Genetic diversity and haplotype structure of 27 Y-STR loci in a Yanbian Korean population from Jilin Province,Northeast China

In this study, 27 Y-STRs were analyzed in 347 male individuals from the Yanbian Korean population. Haplotype diversity (HD) and discrimination capacity (DC) values were calculated. Pairwise R_st values were evaluated in AMOVA analysis and visualized through multidimensional scaling (MDS). Yflier Plus system indicated higher Discrimination Power (DP), HD and DC which is 0.9969, 0.9998 and 0.9769. There is no significant genetic distance between Yanbian Koreans and South Koreans, however, there is a great distance from Chinese Han population. The present results may provide useful information for paternal lineages in forensic cases and increase our understanding of the genetic relationships between Yanbian Korean and other groups.     

Haplotype diversity and phylogenetic relationship analysis of Chinese Yulin Han population using 59 Y-STR loci of two novel Y-STR typing systems

To investigate the genetic polymorphisms of 59 Y-chromosomal short tandem repeat (Y-STR) loci in the Yulin Han population, 229 unrelated healthy male individuals were analyzed using AGCU Y37 kit and AGCU Y-SUPP Plus kit. A total of 227 different haplotypes were obtained at the 59 Y-STR loci. Among them, 225 haplotypes were unique and 2 haplotypes occurred twice. The overall haplotypic diversity and discrimination capacity were 0.9999 and 0.9913, respectively. The phylogenetic relationships between the studied Yulin Han population and 17 previously reported reference populations were evaluated via multidimensional scaling and Neighbor-Joining analyses based on the haplotypic frequencies of ‘YHRD Maximal Loci’. Phylogenetic analysis revealed that Yulin Han population was closely related to Chinese Han and Hunan Yao populations. These results demonstrated that the 59 Y-STR loci were useful for forensic applications and population genetic studies.     

Genetic polymorphisms and haplotypic structure analysis of the Guizhou Gelao ethnic group based on 35 Y-STR loci

In this research, 35 Y-chromosomal short tandem repeat (Y-STR) loci were analyzed in 286 unrelated healthy Gelao male individuals from Guizhou Province, China. Allelic and haplotype frequencies, haplotype diversity (HD), haplotype match probability (HMP), and discrimination capacity (DC) values were computed. Pairwise Rst values were assessed by AMOVA analysis and visualized through multidimensional scaling and neighbor-joining tree construction. A total of 609 alleles were detected at the 35 Y-STR loci, and the allelic frequencies ranged from 0.0035 to 0.8322. The HD, HMP, and DC were 0.9999, 0.0036, and 0.9825, respectively. A total of 281 haplotypes were found at 35 loci in the 286 Gelao individuals, 98.25% of which were unique. Related forensic parameters revealed that this panel of 35 loci had a high level of genetic polymorphisms in the Gelao group. However, the use of multi-copy and rapidly mutating Y-STR loci could significantly increase the discrimination power of a common Y-STR panel. Analyses of population differentiation with the same set of common Y-STR loci demonstrated that the Gelao group has a closer genetic relationship with the Guizhou Han and Guizhou Miao groups than other groups.     

Forensic characteristics and phylogenetic analysis of Hubei Han population in central China using 17 Y-STR loci

Currently, the largest national database within the Y chromosome haplotype reference database (YHRD, https://yhrd.org, release 53) is China, which has approximately 38000 Y chromosomal 17-marker (Yfiler) haplotypes. These haplotype profiles derived from the vast majority of Chinese administrative divisions, but no haplotype data was available for Hubei province, which is located in the Central China region. Herein, 429 unrelated male Chinese Han individuals residing in Hubei province were recruited and genotyped with 17 Y-STR loci. 115 alleles were identified with corresponding allele frequencies spanned from 0.0023 to 07506. The gene diversity (GD) values ranged from 0.3988 at DYS438 to 0.9573 at DYS385a/b. A total of 410 distinct haplotypes were obtained with the overall haplotype diversity (HD) and discrimination capacity (DC) was 0.9995 and 0.9557, respectively. Additionally, genetic relationships along administrative (Han Chinese from different provinces) and ethnic divisions (minority ethnic groups) were analyzed using analysis of molecular variance (AMOVA) tests and visualized by multidimensional scaling plots (MDS). The Han ethnicity including the Hubei Han shows a high genetic homogeneity all across China and significant genetic differences existed between the Hubei Han and some ethnic groups, most prominently for the Kazakhs and the Tibetans.     

