, Ran Q, Huang C, Huang J, Ren Z, Jin X. Insertion/deletion polymorphism for genetic background and forensic performance exploration of the Sui group from Guizhou. Heliyon 2023; 9:e21384. [PMID: 38027767 PMCID: PMC10643464 DOI: 10.1016/j.heliyon.2023.e21384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/08/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Insertion/deletion polymorphisms (InDels) as ideal genetic markers for forensic genetics are appreciated by scholars both nationally and internationally because they integrated the favorable features of single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs). Nevertheless, with the limited identification efficiency of InDels, the multiplex amplification systems of InDels might just be applied as the supplementary methods in paternity testing with respect to commonly used STRs. In the current research, we successfully genotyped 105 unrelated individuals from the Guizhou Sui population based on a six-color fluorescence multiplex panel that could simultaneously detect 64 genetic markers (59 autosomal InDels, two autosomal miniSTRs and three Y chromosomal genetic markers). In addition, frequency distributions and forensic statistical parameters of these loci in the Sui group were assessed using the STRAF software. Phylogenetic relationships among the Sui group and other reference populations were dissected by two methods (principal component analysis and phylogenetic trees) based on 59 InDels. The combined discrimination power and probability of exclusion values of 61 autosomal genetic markers in the Sui group were nearly equal to 1-1.90063 × 10-27 and 0.999998272, respectively. Furthermore, we observed that the Sui group from Guizhou had closer genetic affinities with East Asian populations with respect to other continental populations. In summary, we stated that the multiplex amplification system might be utilized as a prospective independent tool for human individual identification and parentage testing in the Sui group residing in Guizhou.
Collapse
Affiliation(s)
- Xiaoxue Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Qianchong Ran
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Chunli Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Xiaoye Jin
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| |
Collapse
|
5
|
Wang J, Wu J, Sun Q, Wu Q, Li Y, Duan S, Yang L, Wu W, Wang Z, Liu Y, Tang R, Yang J, Wang C, Liu C, Xu J, Wang M, He G. Extensive genetic admixture between Tai-Kadai-speaking people and their neighbours in the northeastern region of the Yungui Plateau inferred from genome-wide variations. BMC Genomics 2023; 24:317. [PMID: 37308851 DOI: 10.1186/s12864-023-09412-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/27/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Yungui Plateau in Southwest China is characterized by multi-language and multi-ethnic communities and is one of the regions with the wealthiest ethnolinguistic, cultural and genetic diversity in East Asia. There are numerous Tai-Kadai (TK)-speaking populations, but their detailed evolutionary history and biological adaptations are still unclear. RESULTS Here, we genotyped genome-wide SNP data of 77 unrelated TK-speaking Zhuang and Dong individuals from the Yungui Plateau and explored their detailed admixture history and adaptive features using clustering patterns, allele frequency differentiation and sharing haplotype patterns. TK-speaking Zhuang and Dong people in Guizhou are closely related to geographically close TK and Hmong-Mien (HM)-speaking populations. Besides, we identified that Guizhou TK-speaking people have a close genetic relationship with Austronesian (AN)-speaking Atayal and Paiwan people, which is supported by the common origin of the ancient Baiyue tribe. We additionally found subtle genetic differences among the newly studied TK people and previously reported Dais via the fine-scale genetic substructure analysis based on the shared haplotype chunks. Finally, we identified specific selection candidate signatures associated with several essential human immune systems and neurological disorders, which could provide evolutionary evidence for the allele frequency distribution pattern of genetic risk loci. CONCLUSIONS Our comprehensive genetic characterization of TK people suggested the strong genetic affinity within TK groups and extensive gene flow with geographically close HM and Han people. We also provided genetic evidence that supported the common origin hypothesis of TK and AN people. The best-fitted admixture models further suggested that ancestral sources from northern millet farmers and southern inland and coastal people contributed to the formation of the gene pool of the Zhuang and Dong people.
