Haplotype analysis of the polymorphic 40 Y-STR markers in Chinese populations

Forty Y-STR loci were analyzed in 1128 males from the following six Chinese ethnic populations: Han (n = 300), Hui (n = 244), Korean (n = 100), Mongolian (n = 100), Uighur (n = 284) and Tibetan (n = 100), utilizing two new generation multiplex Y-STR systems, AGCU Y24 STR and GFS Y24 STR genotyping kits, which allow for the genotyping of 24 loci from a single amplification reaction in each system. The lowest estimates of genetic diversity (below 0.5) correspond to markers DYS391 (0.441658) and DYS437 (0.496977), and the greatest diversity corresponds to markers DYS385a/b (0.969919) and DYS527a/b (0.94676). A considerable number of duplicate and off-ladder alleles were also revealed. Additionally, there were 1111 different haplotypes identified from the total 1128 samples, of which 1095 were unique. Notably, no shared haplotypes between populations were observed. The estimated overall haplotype diversity (HD) was 0.999085, and its discrimination capacity (DC) was 0.970745. An MDS plot based on the genetic distances between populations showed the genetic similarity of the southern Han population to the Northern populations of Hui, Korean, Mongolian and Uighur and a clear genetic departure of the Tibetan population from other populations. For the Y STR markers, population substructure correction was considered when calculating the rarity of the Y STR profile. However, because the haplotype based Fst values are extremely small within the present data (0.000153 with 40 Y-STRs), no substructure correction is required to estimate the rarity of a haplotype comprising 40 markers. In summary, the results of our study indicate that the 40 Y-STRs have a high level of polymorphism in Chinese ethnic groups and could therefore be a powerful tool for forensic applications and population genetic studies.     

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.     

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.     

Population genetics for Y-chromosomal STRs haplotypes of Chinese Xibe ethnic group

Allele and haplotype frequencies of 11 Y-chromosomal short tandem repeats (STRs) included in the PowerPlex^® Y Systems (Promega) were determined in a sample of 280 unrelated healthy autochthonous male individuals of the Chinese Xibe ethnic minority group living in Liaoning (northeast of China). The gene diversity values of the Y-STRs loci ranged from 0.3618 (DYS391) to 0.9686 (DYS385a/b). A total of 237 haplotypes were identified in the Y-STR loci, among which 207 were unique, 22 was found in 2 individuals, 4 were shared in 3 individuals, 3 were shared in 4 individuals, and 1 was shared in 5 individuals. The observed haplotype diversity value and discrimination capacity were 0.9984 and 0.8464, respectively. AMOVA tests demonstrated significant genetic heterogeneity between the Xibes and 16 reference populations from China and other Asian populations, justifying the establishment of local databases in the Chinese Xibe ethnic group for forensic application.     

Population data for 12 Y-chromosome STR loci in a sample from Honduras

Haplotype, allele frequencies and population data of 12 Y-chromosome STR loci DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 were determined from a sample of 128 unrelated male individuals from Honduras, Central America. A total of 112 haplotypes were identified by the 12 Y-STR loci of which 98 were unique. The haplotype diversity (98.99%) and the proportion of different haplotypes (87.50%) were estimated. Genetic distances were calculated between Honduras and other populations from Southern and Central America, Europe and Africa. The analysis of a Multi Dimensional Scaling (MDS) plot, based on pairwise R_ST genetic distances, allowed to conclude that Honduras is highly differentiated from the African samples (0.343  R_ST  0.620; P = 0.000) and from a Native American sample from Argentina, Tobas (R_ST = 0.210, P = 0.000). Honduras showed a lower genetic distance to the European cluster (composed by European and South American general population samples from Brazil, Argentina, Colombia and Venezuela) than to the Central American cluster (Mexico and El Salvador).     

Y-chromosomal STR haplotypes and their applications to forensic and population studies in east Asia

We have analyzed 11 Y-STR loci (DYS19, the two DYS385 loci, DYS388, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DXYS156Y) in 700 males from ten ethnic groups in east Asia in order to evaluate their usefulness for forensic and population genetic studies. A total of 644 different haplotypes were identified, among which 603 (86.14%) were individual-specific. The haplotype diversity averaged over all populations was 0.9997; using only the nine Y-STRs comprising the minimal haplotype (excluding DYS388 and DXYS156Y) it was 0.9996, a value similar to that found in 1924 samples from other Asian populations (0.9996; Lessig et al. Legal Medicine 5(2003) 160–163), and slightly higher than in European populations (0.9976; n=11,610; Roewer et al. For Sci International (2001) 118:103–111). All of the individual east Asian populations examined here had high haplotype diversity (0.997), except for the Mongolians (0.992) and Manchurians (0.960). The most frequent haplotype identified by the nine markers was present at only 1% (7/700). Population comparisons based on _ST or genetic distance measures revealed clustering according to the traditional northeast–southeast distinction, but with exceptions. For example, the Yunnan population from southern China lay among the northern populations, possibly reflecting recent migration, while the Korean population, traditionally considered northern, lay at the boundary between northern and southern populations. An admixture estimate suggested 55(51–59)% northern, 45(41–49)% southern contribution to the Koreans, illustrating the complexity of the genetic history of this region.Electronic Supplementary Material Supplementary material is available for this article at .     

