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Faizov B, Bukayev A, Sabitov Z, Zhabagin M. Population dataset for 23 Y-STR in the Merkit clan form Kazakh population. Data Brief 2024; 53:110160. [PMID: 38384307 PMCID: PMC10879769 DOI: 10.1016/j.dib.2024.110160] [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: 01/11/2024] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
This study presents a comprehensive analysis of 23 Y-STR data for the Merkit clan, a subgroup within the Kerey tribe of the Kazakh people. A total of 64 complete haplotypes were generated using the PowerPlex Y23 System. The data obtained using 23 Y-STR markers has been submitted to the Y Chromosome Haplotype Reference Database (YHRD) at yhrd.org, which will significantly enhance the forensic database for the Kazakh population in Kazakhstan. The research focuses on the distribution of haplotypes within the clan and their genealogical lines, which were visualized using a Median-joining network and Multidimensional scaling plot. The study identifies four distinct haplogroup clusters, revealing important insights into the genetic makeup and historical lineage of the Merkits. This dataset not only enriches our understanding of Kazakh genetic structure but also holds significant value for anthropological and population genetic research, as well as for forensic genetics. This work bridges a notable gap in genetic research on the Merkit clan, contributing to a deeper understanding of Central Asian nomadic tribes.
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Affiliation(s)
- Bekzhan Faizov
- National Center for Biotechnology, Astana 010000, Kazakhstan
| | - Alizhan Bukayev
- National Center for Biotechnology, Astana 010000, Kazakhstan
| | - Zhaxylyk Sabitov
- Research Institute for Jochi Ulus Studies, Astana 010000, Kazakhstan
| | - Maxat Zhabagin
- National Center for Biotechnology, Astana 010000, Kazakhstan
- Research Institute for Jochi Ulus Studies, Astana 010000, Kazakhstan
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Yerezhepov D, Gabdulkayum A, Akhmetova A, Kozhamkulov UA, Rakhimova SE, Kairov UY, Zhunussova G, Kalendar RN, Akilzhanova A. Vitamin D Status, VDR, and TLR Polymorphisms and Pulmonary Tuberculosis Epidemiology in Kazakhstan. Nutrients 2024; 16:558. [PMID: 38398882 PMCID: PMC10892443 DOI: 10.3390/nu16040558] [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: 01/23/2024] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Tuberculosis (TB) and vitamin D deficiency remain major public health problems in Kazakhstan. Due to the high incidence of pulmonary tuberculosis in the country and based on the importance of vitamin D in the modulation of the immune response and the association of its deficiency with many health conditions, the aim of our research was to study the vitamin D status, VDR and TLR gene polymorphisms, and pulmonary tuberculosis epidemiology in Kazakhstan. METHODS A case-control study included 411 individuals diagnosed with pulmonary TB and 686 controls with no family history of pulmonary tuberculosis. Concentrations of serum vitamin D (25-(OH)D) levels were measured by electrochemiluminescence immunoassay. The gene polymorphisms were determined by real-time polymerase chain reaction (PCR) allelic discrimination assay using TaqMan probes. The association between the risk of pulmonary TB and polymorphisms was evaluated using multimodal logistic regression and assessed with the ORs, corresponding to 95% Cis, and the significance level was determined as p < 0.05. RESULTS 1097 individuals were recruited from 3 different regions of Kazakhstan. Biochemical data showed vitamin D deficiency (25-(OH)D < 20 ng/mL) was present in both groups, with the case group accounting for almost 95% and 43.7% in controls. Epidemiological data revealed that socioeconomic factors such as BMI < 25 kg/m2 (p < 0.001), employment (p < 0.001), diabetes (p < 0.001), and vitamin D deficiency (p < 0.001) were statistically different between case and control groups. Logistic regression analysis, adjusted by sex, age, BMI, residence, employment, smoking, alcohol consumption, and diabetes, showed that T/T polymorphism of the VDR gene (rs1544410, OR = 1.97, 95% CI: 1.04-3.72, p = 0.03) and A/A polymorphism of the TLR8 gene (rs3764880, OR = 2.44, 95% CI: 1.20-4.98, p = 0.01) were associated with a high risk of developing pulmonary tuberculosis. CONCLUSIONS Vitamin D deficiency remains prevalent in our study cohort and is associated with TB progression. Socioeconomic determinants such as unemployment, BMI under 25 kg/m2, and diabetes are the main risk factors for the development of pulmonary TB in our study. A/A polymorphism of TLR8 (rs3764880) and T/T polymorphism (BsmI, rs1544410) of VDR genes may act as biomarkers for pulmonary tuberculosis in the Kazakh population.
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Affiliation(s)
- Dauren Yerezhepov
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Aidana Gabdulkayum
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Ainur Akhmetova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Ulan A. Kozhamkulov
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Saule E. Rakhimova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Ulykbek Y. Kairov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | | | - Ruslan N. Kalendar
- Institute of Biotechnology HiLIFE, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland
| | - Ainur Akilzhanova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
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Ashirbekov Y, Zhunussova A, Abaildayev A, Bukayeva A, Sabitov Z, Zhabagin M. Genetic polymorphism of 27 Y-STR loci in Kazakh populations from Central Kazakhstan. Ann Hum Biol 2024; 51:2377571. [PMID: 39051547 DOI: 10.1080/03014460.2024.2377571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/24/2024] [Accepted: 06/28/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND The haplotypes from Northern, Southern, Eastern, and Western Kazakhstan, analysed for 27 Y-STR loci, have been contributed to the Y-Chromosome STR Haplotype Reference Database, while the genetic profile of Central Kazakhstan remains inadequately explored. AIM To investigate the genetic diversity of 27 Y-STR loci in the Kazakh populations from Central Kazakhstan. SUBJECTS AND METHODS A total of 112 unrelated Central Kazakh males were genotyped via the Yfiler Plus kit. Data analysis yielded haplotype and allele frequencies, and forensic parameters. Genetic distances were graphically represented by a multidimensional scaling plot, with genetic linkages further elucidated through Nei's distance dendrograms and Median-joining networks. RESULTS A total of 102 haplotypes were detected, of which 96 were unique. The haplotype diversity and discrimination capacity were 0.997 and 0.91, respectively. Central Kazakhstan displays a unique cluster in analyses, underscoring its distinct Y-chromosome diversity compared to other Kazakh regions. The analysis of the Naiman tribe, predominantly residing in Central, Southern and Eastern Kazakhstan, revealed three genetic clusters of distinct haplogroups associated with their clans. CONCLUSIONS The identified haplotypes will enhance the existing reference database for Y-chromosomal studies in Kazakhstan, offering a robust tool for future research in population genetics, forensic science and genetic genealogy.