Genetic analysis of 27 Y-chromosomal STR loci in a Zimbabwean Shona ethnic group

Buccal swabs from 200 unrelated Zimbabwean males were collected from voluntary participants located in Harare province. The 5-dye SureID® 27Y Human STR Identification Kit was used to perform multiplex polymerase chain reactions (PCR) and generate Y-chromosomal DNA profiles. This kit targets markers DYS456, DYS576, DYS570, DYS481, DYF387S1, DYS627, DYS393, DYS391, DYS390, DYS635, DYS449, DYS533, DYS438, DYS389I, DYS448, DYS389II, DYS19, GATA_H4, DYS518, DYS458, DYS460, DYS437, DYS439, DYS392, and DYS385, similar to the Yfiler® Plus Amplification Kit. A total of 161 haplotypes were generated with the PowerPlex® Y system, whereas 159 complete haplotypes were generated for the Yfiler® Plus system. Haplotype Discrimination Capacity (DC) with the Yfiler® Plus system was determined to be 0.9686, while the Genetic Diversity (GD) of the targeted loci ranged from 0.03748 at DYS392 to 0.867239 at DYS449. One haplotype contained the triallelic pattern 37, 38, and 39 at DYS387S1. In addition, marker DYS387S1 and marker DYS385 had 13 counts of microvariant alleles overall, while 9 null allele counts were noted at marker DYS448. Genetic distances between our population data and 22 other data sets from African countries and people of African descent were estimated and results showed significant genetic variation.     

Genetic substructure and forensic characteristics of Chinese Hui populations using 157 Y-SNPs and 27 Y-STRs

The Hui group is the second largest ethnic minority and one of the most widespread ethnic groups in China. However, the genetic architecture of the Hui population remains largely unexplored, particularly with respect to the male-specific region of the Y chromosome. Here, we studied nine Hui populations (Xinjiang, Qinghai, Gansu, Ningxia, Shaanxi, Henan, Shandong, Sichuan, Yunnan) using 157 Y-chromosome single nucleotide polymorphisms (Y-SNPs) and 27 short tandem repeats (Y-STRs) to unravel their genetic substructure and forensic characteristics. A total of 650 unrelated male samples from the Hui populations were genotyped by SNaPshot^®, a single base extension (SBE) assay. Finally, 95 terminal haplogroups and high haplotype diversity (0.9999) were observed in Hui populations. Frequency heat map matrices, genetic distance (F_ST) and network analysis within Hui populations indicated that these nine Hui populations can be divided into three groups: Hui populations from the northwest (NWH), Hui populations from Sichuan and Shandong (SSH), and Hui populations from Yunnan (YNH). Our results suggested that we should use different databases for different Hui samples in forensic cases. Comparison with other populations that used different population genetic analysis revealed that the Hui populations had close relationships with East Asian populations, especially Chinese Han population. Overall, the high-resolution panel with Y-SNPs and Y-STRs gives new and complete insight into Hui populations, which can be used to interpret the genetic substructure of Hui populations and affect the utility of forensic databases.     

Y-SNP and Y-STR analysis in a Japanese population

In this study, four Y-SNPs (M122, P31, M174 and M216) were analyzed in 207 Japanese males (Gunma, Fukui, Kagoshima and Tokushima Prefecture). Eleven Y-STRs, including DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS389, DYS385 and YCAII were also investigated in each prefecture. As a new technique, we used Cycleave PCR method with real-time PCR, which allows detection of Y-SNPs by an easier and faster method. Regarding Y-SNPs, each region in Japan could be almost classified based on two types, the D and O type. We found that the O type was remarkably higher in Kagoshima Prefecture than in other areas. Moreover, the D type was more prevalent than the O type in Gunma Prefecture, which is geographically located at the center of Japan. These findings of geographical differences may be related to the historical background and population movements of Japanese. Y-STRs were analyzed and data from Tokushima Prefecture that we previously reported was included in the analyses. As a result, DYS385 showed the highest gene diversity (GD) value (GD = 0.953), while DYS391 showed the lowest GD value (GD = 0.288). Haplotype diversity (HD) value of only Y-STRs (Extended haplotype) was estimated at 0.99981, whereas the HD value of Y-SNPs/Y-STRs was 0.9988.     

Genetic polymorphisms of 24 Y-STR loci in Hani ethnic minority from Yunnan Province,Southwest China

International Journal of Legal Medicine - In the present study, 24 Y-chromosomal short tandem repeat (Y-STR) loci were analyzed in 250 unrelated Hani male individuals from Lvchun county, Honghe...     

Genetic analysis of 17 Y-STR loci in Han and Korean populations from Jilin Province,Northeast China

In this study, 17 Y chromosomal short tandem repeats (Y-STRs) were analyzed in 302 male individuals from the Chinese Han and Korean populations of Jilin Province. The haplotype diversities of two populations reached 0.99969 and 0.99874, respectively. The Jilin Han and Korean populations differed from each other significantly. The Jilin Han population showed no significant difference from almost any other Han population, but it did show significant differences from most other Chinese ethnic populations. The haplotype frequencies in the Jilin Korean population studied here showed significant differences from all reference populations in earlier reports. These data provide a reference for the Y-STR database in Jilin Province, and they may be valuable for population genetic analysis.     