Collapse
Affiliation(s)
- Jiawen Wang
- School of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, China.
| | - Jun Wu
- School of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, China
| | - Qiuxia Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Qian Wu
- Qiannan Prefecture People's Hospital, Buyi and Miao Autonomous Prefecture of QianNan, Buyi and Miao Autonomous Prefecture of QianNan, 558000, China
| | - Youjing Li
- Congjiang People's Hospital, Congjiang, 557499, China
| | - Shuhan Duan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000, China
| | - Lin Yang
- School of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, China
| | - Wenxin Wu
- School of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000, China
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Junbao Yang
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000, China
| | - Chuanchao Wang
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, Xiamen University, Xiamen, 361000, China
| | - Chao Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jianwei Xu
- Department of Pharmacology, School of Basic Medicine, Guizhou Medical University, Guiyang, 550004, China.
| | - Mengge Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
| |
Collapse
|
6
|
Zhou J, Zhang X, Li X, Sui J, Zhang S, Zhong H, Zhang Q, Zhang X, Huang H, Wen Y. Genetic structure and demographic history of Northern Han people in Liaoning Province inferred from genome-wide array data. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1014024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this study, we used typical and advanced population genetic analysis methods [principal component analysis (PCA), ADMIXTURE, FST, f3-statistics, f4-statistics, qpAdm/qpWave, qpGraph, ALDER (Admixture-induced Linkage Disequilibrium for Evolutionary Relationships) and TreeMix] to explore the genetic structure of 80 Han individuals from four different cities in Liaoning Province and reconstruct their demographic history based on the newly generated genome-wide data. We found that Liaoning Han people have genetic similarities with other northern Han people (Shandong, Henan, and Shanxi) and Liaoning Manchu people. Millet farmers in the Yellow River Basin (YRB) and the West Liao River Basin (WLRB) (57–98%) and hunter-gatherers in the Mongolian Plateau (MP) and the Amur River Basin (ARB) (40–43%) are the main ancestral sources of the Liaoning Han people. Our study further supports the “northern origin hypothesis”; YRB-related ancestry accounts for 83–98% of the genetic makeup of the Liaoning Han population. There are clear genetic influences of northern East Asian populations in the Liaoning Han people, ancient Northeast Asian-related ancestry is another dominant ancestral component, and large-scale population admixture has happened between Tungusic Manchu people and Han people. There are genetic differences among the Liaoning Han people, and we found that these differences are associated with different migration routes of Hans during the “Chuang Guandong” period in historical records.
Collapse
|
7
|
Huang T, Li J, Zhao H, Ngamphiw C, Tongsima S, Kantaputra P, Kittitharaphan W, Wang SM. Core promoter in TNBC is highly mutated with rich ethnic signature. Brief Funct Genomics 2022; 22:9-19. [PMID: 36307127 PMCID: PMC9853936 DOI: 10.1093/bfgp/elac035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/23/2022] [Accepted: 09/28/2022] [Indexed: 01/25/2023] Open
Abstract
The core promoter plays an essential role in regulating transcription initiation by controlling the interaction between transcriptional factors and sequence motifs in the core promoter. Although mutation in core promoter sequences is expected to cause abnormal gene expression leading to pathogenic consequences, limited supporting evidence showed the involvement of core promoter mutation in diseases. Our previous study showed that the core promoter is highly polymorphic in worldwide human ethnic populations in reflecting human history and adaptation. Our recent characterization of the core promoter in triple-negative breast cancer (TNBC), a subtype of breast cancer, in a Chinese TNBC cohort revealed the wide presence of core promoter mutation in TNBC. In the current study, we analyzed the core promoter in a Thai TNBC cohort. We also observed rich core promoter mutation in the Thai TNBC patients. We compared the core promoter mutations between Chinese and Thai TNBC cohorts. We observed substantial differences of core promoter mutation in TNBC between the two cohorts, as reflected by the mutation spectrum, mutation-effected gene and functional category, and altered gene expression. Our study confirmed that the core promoter in TNBC is highly mutable, and is highly ethnic-specific.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - San Ming Wang
- Corresponding author: S.M. Wang, Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China. Tel.: +(853) 8822-4836; E-mail:
| |
Collapse
|
8
|
Chen H, Lin R, Lu Y, Zhang R, Gao Y, He Y, Xu S. Tracing Bai-Yue Ancestry in Aboriginal Li People on Hainan Island. Mol Biol Evol 2022; 39:6731089. [PMID: 36173765 PMCID: PMC9585476 DOI: 10.1093/molbev/msac210] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
As the most prevalent aboriginal group on Hainan Island located between South China and the mainland of Southeast Asia, the Li people are believed to preserve some unique genetic information due to their isolated circumstances, although this has been largely uninvestigated. We performed the first whole-genome sequencing of 55 Hainan Li (HNL) individuals with high coverage (∼30-50×) to gain insight into their genetic history and potential adaptations. We identified the ancestry enriched in HNL (∼85%) is well preserved in present-day Tai-Kadai speakers residing in South China and North Vietnam, that is, Bai-Yue populations. A lack of admixture signature due to the geographical restriction exacerbated the bottleneck in the present-day HNL. The genetic divergence among Bai-Yue populations began ∼4,000-3,000 years ago when the proto-HNL underwent migration and the settling of Hainan Island. Finally, we identified signatures of positive selection in the HNL, some outstanding examples included FADS1 and FADS2 related to a diet rich in polyunsaturated fatty acids. In addition, we observed that malaria-driven selection had occurred in the HNL, with population-specific variants of malaria-related genes (e.g., CR1) present. Interestingly, HNL harbors a high prevalence of malaria leveraged gene variants related to hematopoietic function (e.g., CD3G) that may explain the high incidence of blood disorders such as B-cell lymphomas in the present-day HNL. The results have advanced our understanding of the genetic history of the Bai-Yue populations and have provided new insights into the adaptive scenarios of the Li people.