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Affiliation(s)
- Yeldar Ashirbekov
- M. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Republic of Kazakhstan
| | | | - Arman Abaildayev
- M. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Republic of Kazakhstan
| | - Ayagoz Bukayeva
- National Center for Biotechnology, Almaty, Republic of Kazakhstan
| | - Zhaxylyk Sabitov
- Research Institute for Jochi Ulus Studies, Republic of Kazakhstan
| | - Maxat Zhabagin
- National Center for Biotechnology, Almaty, Republic of Kazakhstan
- Research Institute for Jochi Ulus Studies, Republic of Kazakhstan
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4
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Ashirbekov Y, Seidualy M, Abaildayev A, Maxutova A, Zhunussova A, Akilzhanova A, Sharipov K, Sabitov Z, Zhabagin M. Genetic polymorphism of Y-chromosome in Kazakh populations from Southern Kazakhstan. BMC Genomics 2023; 24:649. [PMID: 37891458 PMCID: PMC10612363 DOI: 10.1186/s12864-023-09753-z] [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: 09/18/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND The Kazakhs are one of the biggest Turkic-speaking ethnic groups, controlling vast swaths of land from the Altai to the Caspian Sea. In terms of area, Kazakhstan is ranked ninth in the world. Northern, Eastern, and Western Kazakhstan have already been studied in relation to genetic polymorphism 27 Y-STR. However, current information on the genetic polymorphism of the Y-chromosome of Southern Kazakhstan is limited only by 17 Y-STR and no geographical study of other regions has been studied at this variation. RESULTS The Kazakhstan Y-chromosome Haplotype Reference Database was expanded with 468 Kazakh males from the Zhambyl and Turkestan regions of South Kazakhstan by having their 27 Y-STR loci and 23 Y-SNP markers analyzed. Discrimination capacity (DC = 91.23%), haplotype match probability (HPM = 0.0029) and haplotype diversity (HD = 0.9992) are defined. Most of this Y-chromosome variability is attributed to haplogroups C2a1a1b1-F1756 (2.1%), C2a1a2-M48 (7.3%), C2a1a3-F1918 (33.3%) and C2b1a1a1a-M407 (6%). Median-joining network analysis was applied to understand the relationship between the haplotypes of the three regions. In three genetic layer can be described the position of the populations of the Southern region of Kazakhstan-the geographic Kazakh populations of Kazakhstan, the Kazakh tribal groups, and the people of bordering Asia. CONCLUSION The Kazakhstan Y-chromosome Haplotype Reference Database was formed for 27 Y-STR loci with a total sample of 1796 samples of Kazakhs from 16 regions of Kazakhstan. The variability of the Y-chromosome of the Kazakhs in a geographical context can be divided into four main clusters-south, north, east, west. At the same time, in the genetic space of tribal groups, the population of southern Kazakhs clusters with tribes from the same region, and genetic proximity is determined with the populations of the Hazaras of Afghanistan and the Mongols of China.
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Affiliation(s)
- Yeldar Ashirbekov
- M. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
| | - Madina Seidualy
- National Center for Biotechnology, Astana, Kazakhstan
- Nazarbayev University, Astana, Kazakhstan
| | - Arman Abaildayev
- M. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
| | | | | | | | - Kamalidin Sharipov
- M. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
| | - Zhaxylyk Sabitov
- Research Institute for Jochi Ulus Studies, Astana, Republic of Kazakhstan
- L.N. Gumilyov Eurasian National University, Astana, Republic of Kazakhstan
| | - Maxat Zhabagin
- National Center for Biotechnology, Astana, Kazakhstan.
- Nazarbayev University, Astana, Kazakhstan.
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5
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Ashirbekov Y, Nogay A, Abaildayev A, Zhunussova A, Sabitov Z, Zhabagin M. Genetic polymorphism of 27 Y-STR loci in Kazakh populations from Eastern Kazakhstan. Ann Hum Biol 2023; 50:48-51. [PMID: 36650935 DOI: 10.1080/03014460.2023.2170465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND The establishment of a national haplotype database is important for forensic and genetic applications and requires studying genetic polymorphisms at Y-STR sites. However, the genetic structure of the Eastern Kazakhstan population is poorly characterised. AIM To investigate the genetic polymorphisms of 27 Y-STR loci in the Kazakh population from Eastern Kazakhstan and analyse the population genetic relationships of the Eastern Kazakhs with other populations. SUBJECTS AND METHODS The Yfiler Plus kit was utilised to genotype 246 healthy, unrelated males from Eastern Kazakhstan. Based on the raw data, haplotype and allele frequencies along with forensic parameters were calculated, and an MDS plot was constructed. RESULTS A total of 207 haplotypes were detected, of which 186 were unique. The haplotype diversity and discrimination capacity were 0.997 and 0.841, respectively. Population comparisons showed that Eastern Kazakhs have close genetic relationships with Kazakhs from Xinjiang, China. At the same time, a difference was found between the studied population and the previous one in the same part of Kazakhstan. CONCLUSIONS The obtained haplotypes will help to expand the Kazakhstan Y-chromosome reference database and will be useful for future genetic research and forensic applications.