Genetic polymorphism of 17 Y chromosomal STRs in Kazakh and Uighur populations from Xinjiang,China

To evaluate the utility of Y-STR data for DNA testing in two ethnic populations of Xinjiang province, a sample of 338 subjects (121 Kazakhs and 217 Uighurs) was tested. In the Kazakh and Uighur populations, the haplotype diversity was 0.868 and 0.996, respectively, and the discrimination capacity was 0.5950 and 0.8940, respectively. High numbers of singleton haplotypes were observed among Xinjiang Uighurs, but fewer were found in Kazakhs. Our results were also compared with geographically and linguistically close populations.     

Analysis of 36 Y-STR marker units including a concordance study among 2085 Dutch males

The genotypes of 36 Y-chromosomal short tandem repeat (Y-STR) marker units were analysed in a Dutch population sample of 2085 males. Profiling results were compared for several partially overlapping kits, i.e. PowerPlex Y, Yfiler, PowerPlex Y23, and two in-house designed multiplexes with rapidly mutating Y-STRs. Nineteen Y-STR marker units, of which two are rapidly mutating, reside in at least two of these multiplexes, and for these markers concordance testing was performed. Two samples showed discordant genotyping results and the probable causative base change was revealed by Sanger sequencing. In addition, we encountered concordant, but aberrant genotyping results including one allele with low peak height and several null alleles. For 12 samples, this involved a null allele in two adjacent loci suggesting a large and recurrent deletion as the samples represent three distinct haplogroups. For each marker unit, the allele counts and frequencies are presented, as are the haplotype counts and haplotype diversities for several combinations of markers.     

Genetic analysis of 17 Y-chromosomal STR loci of Chinese Tujia ethnic group residing in Youyang Region of Southern China

Y-STR haplotype data were obtained in a population sample of 197 unrelated healthy male individuals of Chinese Tujia ethnic minority group residing in an autonomous county of Southern China using 17 Y-chromosome STR markers. A total of 197 haplotypes were identified in the set of Y-STR loci. The overall haplotype diversity for the Tujia population at 17 Y-STR loci was 1.0000 ± 0.0005. Genetic distance was estimated between this population and other 14 Chinese populations including Paiwan and Atayal populations of Taiwan, and Southern Han, Dong, Jing, Miao, Yao, Zhuang, Yi, Maonan, She, Hui, Sala, and Tibetan ethnic groups. The results demonstrated that the 17 Y-STR loci analyzed were highly polymorphic in Tujia ethnic group examined and hence useful for forensic cases, paternity testing, and population genetic studies.     

Haplotype analysis of the polymorphic 24 Y-STR markers in six ethnic populations from China

Twenty-four Y-STR loci were analysed in 1446 males from the following six Chinese ethnic populations: Guangxi Han (n=600), Gin (n=161), Maonan (n=135), Miao (n=186), Zhuang (n=226) and Yao (n=138) using the AGCU Y24 STR amplification kit. The lowest estimates of genetic diversity (below 0.5) correspond to markers DYS391 (0.4006), DYS438 (0.4300), and DS388 (0.4907), and the greatest diversity corresponds to markers DYS385a/b (0.9636) and DYS527a/b (0.9439). Moreover, there were 1331 different haplotypes identified from the 1446 total samples, of which 1233 were unique. Notably, we observed shared haplotypes between the four ethnic populations (Maonan, Miao, Zhuang, Yao ethnic population), except between the Guangxi Han and Gin population. The estimated overall haplotype diversity (HD) was 0.9997. A multidimensional scaling (MDS) plot based on the genetic distances between populations demonstrates the genetic similarity of the Maonan, Miao and Zhuang populations with genetic distance below 3.0. No substructure correction is required to estimate the rarity of a haplotype comprising 24 markers. In summary, the results of our study indicate that the 24 Y-STRs have a high level of polymorphism in these six Chinese ethnic populations and could therefore be a powerful tool for forensic applications and population genetic studies.     

Genetic analysis of 29 Y-STR loci in Han population from Dongfang,Southern China

International Journal of Legal Medicine - In the present study, blood samples of 984 unrelated Han individuals were collected from Dongfang, Southern China, after informed consent. A total of 29...     

Genetic analysis of 50 Y-STR loci in Dong,Miao, Tujia,and Yao populations from Hunan

International Journal of Legal Medicine - To investigate the genetic polymorphism of Y chromosome short tandem repeat (Y-STR) loci in Dong, Miao, Tujia, and Yao minority populations from Hunan...