Collapse
Affiliation(s)
| | | | - Yan Lu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China,Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
| | - Rui Zhang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yang Gao
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
| | | | | |
Collapse
|
9
|
Ren Z, Yang M, Jin X, Wang Q, Liu Y, Zhang H, Ji J, Wang CC, Huang J. Genetic substructure of Guizhou Tai-Kadai-speaking people inferred from genome-wide single nucleotide polymorphisms data. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.995783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The genome-wide characteristics and admixture history of the Tai-Kadai-speaking populations are essential for understanding the population genetic diversity in southern China. We genotyped about 700,000 single nucleotide polymorphisms (SNPs) of 239 individuals from six Tai-Kadai-speaking populations residing in the mountainous Guizhou Province of southwestern China. We merged the genome-wide data with available populations and ancients in East and Southeast Asia to infer Tai-Kadai-speaking populations’ admixture history and genetic structure. We observed a genetic substructure within the studied six populations in the PCA, ADMIXTURE, ChromoPainter, GLOBETROTTER, f-statistics, and qpWave analysis. The Dong, Zhuang, and Bouyei people had a strong genetic affinity with other Tai-Kadai-speaking and Austronesian groups in the surrounding area. However, Gelao showed an affinity to Sino-Tibetan groups, and Mulao people were genetically close to Hmong-Mien populations. qpAdm further illuminated that Gelao and Dong_Tongren composited more Han-related ancestry than Dong, Zhuang, Bouyei, and Mulao people. Meanwhile, we observed high frequencies of Y-chromosome haplogroup O in studied Tai-Kadai-speaking groups except for Gelao people with a high haplogroup N frequency. From the maternal side, haplogroup M7 was frequent in studied populations except for Tongren Dong, who had a high frequency of haplogroup B5. Our newly reported data are helpful for further exploring population dynamics in southern China.
Collapse
|
10
|
Yang M, He G, Ren Z, Wang Q, Liu Y, Zhang H, Zhang H, Chen J, Ji J, Zhao J, Guo J, Zhu K, Yang X, Wang R, Ma H, Wang CC, Huang J. Genomic Insights Into the Unique Demographic History and Genetic Structure of Five Hmong-Mien-Speaking Miao and Yao Populations in Southwest China. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.849195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Southern China was the original center of multiple ancestral populations related to modern Hmong-Mien, Tai-Kadai, Austroasiatic, and Austronesian people. More recent genetic surveys have focused on the fine-scale genetic structure and admixture history of southern Chinese populations, but the genetic formation and diversification of Hmong-Mien speakers are far from clear due to the sparse genetic sampling. Here, we reported nearly 700,000 single-nucleotide polymorphisms (SNPs) data from 130 Guizhou Miao and Yao individuals. We used principal component analysis, ADMIXTURE, f-statistics, qpAdm, phylogenetic tree, fineSTRUCTURE, and ALDER to explore the fine-scale population genetic structure and admixture pattern of Hmong-Mien people. The sharing allele patterns showed that our studied populations had a strong genetic affinity with ancient and modern groups from southern and southeastern East Asia. We identified one unique ancestry component maximized in Yao people, which widely existed in other Hmong-Mien-speaking populations in southern China and Southeast Asia and ancient samples of Guangxi. Guizhou Hmong-Mien speakers harbored the dominant proportions of ancestry related to southern indigenous East Asians and minor proportions of northern ancestry related to Yellow River farmers, suggesting the possibility of genetic admixture between Hmong-Mien people and recent southward Sino-Tibetan-related populations. Furthermore, we found a genetic substructure among geographically different Miao and Yao people in Leishan and Songtao. The Yao and Miao people in Leishan harbored more southern East Asian ancestry, but Miao in Songtao received more northern East Asian genetic influence. We observed high mtDNA but low Y-chromosome diversity in studied Hmong-Mien groups, supporting the role of sex-specific residence in influencing human genetic variation. Our data provide valuable clues for further exploring population dynamics in southern China.