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Affiliation(s)
- Yeldar Ashirbekov
- M. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Republic of Kazakhstan
| | - Anastassiya Nogay
- National Center for Biotechnology, Astana, Republic of Kazakhstan.,School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
| | - Arman Abaildayev
- M. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Republic of Kazakhstan
| | - Aigul Zhunussova
- National Center for Biotechnology, Astana, Republic of Kazakhstan
| | - Zhaxylyk Sabitov
- National Center for Biotechnology, Astana, Republic of Kazakhstan.,L.N. Gumilyov Eurasian National University, Astana, Republic of Kazakhstan.,Research Institute for Jochi Ulus Studies, Astana, Republic of Kazakhstan
| | - Maxat Zhabagin
- National Center for Biotechnology, Astana, Republic of Kazakhstan
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Genetic Polymorphism of 27 Y-STR Loci in the Western Kazakh Tribes from Kazakhstan and Karakalpakstan, Uzbekistan. Genes (Basel) 2022; 13:genes13101826. [PMID: 36292713 PMCID: PMC9601638 DOI: 10.3390/genes13101826] [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: 09/02/2022] [Revised: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 11/04/2022] Open
Abstract
Data on the genetic polymorphism of 27 Y-STR in Kazakhs of the Junior Zhuz has been presented and analyzed in relation to forensic features. A total of 464 representatives of the Western Kazakh tribes of Kazakhstan (Western Kazakhs, n = 405) and Uzbekistan (Karakalpakstan Kazakhs, n = 59) were examined by the Yfiler Plus set. The data are available in the YHRD under accession numbers YA006010 and YA006009. Genetic analysis (AMOVA and MDS) did not show significant differences between the two groups (Kazakhstan and Karakalpakstan Kazakhs) in terms of Y-chromosome diversity. Both groups are characterized by haplogroup C2a1a2 as a founder effect, which dominated two of the three tribes: Alimuly (67%), Baiuly (74.6%), and Zhetiru (25.8%). At the same time, the phylogenetic network for each tribe found its own clusters within C2a1a2. Western Kazakhs and Karakalpakstan Kazakhs present high values of unique haplotypes (84.44% and 96.61%), discrimination capacity (90.37% and 98.30%), and haplotype diversity (0.9991 and 0.9994). A set of 27 Y-STR loci distinguishes closely related individuals within the Western Kazakh tribes quite well. It is suitable for forensic application, and is also optimal for population genetics studies.
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Kairov U, Molkenov A, Sharip A, Rakhimova S, Seidualy M, Rhie A, Kozhamkulov U, Zhabagin M, Kim JI, Lee JH, Terwilliger JD, Seo JS, Zhumadilov Z, Akilzhanova A. Whole-Genome Sequencing and Genomic Variant Analysis of Kazakh Individuals. Front Genet 2022; 13:902804. [PMID: 35899193 PMCID: PMC9309552 DOI: 10.3389/fgene.2022.902804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/06/2022] [Indexed: 11/30/2022] Open
Abstract
Kazakhstan, the ninth-largest country in the world, is located along the Great Silk Road and connects Europe with Asia. Historically, its territory has been inhabited by nomadic tribes, and modern-day Kazakhstan is a multiethnic country with a dominant Kazakh population. We sequenced and analyzed the genomes of five ethnic Kazakhs at high coverage using the Illumina HiSeq2000 next-generation sequencing platform. The five Kazakhs yielded a total number of base pairs ranging from 87,308,581,400 to 107,526,741,301. On average, 99.06% were properly mapped. Based on the Het/Hom and Ti/Tv ratios, the quality of the genomic data ranged from 1.35 to 1.49 and from 2.07 to 2.08, respectively. Genetic variants were identified and annotated. Functional analysis of the genetic variants identified several variants that were associated with higher risks of metabolic and neurogenerative diseases. The present study showed high levels of genetic admixture of Kazakhs that were comparable to those of other Central Asians. These whole-genome sequence data of healthy Kazakhs could contribute significantly to biomedical studies of common diseases as their findings could allow better insight into the genotype–phenotype relations at the population level.
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Affiliation(s)
- Ulykbek Kairov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
- *Correspondence: Ulykbek Kairov, ; Ainur Akilzhanova,
| | - Askhat Molkenov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Aigul Sharip
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Saule Rakhimova
- Laboratory of Genomic and Personalized Medicine, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Madina Seidualy
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Arang Rhie
- Ilchun Genomic Medicine Institute, Seoul National University, Seoul, Korea
| | - Ulan Kozhamkulov
- Laboratory of Genomic and Personalized Medicine, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Maxat Zhabagin
- Laboratory of Genomic and Personalized Medicine, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Jong-Il Kim
- Ilchun Genomic Medicine Institute, Seoul National University, Seoul, Korea
| | - Joseph H. Lee
- Sergievsky Center, Departments of Neurology and Epidemiology, Taub Institute, Columbia University, New York City, NY, United States
| | - Joseph D. Terwilliger
- Departments of Genetics and Development and Psychiatry, Sergievsky Center, Columbia University, New York City, NY, United States
| | - Jeong-Sun Seo
- Ilchun Genomic Medicine Institute, Seoul National University, Seoul, Korea
| | - Zhaxybay Zhumadilov
- Laboratory of Genomic and Personalized Medicine, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
- School of Medicine, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ainur Akilzhanova
- Laboratory of Genomic and Personalized Medicine, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
- *Correspondence: Ulykbek Kairov, ; Ainur Akilzhanova,
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Ashirbekov Y, Abaildayev A, Neupokoyeva A, Sabitov Z, Zhabagin M. Genetic polymorphism of 27 Y-STR loci in Kazakh populations from Northern Kazakhstan. Ann Hum Biol 2022; 49:87-89. [PMID: 35132894 DOI: 10.1080/03014460.2022.2039292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
BACKGROUND Previous studies of the genetic polymorphism of the Y-chromosome of Kazakhs were focused on the Eastern, Central, Southern, and Western regions of Kazakhstan. In addition, many of these studies were limited to 17 Y-STR loci from the Yfiler. AIM To enrich the existing Kazakhstan Y-chromosome Haplotype Reference Database from the Northern Kazakh population data by a wide set of 27 Y-STR and investigate the population genetic relationships with previously published data. SUBJECTS AND METHODS 27 Y-STR loci from the Yfiler Plus PCR Amplification Kit were analysed in 382 healthy unrelated Kazakh males from Northern Kazakhstan. Genetic polymorphism was analysed using Arlequin software. RESULTS A total of 326 distinct haplotypes of the 27 Y-STR loci were observed in 382 individuals. The discrimination capacity (0.9982) and haplotype diversity (0.8534) were computed. A total of 168 alleles at single-copy loci were observed, and their frequencies ranged from 0.003 to 0.843. The pairwise genetic distance (RST) showed that the Northern Kazakh population is genetically distinct from the Chinese Kazakh population. CONCLUSIONS Genetic polymorphism shows that the potential value of 27 Y-STR loci for forensic casework in the Northern Kazakh population, and the current findings, might be beneficial for paternal lineages in the study of population genetics.