Y-chromosomal STR haplotypes in Chinese Uigur ethnic group

We have already coamplified minimal haplotypes (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385I/II), two additional loci, namely, DYS438, DYS439, and Amelogenin, in a single PCR using the Y-PLEX 12 kit. We investigated 107 unrelated male individuals from the Uigur ethnic group and studied the allelic frequency distribution and haplotype diversity of 11 Y-chromosomal STRs. A number of 43 alleles (nine STR loci) and 27 phenotypes (including DYS385) were detected, with frequencies ranging from 0.0092 to 0.6296. A total of 103 haplotypes were identified, among which 99 were individual-specific and four haplotypes were found twice. The haplotype diversity for these 12 Y-STR loci was 0.9993.     

Human Y-chromosomal STR types in north Thailand

A north Thai Y-haplotype database consisting of the loci DYS19, DXYS156-Y, DYS390, DYS391, DYS392, DYS393, and the four subsegments of DYS389 is presented. We observed 44 Y-types in 50 unrelated Thais, and the haplotype diversity was calculated to be 97.36%. No Y-types were shared with a sample of 55 Japanese, but 3 matches were found in a sample of 61 Han Chinese, and there was one Thai-German match in a larger west German sample (n = 179).     

Forensic characteristics and genetic analysis of both 27 Y-STRs and 143 Y-SNPs in Eastern Han Chinese population

Y-chromosome short tandem repeat (Y-STR) and Y-chromosome single nucleotide polymorphism (Y-SNP) frequency distributions provide resources for assessment of male population stratification among world-wide populations. Currently, the Y-STR Haplotype Reference Database (YHRD) contains numerous Y-chromosome haplotype profiles from various populations and countries around the world. However, for many of the recently discovered and already phylogenetically mapped Y-SNPs, the population data are scarce. Herein, the typing of 27 Y-STRs (Yfiler Plus) and 143 Y-SNPs (self-designed Y-SNP panel) was performed on 1269 unrelated males from 11 Han Chinese populations. Haplogroup O-M175 was the most predominant haplogroup in our Han Chinese data, ranging from 67.34% (Henan Han) to 93.16% (Guangdong Han). The highest haplogroup diversity (0.967056) was observed in Heilongjiang Han, with a discrimination capacity (DC) value of 0.3723. The number of alleles at single-copy loci varied from 2 for DYS391 (Guangdong Han) to 16 for DYS518 (Henan Han). For the majority of the populations (8/11), both the haplotype diversity and DC values are 1.0000. Furthermore, genetic differentiations were observed between Northern and Southern Han Chinese. These genetic differences were mainly reflected in haplogroup distribution and frequency, and they were confirmed by statistical analysis.     

Haplotype and mutation analysis for newly suggested Y-STRs in Korean father–son pairs

In this study, 363 Korean father–son haplotype transfers in 351 families were analyzed using an in-house multiplex PCR system for 14 Y-STRs (DYS385a/b, DYF387S1, DYS391, DYS449, DYS460, DYS481, DYS518, DYS533, DYS549, DYS570, DYS576, DYS627 and DYS643), that included 11 loci newly added to the PowerPlex Y23 system or the Yfiler Plus system. The Y-STRs showed gene diversity values ranging from 0.2499 to 0.9612; the multicopy Y-STR loci DYS385 and DYF387S1 had high gene diversity of 0.9612 and 0.9457, respectively. In addition, DYF387S1, which has two copies, showed three alleles in seven individuals, and micro-variant alleles were observed in 14 individuals at four loci (DYS448, DYS518, DYS570 and DYS627). Among 351 haplotypes for the 11 newly added Y-STRs, 350 different haplotypes were observed, with an overall haplotype diversity of 0.9999 and discrimination capacity of 99.72%. In 363 haplotype transfers from 351 pedigrees, 29 single-step mutations were observed at 11 Y-STRs. Locus-specific mutation rate estimates varied from 0.0 to 1.93 × 10⁻², with an average estimated mutation rate of 6.66 × 10⁻³. Two father–son pairs had mutations at two different loci in 11 Y-STRs. The number of pairs with mutations at multiple loci increased to five when the mutation event was investigated for haplotype transfer at 28 Y-STRs including 17 Yfiler loci and 11 Y-STRs examined in this study: four father–son pairs had mutations at two loci, and one pair had mutations at three loci. Overall, mutations were frequently observed at DYS449, DYS576 and DYS627 loci, which are known to be rapidly mutating Y-STRs. Mutation rate estimates at most loci were not significantly different from rates in other populations, but estimates for DYF387S1, DYS518 and DYS570 were considerably lower in the Korean population than in other populations.     