Collapse
|
11
|
Yang M, Yang X, Ren Z, He G, Zhang H, Wang Q, Liu Y, Zhang H, Ji J, Chen J, Guo J, Huang J, Wang CC. Genetic Admixture History and Forensic Characteristics of Guizhou Sui People Inferred From Autosomal Insertion/Deletion and Genome-Wide Single-Nucleotide Polymorphisms. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.844761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Insertion-deletion (Indel) serves as one of the important markers in forensic personal identification and parentage testing, especially for cases with degraded samples. However, the genetic diversity and forensic features in ethnolinguistically diverse southwestern Chinese populations remain to be explored. Sui, one Tai-Kadai-speaking population residing in Guizhou, has a complex genetic history based on linguistic, historic, and anthropological evidence. In this study, we genotyped 30 Indels from 511 Guizhou Sui individuals and obtained approximately 700,000 genome-wide single-nucleotide polymorphisms (SNPs) in 15 representative Sui individuals to comprehensively characterize the genetic diversity, forensic characteristics, and genomic landscape of Guizhou Sui people. The estimated forensic statistically allele frequency spectrum and parameters demonstrated that this Indels panel was polymorphic and informative in Tai-Kadai populations in southern China. Results of principal component analysis (PCA), STRUCTURE, and phylogenetic trees showed that Guizhou Sui had a close genetic relationship with geographically close Tai-Kadai and Hmong-Mien people. Furthermore, genomic analysis based on the Fst and f4-statistics further suggested the genetic affinity within southern Chinese Tai-Kadai-speaking populations and a close relationship with geographically adjoining Guizhou populations. Admixture models based on the ADMIXTURE, f4, three-way qpAdm, and ALDER results demonstrated the interaction between the common ancestor for Tai-Kadai/Austronesian, Hmong-Mien, and Austroasiatic speaking populations played a significant role in the formation of modern Tai-Kadai people. We observed a sex-biased influence in Sui people by finding that the dominant Y chromosomal type was a Hmong-Mien specific lineage O2a2a1a2a1a2-N5 but the mtDNA lineages were commonly found in Tai-Kadai populations. The additional southward expansion of millet farmers in the Yellow River Basin has impacted the gene pool of southern populations including Tai-Kadai. The whole-genome sequencing in the future will shed more light on the finer genetic profile of Guizhou populations.
Collapse
|
12
|
Chen J, He G, Ren Z, Wang Q, Liu Y, Zhang H, Yang M, Zhang H, Ji J, Zhao J, Guo J, Chen J, Zhu K, Yang X, Wang R, Ma H, Tao L, Liu Y, Shen Q, Yang W, Wang CC, Huang J. Fine-Scale Population Admixture Landscape of Tai–Kadai-Speaking Maonan in Southwest China Inferred From Genome-Wide SNP Data. Front Genet 2022; 13:815285. [PMID: 35251126 PMCID: PMC8891617 DOI: 10.3389/fgene.2022.815285] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/27/2022] [Indexed: 12/27/2022] Open
Abstract
Guizhou Province harbors extensive ethnolinguistic and cultural diversity with Sino-Tibetan-, Hmong–Mien-, and Tai–Kadai-speaking populations. However, previous genetic analyses mainly focused on the genetic admixture history of the former two linguistic groups. The admixture history of Tai–Kadai-speaking populations in Guizhou needed to be characterized further. Thus, we genotyped genome-wide SNP data from 41 Tai–Kadai-speaking Maonan people and made a comprehensive population genetic analysis to explore their genetic origin and admixture history based on the pattern of the sharing alleles and haplotypes. We found a genetic affinity among geographically different Tai–Kadai-speaking populations, especially for Guizhou Maonan people and reference Maonan from Guangxi. Furthermore, formal tests based on the f3/f4-statistics further identified an adjacent connection between Maonan and geographically adjacent Hmong–Mien and Sino-Tibetan people, which was consistent with their historically documented shared material culture (Zhang et al., iScience, 2020, 23, 101032). Fitted qpAdm-based two-way admixture models with ancestral sources from northern and southern East Asians demonstrated that Maonan people were an admixed population with primary ancestry related to Guangxi historical people and a minor proportion of ancestry from Northeast Asians, consistent with their linguistically supported southern China origin. Here, we presented the landscape of genetic structure and diversity of Maonan people and a simple demographic model for their evolutionary process. Further whole-genome-sequence–based projects can be presented with more detailed information about the population history and adaptative history of the Guizhou Maonan people.