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Affiliation(s)
- Yeldar Ashirbekov
- M. Aitkhozhin Institute of Molecular Biology and Biochemistry, Republic of Kazakhstan
| | - Arman Abaildayev
- M. Aitkhozhin Institute of Molecular Biology and Biochemistry, Republic of Kazakhstan
| | | | - Zhaxylyk Sabitov
- National Center for Biotechnology, Republic of Kazakhstan.,L.N. Gumilyov Eurasian National University, Republic of Kazakhstan
| | - Maxat Zhabagin
- National Center for Biotechnology, Republic of Kazakhstan.,Young Researchers Alliance, Republic of Kazakhstan
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Khussainova E, Kisselev I, Iksan O, Bekmanov B, Skvortsova L, Garshin A, Kuzovleva E, Zhaniyazov Z, Zhunussova G, Musralina L, Kahbatkyzy N, Amirgaliyeva A, Begmanova M, Seisenbayeva A, Bespalova K, Perfilyeva A, Abylkassymova G, Farkhatuly A, Good SV, Djansugurova L. Genetic Relationship Among the Kazakh People Based on Y-STR Markers Reveals Evidence of Genetic Variation Among Tribes and Zhuz. Front Genet 2022; 12:801295. [PMID: 35069700 PMCID: PMC8777105 DOI: 10.3389/fgene.2021.801295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/10/2021] [Indexed: 11/21/2022] Open
Abstract
Ethnogenesis of Kazakhs took place in Central Asia, a region of high genetic and cultural diversity. Even though archaeological and historical studies have shed some light on the formation of modern Kazakhs, the process of establishment of hierarchical socioeconomic structure in the Steppe remains contentious. In this study, we analyzed haplotype variation at 15 Y-chromosomal short-tandem-repeats obtained from 1171 individuals from 24 tribes representing the three socio-territorial subdivisions (Senior, Middle and Junior zhuz) in Kazakhstan to comprehensively characterize the patrilineal genetic architecture of the Kazakh Steppe. In total, 577 distinct haplotypes were identified belonging to one of 20 haplogroups; 16 predominant haplogroups were confirmed by SNP-genotyping. The haplogroup distribution was skewed towards C2-M217, present in all tribes at a global frequency of 51.9%. Despite signatures of spatial differences in haplotype frequencies, a Mantel test failed to detect a statistically significant correlation between genetic and geographic distance between individuals. An analysis of molecular variance found that ∼8.9% of the genetic variance among individuals was attributable to differences among zhuzes and ∼20% to differences among tribes within zhuzes. The STRUCTURE analysis of the 1164 individuals indicated the presence of 20 ancestral groups and a complex three-subclade organization of the C2-M217 haplogroup in Kazakhs, a result supported by the multidimensional scaling analysis. Additionally, while the majority of the haplotypes and tribes overlapped, a distinct cluster of the O2 haplogroup, mostly of the Naiman tribe, was observed. Thus, firstly, our analysis indicated that the majority of Kazakh tribes share deep heterogeneous patrilineal ancestries, while a smaller fraction of them are descendants of a founder paternal ancestor. Secondly, we observed a high frequency of the C2-M217 haplogroups along the southern border of Kazakhstan, broadly corresponding to both the path of the Mongolian invasion and the ancient Silk Road. Interestingly, we detected three subclades of the C2-M217 haplogroup that broadly exhibits zhuz-specific clustering. Further study of Kazakh haplotypes variation within a Central Asian context is required to untwist this complex process of ethnogenesis.
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Affiliation(s)
| | - Ilya Kisselev
- Institute of Genetics and Physiology, Almaty, Kazakhstan
- The University of Winnipeg, Winnipeg, MB, Canada
| | - Olzhas Iksan
- Institute of Genetics and Physiology, Almaty, Kazakhstan
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Bakhytzhan Bekmanov
- Institute of Genetics and Physiology, Almaty, Kazakhstan
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | | | - Alexander Garshin
- Institute of Genetics and Physiology, Almaty, Kazakhstan
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | | | | | | | - Lyazzat Musralina
- Institute of Genetics and Physiology, Almaty, Kazakhstan
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | | | | | | | | | - Kira Bespalova
- Institute of Genetics and Physiology, Almaty, Kazakhstan
| | | | | | | | - Sara V. Good
- The University of Winnipeg, Winnipeg, MB, Canada
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Fan H, Zeng Y, Wu W, Liu H, Xu Q, Du W, Hao H, Liu C, Ren W, Wu W, Chen L, Liu C. The Y-STR landscape of coastal southeastern Han: Forensic characteristics, haplotype analyses, mutation rates, and population genetics. Electrophoresis 2021; 42:1578-1593. [PMID: 34018209 DOI: 10.1002/elps.202100037] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/16/2021] [Accepted: 05/15/2021] [Indexed: 11/09/2022]
Abstract
The Y-STR landscape of Coastal Southeastern Han (CSEH) living in Chinese southeast areas (including Guangdong, Fujian, and Zhejiang provinces) is still unclear. We investigated 62 Y-STR markers in a reasonably large number of 1021 unrelated males and 1027 DNA-confirmed father-son pairs to broaden the genetic backgrounds of CSEH. In total, 85 null alleles, 121 off-ladder alleles, and 95 copy number variants were observed, and 1012 distinct haplotypes were determined with the overall HD and DC values of 0.999974 and 0.9912. We observed 369 mutations in 76 099 meiotic transfers, and the average estimated Y-STR mutation rate was 4.85 × 10-3 (95% CI, 4.4 × 10-3 -5.4 × 10-3 ). The Spearman correlation analyses indicated that GD values (R2 = 0.6548) and average allele sizes (R2 = 0.5989) have positive correlations with Y-STR mutation rates. Our RM Y-STR set including 8 candidate RM Y-STRs, of which DYS534, DYS630, and DYS713 are new candidates in CSEH, distinguished 18.52% of father-son pairs. This study also clarified the population structures of CSEH which isolated in population-mixed South China relatively. The strategy, SM Y-STRs for familial searching and RM Y-STRs for individual identification regionally, could be applicable based on enough knowledge of the Y-STR mutability of different populations.
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Affiliation(s)
- Haoliang Fan
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Ying Zeng
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Weiwei Wu
- Zhejiang Key Laboratory of Forensic Science and Technology, Institute of Forensic Science of Zhejiang Provincial Public Security Bureau, Hangzhou, P. R. China
| | - Hong Liu
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Quyi Xu
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Weian Du
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Honglei Hao
- Zhejiang Key Laboratory of Forensic Science and Technology, Institute of Forensic Science of Zhejiang Provincial Public Security Bureau, Hangzhou, P. R. China
| | - Changhui Liu
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Wenyan Ren
- Zhejiang Key Laboratory of Forensic Science and Technology, Institute of Forensic Science of Zhejiang Provincial Public Security Bureau, Hangzhou, P. R. China
| | - Weibin Wu
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Ling Chen
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Chao Liu
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China.,Guangzhou Forensic Science Institute, Guangzhou, P. R. China
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11
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Luo C, Duan L, Li Y, Xie Q, Wang L, Ru K, Nazir S, Jawad M, Zhao Y, Wang F, Du Z, Peng D, Wen SQ, Qiu P, Fan H. Insights From Y-STRs: Forensic Characteristics, Genetic Affinities, and Linguistic Classifications of Guangdong Hakka and She Groups. Front Genet 2021; 12:676917. [PMID: 34108995 PMCID: PMC8181459 DOI: 10.3389/fgene.2021.676917] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 04/06/2021] [Indexed: 12/02/2022] Open
Abstract
Guangdong province is situated in the south of China with a population size of 113.46 million. Hakka is officially recognized as a branch of Han Chinese, and She is the official minority group in mainland China. There are approximately 25 million Hakka people who mainly live in the East and North regions of China, while there are only 0.7 million She people. The genetic characterization and forensic parameters of these two groups are poorly defined (She) or still need to be explored (Hakka). In this study, we have genotyped 475 unrelated Guangdong males (260 Hakka and 215 She) with Promega PowerPlex® Y23 System. A total of 176 and 155 different alleles were observed across all 23 Y-STRs for Guangdong Hakka (with a range of allele frequencies from 0.0038 to 0.7423) and Guangdong She (0.0047–0.8605), respectively. The gene diversity ranged from 0.4877 to 0.9671 (Guangdong Hakka) and 0.3277–0.9526 (Guangdong She), while the haplotype diversities were 0.9994 and 0.9939 for Guangdong Hakka and Guangdong She, with discrimination capacity values of 0.8885 and 0.5674, respectively. With reference to geographical and linguistic scales, the phylogenetic analyses showed us that Guangdong Hakka has a close relationship with Southern Han, and the genetic pool of Guangdong Hakka was influenced by surrounding Han populations. The predominant haplogroups of the Guangdong She group were O2-M122 and O2a2a1a2-M7, while Guangdong She clustered with other Tibeto-Burman language-speaking populations (Guizhou Tujia and Hunan Tujia), which shows us that the Guangdong She group is one of the branches of Tibeto-Burman populations and the Huonie dialect of She languages may be a branch of Tibeto-Burman language families.
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Affiliation(s)
- Chunfang Luo
- School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Heyuan Municipal Public Security Bureau, Heyuan, China
| | - Lizhong Duan
- Beijing Municipal Public Security Bureau, Beijing, China
| | - Yanning Li
- School of Forensic Medicine, Southern Medical University, Guangzhou, China.,School of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Qiqian Xie
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Lingxiang Wang
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Kai Ru
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Shahid Nazir
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Muhammad Jawad
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Yifeng Zhao
- Nanjing Zhenghong Judicial Identification Institute, Nanjing, China
| | - Fenfen Wang
- First Clinical Medical College, Hainan Medical University, Haikou, China
| | - Zhengming Du
- First Clinical Medical College, Hainan Medical University, Haikou, China
| | - Dehua Peng
- Heyuan Municipal Public Security Bureau, Heyuan, China
| | - Shao-Qing Wen
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Pingming Qiu
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Haoliang Fan
- School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Institute of Archaeological Science, Fudan University, Shanghai, China.,School of Basic Medicine and Life Science, Hainan Medical University, Haikou, China
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12
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Song Z, Wang Q, Zhang H, Tang J, Wang Q, Zhang H, Yang M, Ji J, Ren Z, Wu Y, Huang J. Genetic structure and forensic characterization of 36 Y-chromosomal STR loci in Tibeto-Burman-speaking Yi population. Mol Genet Genomic Med 2021; 9:e1572. [PMID: 33448700 PMCID: PMC8077142 DOI: 10.1002/mgg3.1572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/05/2020] [Accepted: 11/20/2020] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Male-specifically inherited Y-STRs have been widely used in population genetics and forensic investigations. METHODS We genotyped and analyzed Y chromosome haplotypes of 408 unrelated Tibeto-Burman-speaking Yi male individuals from Guizhou using Goldeneye® Y-PLUS kit. Population comparisons between the Guizhou Yi and 67 reference groups were performed via the AMOVA, MDS, and phylogenetic relationship reconstruction. RESULTS A total of 389 alleles and 396 haplotypes could be detected, and the allelic frequencies ranged from 0.0025 to 0.9875. The haplotype diversity, random match probability, and discrimination capacity values were 0.9999, 0.0026, and 0.9900, respectively. The gene diversity (GD) of 36 Y-STR loci in the studied group ranged from 0.0248 (DYS645) to 0.9601 (DYS385a/b). Our newly genotyped Yi samples show a close affinity with other Tibeto-Burman speaking groups in China and Southeast Asia. CONCLUSIONS The population stratification was almost consistent with the geographic distribution and language-family, both among Chinese and worldwide ethnic groups. Our data may provide useful information for paternal lineage in the forensic application and population genetics, as well as evidence for archaeological and historical research.