Collapse
Affiliation(s)
- Jing Chen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Guanglin He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- Institute Of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jing Zhao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Jianxin Guo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Jinwen Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Kongyang Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Xiaomin Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Hao Ma
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Le Tao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Yilan Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Qu Shen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Wenjiao Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- *Correspondence: Chuan-Chao Wang, ; Jiang Huang,
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
- *Correspondence: Chuan-Chao Wang, ; Jiang Huang,
| |
Collapse
|
13
|
Liu Y, Xie J, Wang M, Liu C, Zhu J, Zou X, Li W, Wang L, Leng C, Xu Q, Yeh HY, Wang CC, Wen X, Liu C, He G. Genomic Insights Into the Population History and Biological Adaptation of Southwestern Chinese Hmong-Mien People. Front Genet 2022; 12:815160. [PMID: 35047024 PMCID: PMC8762323 DOI: 10.3389/fgene.2021.815160] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/03/2021] [Indexed: 01/19/2023] Open
Abstract
Hmong-Mien (HM) -speaking populations, widely distributed in South China, the north of Thailand, Laos, and Vietnam, have experienced different settlement environments, dietary habits, and pathogenic exposure. However, their specific biological adaptation remained largely uncharacterized, which is important in the population evolutionary genetics and Trans-Omics for regional Precision Medicine. Besides, the origin and genetic diversity of HM people and their phylogenetic relationship with surrounding modern and ancient populations are also unknown. Here, we reported genome-wide SNPs in 52 representative Miao people and combined them with 144 HM people from 13 geographically representative populations to characterize the full genetic admixture and adaptive landscape of HM speakers. We found that obvious genetic substructures existed in geographically different HM populations; one localized in the HM clines, and others possessed affinity with Han Chinese. We also identified one new ancestral lineage specifically existed in HM people, which spatially distributed from Sichuan and Guizhou in the north to Thailand in the south. The sharing patterns of the newly identified homogenous ancestry component combined the estimated admixture times via the decay of linkage disequilibrium and haplotype sharing in GLOBETROTTER suggested that the modern HM-speaking populations originated from Southwest China and migrated southward in the historic period, which is consistent with the reconstructed phenomena of linguistic and archeological documents. Additionally, we identified specific adaptive signatures associated with several important human nervous system biological functions. Our pilot work emphasized the importance of anthropologically informed sampling and deeply genetic structure reconstruction via whole-genome sequencing in the next step in the deep Chinese Population Genomic Diversity Project (CPGDP), especially in the regions with rich ethnolinguistic diversity.
Collapse
Affiliation(s)
- Yan Liu
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, China.,Medical Imaging Key Laboratory of Sichuan Province, North Sichuan Medical College, Nanchong, China
| | - Jie Xie
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, China
| | - Mengge Wang
- Guangzhou Forensic Science Institute, Guangzhou, China.,Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Changhui Liu
- Guangzhou Forensic Science Institute, Guangzhou, China
| | - Jingrong Zhu
- Department of Anthropology and Ethnology, Xiamen University, Xiamen, China
| | - Xing Zou
- College of Medicine, Chongqing University, Chongqing, China
| | - Wenshan Li
- College of Medical Imaging, North Sichuan Medical College, Nanchong, China
| | - Lin Wang
- College of Clinical Medicine, North Sichuan Medical College, Nanchong, China
| | - Cuo Leng
- College of Medical Imaging, North Sichuan Medical College, Nanchong, China
| | - Quyi Xu
- Guangzhou Forensic Science Institute, Guangzhou, China
| | - Hui-Yuan Yeh
- School of Humanities, Nanyang Technological University, Singapore, Singapore
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Xiaohong Wen
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, China
| | - Chao Liu
- Guangzhou Forensic Science Institute, Guangzhou, China.,Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Guanglin He
- School of Humanities, Nanyang Technological University, Singapore, Singapore.,State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| |
Collapse
|