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Affiliation(s)
- Zhengyang Song
- Department of Forensic MedicineGuizhou Medical UniversityGuiyangChina
| | - Qian Wang
- Guiyang Judicial Expertise Center of Public SecurityGuiyangChina
| | - Han Zhang
- Department of Forensic MedicineGuizhou Medical UniversityGuiyangChina
| | - Jing Tang
- Guiyang Judicial Expertise Center of Public SecurityGuiyangChina
| | - Qiyan Wang
- Department of Forensic MedicineGuizhou Medical UniversityGuiyangChina
| | - Hongling Zhang
- Department of Forensic MedicineGuizhou Medical UniversityGuiyangChina
| | - Meiqing Yang
- Department of Forensic MedicineGuizhou Medical UniversityGuiyangChina
| | - Jingyan Ji
- Department of Forensic MedicineGuizhou Medical UniversityGuiyangChina
| | - Zheng Ren
- Department of Forensic MedicineGuizhou Medical UniversityGuiyangChina
| | - Yan Wu
- Department of Forensic MedicineGuizhou Medical UniversityGuiyangChina
| | - Jiang Huang
- Department of Forensic MedicineGuizhou Medical UniversityGuiyangChina
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13
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Zhabagin M, Sabitov Z, Tazhigulova I, Alborova I, Agdzhoyan A, Wei LH, Urasin V, Koshel S, Mustafin K, Akilzhanova A, Li H, Balanovsky O, Balanovska E. Medieval Super-Grandfather founder of Western Kazakh Clans from Haplogroup C2a1a2-M48. J Hum Genet 2021; 66:707-716. [PMID: 33510364 DOI: 10.1038/s10038-021-00901-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/09/2020] [Accepted: 11/24/2020] [Indexed: 11/09/2022]
Abstract
Western Kazakhstan is populated by three clans totaling 2 million people. Since the clans are patrilineal, the Y-chromosome is the most informative genetic system for tracing their origin. We genotyped 40 Y-SNP and 17 Y-STR markers in 330 Western Kazakhs. High phylogenetic resolution within haplogroup C2a1a2-M48 was achieved by using additional SNPs. Three lines of evidence indicate that the Alimuly and Baiuly clans (but not the Zhetiru clan) have a common founder placed 700 ± 200 years back by the STR data and 500 ± 200 years back by the sequencing data. This supports traditional genealogy claims about the descent of these clans from Emir Alau, who lived 650 years ago and whose lineage might be carried by two-thirds of Western Kazakhs. There is accumulation of specific haplogroups in the subclans representing other lineages, confirming that the clan structure corresponds with the paternal genetic structure of the steppe population.
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Affiliation(s)
- Maxat Zhabagin
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan. .,MOE Key Laboratory of Contemporary Anthropology and B&R International Joint Laboratory for Eurasian Anthropology, School of Life Sciences, Fudan University, Shanghai, China. .,National Center for Biotechnology, Nur-Sultan, Kazakhstan.
| | - Zhaxylyk Sabitov
- L.N. Gumilyov Eurasian National University, Nur-Sultan, Kazakhstan
| | - Inkar Tazhigulova
- Forensic science center of the Ministry of Justice of the Republic of Kazakhstan, Nur-Sultan, Kazakhstan
| | - Irina Alborova
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anastasiya Agdzhoyan
- Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Lan-Hai Wei
- MOE Key Laboratory of Contemporary Anthropology and B&R International Joint Laboratory for Eurasian Anthropology, School of Life Sciences, Fudan University, Shanghai, China.,Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | | | - Sergey Koshel
- Faculty of Geography, Lomonosov Moscow State University, Moscow, Russia
| | - Kharis Mustafin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ainur Akilzhanova
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology and B&R International Joint Laboratory for Eurasian Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Oleg Balanovsky
- Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia
| | - Elena Balanovska
- Biobank of North Eurasia, Moscow, Russia.,Research Centre for Medical Genetics, Moscow, Russia
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14
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Zhabagin M, Sabitov Z, Tarlykov P, Tazhigulova I, Junissova Z, Yerezhepov D, Akilzhanov R, Zholdybayeva E, Wei LH, Akilzhanova A, Balanovsky O, Balanovska E. The medieval Mongolian roots of Y-chromosomal lineages from South Kazakhstan. BMC Genet 2020; 21:87. [PMID: 33092538 PMCID: PMC7583311 DOI: 10.1186/s12863-020-00897-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 08/05/2020] [Indexed: 12/02/2022] Open
Abstract
Background The majority of the Kazakhs from South Kazakhstan belongs to the 12 clans of the Senior Zhuz. According to traditional genealogy, nine of these clans have a common ancestor and constitute the Uissun tribe. There are three main hypotheses of the clans’ origin, namely, origin from early Wusuns, from Niru’un Mongols, or from Darligin Mongols. We genotyped 490 samples of South Kazakhs by 35 Y-chromosomal SNPs (single nucleotide polymorphism) and 17 STRs (short tandem repeat). Additionally, 133 samples from citizen science projects were included into the study. Results We found that three Uissun clans have unique Y-chromosomal profiles, but the remaining six Uissun clans and one non-Uissun clan share a common paternal gene pool. They share a high frequency (> 40%) of the C2*-ST haplogroup (marked by the SNP F3796), which is associated with the early Niru’un Mongols. Phylogenetic analysis of this haplogroup carried out on 743 individuals from 25 populations of Eurasia has revealed a set of haplotype clusters, three of which contain the Uissun haplotypes. The demographic expansion of these clusters dates back to the 13-fourteenth century, coinciding with the time of the Uissun’s ancestor Maiky-biy known from historical sources. In addition, it coincides with the expansion period of the Mongol Empire in the Late Middle Ages. A comparison of the results with published aDNA (ancient deoxyribonucleic acid) data and modern Y haplogroups frequencies suggest an origin of Uissuns from Niru’un Mongols rather than from Wusuns or Darligin Mongols. Conclusions The Y-chromosomal variation in South Kazakh clans indicates their common origin in 13th–14th centuries AD, in agreement with the traditional genealogy. Though genetically there were at least three ancestral lineages instead of the traditional single ancestor. The majority of the Y-chromosomal lineages of South Kazakhstan was brought by the migration of the population related to the medieval Niru’un Mongols.
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Affiliation(s)
- Maxat Zhabagin
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan. .,National Center for Biotechnology, Nur-Sultan, Kazakhstan.
| | - Zhaxylyk Sabitov
- L.N. Gumilyov Eurasian National University, Nur-Sultan, Kazakhstan.,Young Researchers Alliance, Nur-Sultan, Republic of Kazakhstan
| | - Pavel Tarlykov
- National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | - Inkar Tazhigulova
- Forensic Science Center of the Ministry of Justice of the Republic of Kazakhstan, Nur-Sultan, Kazakhstan
| | - Zukhra Junissova
- Research Institute of Archeology named after K.A. Akishev, Nur-Sultan, Republic of Kazakhstan
| | - Dauren Yerezhepov
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | | | | | - Lan-Hai Wei
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China.,Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Ainur Akilzhanova
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Oleg Balanovsky
- Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia.,Research Centre for Medical Genetics, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia
| | - Elena Balanovska
- Research Centre for Medical Genetics, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia
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15
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Li X, Zhang J, Li L, Zha L, Shi M, Ding M. Genetic polymorphism of 24 Y-STR loci in Altay Hui and Kazakh populations from northwest China. Leg Med (Tokyo) 2020; 47:101760. [PMID: 32739877 DOI: 10.1016/j.legalmed.2020.101760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/30/2020] [Accepted: 07/10/2020] [Indexed: 11/26/2022]
Abstract
24 Y-STR loci were analyzed in 223 Altay Hui individuals and 209 Altay Kazakh individuals. Haplotype diversity (HD) and discrimination capacity (DC) values were calculated. Population pairwise genetic distances (Rst) were evaluated in AMOVA analysis and compared between two studied populations and other populations. The relationships between populations were visualized through multidimensional scaling (MDS) and neighbor-joining (NJ) tree. The results indicated higher discrimination power in the Altay Kazakh and Hui populations. The Altay Kazakh was the most distantly related to Xishuangbanna Dai, while Altay Kazakh was the most closely related to Gansu Kazakh. The results may provide useful information for paternal lineages and increase our understanding of genetic relationships between two studied populations and other populations.
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Affiliation(s)
- XueBo Li
- Key Laboratory of Evidence Identification in Universities of Shandong Province, Shandong University of Political Science and Law, Jinan 250014, Shandong, PR China; Institute of Forensic Science, Shandong University of Political Science and Law, Jinan 250014, Shandong, PR China
| | - Jiashuo Zhang
- Key Laboratory of Evidence Identification in Universities of Shandong Province, Shandong University of Political Science and Law, Jinan 250014, Shandong, PR China; Institute of Forensic Science, Shandong University of Political Science and Law, Jinan 250014, Shandong, PR China
| | - Liangliang Li
- Key Laboratory of Evidence Identification in Universities of Shandong Province, Shandong University of Political Science and Law, Jinan 250014, Shandong, PR China; Institute of Forensic Science, Shandong University of Political Science and Law, Jinan 250014, Shandong, PR China
| | - Lagabaiyila Zha
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No 172. Tongzipo Road, Changsha, Hunan Province, 410013, PR China
| | - Meisen Shi
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, 25 Xitucheng Road, Beijing 100088, PR China.
| | - Mingxia Ding
- Laboratory of Genetics and Prenatal Diagnosis, The Second Hospital Of Shandong University, Jinan 250001, Shandong, PR China.
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16
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Tang J, Yang M, Wang X, Wang Q, Wang Q, Zhang H, Qian E, Zhang H, Ji J, Ren Z, Wu Y, Huang J. Genetic structure and forensic characterisation of 36 Y-chromosomal STR loci in Hmong-Mien-speaking Miao population. Ann Hum Biol 2020; 47:541-548. [PMID: 32597239 DOI: 10.1080/03014460.2020.1788159] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
BACKGROUND Y-chromosomal short tandem repeats (Y-STRs) are widely used in paternity identification, pedigree investigation, and human population genetic history. AIM To investigate the Y-STR polymorphisms in a typical Miao population, and explore the genetic differentiation between the Miao population and reference groups. SUBJECTS AND METHODS We detected 36 Y-STRs genotyping in 455 unrelated Miao individuals from Guizhou province, and analysed genetic differentiation between the Miao population and 76 reference groups. RESULTS A total of 369 alleles were obtained, and the allele frequencies ranged from 0.0022 to 0.9802. In addition, the haplotype diversity, random match probability, and discrimination capacity values were 0.99997, 0.0022, and 0.9934, respectively. Moreover, the genetic relationships between Guizhou Miao and 76 ethnic populations showed that the population stratification was almost consistent with geographic distribution and language-family. CONCLUSIONS The 36 Y-STR loci in this study have good polymorphism distributions in the Guizhou Miao population, and therefore would be a useful tool in forensic identification and male parentage testing and even pedigree investigation.
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Affiliation(s)
- Jing Tang
- Guiyang Judicial Expertise Center of Public Security, Guiyang, Guizhou, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaojuan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Qian Wang
- Guiyang Judicial Expertise Center of Public Security, Guiyang, Guizhou, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Enfang Qian
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yan Wu
- Guiyang Judicial Expertise Center of Public Security, Guiyang, Guizhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
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17
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Y-chromosome evidence confirmed the Kerei-Abakh origin of Aksay Kazakhs. J Hum Genet 2020; 65:797-803. [PMID: 32313196 DOI: 10.1038/s10038-020-0759-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/14/2020] [Accepted: 04/02/2020] [Indexed: 11/08/2022]
Abstract
Aksay Kazakhs are the easternmost branch of Kazakhs, residing in Jiuquan city, the forefront of the ancient Silk Road. However, the genetic diversity of Aksay Kazakhs and its relationships with other Kazakhs still lack attention. To clarify this issue, we analyzed the non-recombining portion of the Y-chromosome from 93 Aksay Kazakhs samples, using a high-resolution analysis of 106 biallelic markers and 17 STRs. The lowest haplogroup diversity (0.38) was observed in Aksay Kazakhs among all studied Kazakh populations. The social and cultural traditions of the Kazakhs shaped their current pattern of genetic variation. Aksay Kazakhs tended to migrate with clans and had limited paternal admixture with neighboring populations. Aksay Kazakhs had the highest frequency (80%) of haplogroup C2b1a3a1-F3796 (previous C3*-Star Cluster) among the investigated Eurasian steppe populations, which was now seen as the genetic marker of Kerei clan. Furthermore, NETWORK analysis indicated that Aksay Kazakhs originated from sub-clan Kerei-Abakh in Kazakhstan with DYS448 = 23. TMRCA estimates of three recent descent clusters detected in C2*-M217 (xM48) network, one of which incorporate nearly all of the C2b1a3a1-F3796 Aksay Kazakhs samples, gave the age range of 976-1405 YA for DC1, 1059-1314 YA for DC2, and 1139-1317 YA for DC3, respectively; this is coherent with the 7th to the 11th centuries Altaic-speaking pastoral nomadic population expansion.
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18
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Liu Y, Yu T, Mei S, Jin X, Lan Q, Zhou Y, Fang Y, Xie T, Huang J, Zhu B. Forensic characteristics and genetic affinity analyses of Xinjiang Mongolian group using a novel six fluorescent dye-labeled typing system including 41 Y-STRs and 3 Y-InDels. Mol Genet Genomic Med 2020; 8:e1097. [PMID: 31876394 PMCID: PMC7005640 DOI: 10.1002/mgg3.1097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/25/2019] [Accepted: 12/02/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Y-chromosomal genetic marker haplotypes of individuals can define the paternal kinship or genealogies to which they belong and further provide clues for forensic individual identifications. Studying the genetic structure of the Mongolian group will help to bring to light the Mongolian ethnic origin, and explicate the genetic affinities among the studied and compared populations. Some forensic scientists have studied the genetic background of the Mongolian group based on different molecular genetic markers. These studies were of very great reference significance for the Mongolian group genetic research, whereas the investigation of Y-STR haplotype data in the Xinjiang Mongolian group is still insufficient. METHODS Genetic characteristics of 182 unrelated healthy male Mongolian individuals were revealed by 41 Y-chromosomal short tandem repeat and 3 insertion/deletion molecular genetic markers. Furthermore, analyses of molecular variance programs, multi-dimensional scaling plots, and phylogenetic tree reconstructions were operated to explore the genetic relationships of the Xinjiang Mongolian group with comparative 23 populations from China and 33 populations from worldwide nations. RESULTS The genetic diversity values ranged from 0.0641 (rs771783753) to 0.9502 (DYF387S1). A total of 165 distinct haplotypes were identified, of which 150 (90.91%) were unique. The discrimination capacity, match probability, and haplotype diversity of 44 loci were 0.9066, 0.0067, and 0.9988, respectively. Additionally, the Mongolian group had the most intimate relationship with Gansu Dongxiang (RST = 0.0165), followed by HulunBuir Mongolian (RST = 0.0187), Inner Mongolia Daur (RST = 0.0202) as well as other three minority ethnic groups from the Xinjiang region (RST < 0.05) in all compared Chinese populations, and clustered together with the majority of Asian populations in a worldwide scale. CONCLUSIONS Consequently, the 44 loci could be well applied in forensic applications of the Mongolian group. The haplotypes available in here made new contributions to the existing population genetic information and would be of great value in population studies.
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Affiliation(s)
- Yanfang Liu
- Department of Forensic GeneticsSchool of Forensic MedicineSouthern Medical UniversityGuangzhouChina
- Department of Laboratory MedicineNanhai HospitalSouthern Medical UniversityFoshanChina
- Multi‐Omics Innovative Research Center of Forensic IdentificationSouthern Medical UniversityGuangzhouChina
| | | | - Shuyan Mei
- Department of Forensic GeneticsSchool of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong UniversityXi'anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong UniversityXi'anChina
- College of Forensic MedicineXi'an Jiaotong University Health Science CenterXi'anChina
| | - Qiong Lan
- Department of Forensic GeneticsSchool of Forensic MedicineSouthern Medical UniversityGuangzhouChina
- Multi‐Omics Innovative Research Center of Forensic IdentificationSouthern Medical UniversityGuangzhouChina
| | - Yongsong Zhou
- Department of Forensic GeneticsSchool of Forensic MedicineSouthern Medical UniversityGuangzhouChina
- Multi‐Omics Innovative Research Center of Forensic IdentificationSouthern Medical UniversityGuangzhouChina
| | - Yating Fang
- Department of Forensic GeneticsSchool of Forensic MedicineSouthern Medical UniversityGuangzhouChina
- Multi‐Omics Innovative Research Center of Forensic IdentificationSouthern Medical UniversityGuangzhouChina
| | - Tong Xie
- Department of Forensic GeneticsSchool of Forensic MedicineSouthern Medical UniversityGuangzhouChina
- Multi‐Omics Innovative Research Center of Forensic IdentificationSouthern Medical UniversityGuangzhouChina
| | | | - Bofeng Zhu
- Department of Forensic GeneticsSchool of Forensic MedicineSouthern Medical UniversityGuangzhouChina
- Multi‐Omics Innovative Research Center of Forensic IdentificationSouthern Medical UniversityGuangzhouChina
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong UniversityXi'anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong UniversityXi'anChina
- College of Forensic MedicineXi'an Jiaotong University Health Science CenterXi'anChina
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19
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Wang CZ, Su MJ, Li Y, Chen L, Jin X, Wen SQ, Tan J, Shi MS, Li H. Genetic polymorphisms of 27 Yfiler® Plus loci in the Daur and Mongolian ethnic minorities from Hulunbuir of Inner Mongolia Autonomous Region, China. Forensic Sci Int Genet 2019; 40:e252-e255. [DOI: 10.1016/j.fsigen.2019.02.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 01/22/2019] [Accepted: 02/03/2019] [Indexed: 11/28/2022]
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20
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Zhang J, Tao R, Zhong J, Sun D, Qiao L, Shan S, Yang Z, Zhang J, Zhang S, Li C. Genetic polymorphisms of 27 Y-STR loci in the Dezhou Han population from Shandong province, Eastern China. Forensic Sci Int Genet 2019; 39:e26-e28. [DOI: 10.1016/j.fsigen.2018.11.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/26/2018] [Accepted: 11/26/2018] [Indexed: 11/30/2022]
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