Population genetics for 17 Y-STR loci(AmpFISTR®Y-filerTM) in Luzhou Han ethnic group

In this study, 17 Y-STR loci(AmpFISTR^®Y-filerTM)—DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y-GATA H4, DYS437, DYS438, DYS448 were analyzed in 424 unrelated males from Luzhou Han ethnic group, Southwest China. 365 haplotypes were observed. The discrimination capacity was 0.8608 and the haplotype diversity was 0.9992.     

Genetic sub-structure in western Mediterranean populations revealed by 12 Y-chromosome STR loci

Haplotype and allele frequencies of 12 Y-chromosome short tandem repeat (Y-STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385 a/b, DYS437, DYS438 and DYS439) included in the Powerplex® Y System were determined in seven western Mediterranean populations from Valencia, Majorca, Ibiza (eastern Spain), Sicily and three Calabrian provinces (southern Italy). Amongst the 554 males included in the study, 443 different haplotypes were observed of which 372 were only observed once. The other haplotypes were shared by two to seven men. The overall haplotype diversity was 0.9988?±?0.0002. These Y-STRs markers showed a low capacity of discrimination (56.3%) in the Ibiza population probably due to genetic drift. Comparisons between the populations studied and other neighbouring populations showed a clear genetic sub-structure in the western Mediterranean area.     

Haplotype diversity of 17 Y-STR loci in a Chinese Han population sample from Shanxi Province,Northern China

The distribution of 17 Y-chromosome STR loci DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y-GATA-H4, DYS437, DYS438, and DYS448 haplotypes was determined in a population sample of 222 unrelated Chinese Han from Shanxi Province, Northern China. A total of 219 haplotypes were observed, and of these, 216 were unique, while 3 were found two times. The overall haplotype diversity was 0.9999 and the discrimination capacity was 0.9865, indicating a high potential for differentiating between male individuals in this population. Comparison analysis via Analysis of Molecular Variance (AMOVA) and construction of MDS plot revealed that Shanxi Han sample clusters with Chinese origin populations and stands far apart of the non-Chinese populations, justifying the establishment of local databases in Shanxi Han population for any future forensic and genetic epidemiology efforts in this region.     

Fourteen short tandem repeat loci Y chromosome haplotypes: Genetic analysis in populations from northern Brazil

Fourteen Y-STR loci (DYS458, DYS439, Y-GATA H4, DYS576, DYS447, DYS460, DYS456, YGATA A10, DYS437, DYS449, DYS570, DYS635 or Y-GATA C4, DYS448 and DYS438) were analysed in 873 males from eight northern Brazil populations: Belém (N=400), Santarém (N=69), Manaus (N=75), Macapá (N=65), Palmas (N=30), Rio Branco (N=32), Porto Velho (N=135) and Boa Vista (N=67). A total of 871 different haplotypes were identified, of which 869 were unique. The panel's estimated total haplotype diversity (HD) is 0.9988, and its discrimination capacity (DC) is 0.9980. The lowest estimates of genetic diversity correspond to markers Y-GATA H4 (0.550) and DYS460 (0.581), and the greatest (above 0.700) to markers DYS458, DYS576, DYS447, YS449, DYS570 and DYS635. The genetic parameters obtained were higher for the 14-Y-STR panel than that for the minimum haplotype set (HD=0.9969; DC=0.76) and the parameters were similar to those obtained with the panel of 17 YSTR of YHRD (HD=0.9987; DC=0. 9870). The analysis of molecular variance (AMOVA) indicated that most of the genetic variance is found within populations and a smaller, but significant part, is found among populations (R(ST)=0.027, p value=0.009). The data when compared with those from African, Amerindian and European populations have shown no significant genetic distance between northern Brazil populations and Europeans, but there is a significant genetic distance when compared to Africans and Amerindians. The discrimination capacity of the markers shows a high potential for forensic analysis.     

Genetic analysis of 39 Y-STR loci in a Han population from Henan province,central China

A total of 39 Y-chromosomal short tandem repeat (Y-STR) loci included in the advanced commercial six-dye multiplex system (AGCU Database Y30 kit) and a custom-designed four-dye multiplex system were investigated in 259 unrelated healthy Chinese males residing in Henan Province, central China. The haplotype diversity (HD) values were 0.99997 and 1.0000 for the six and four fluorescent-multiplex amplification systems, respectively. The discrimination capacity (DC) values were 0.9961 and 1.0000, respectively. When the 39 Y-STR loci were considered, 259 unique haplotypes were obtained in Henan Han individuals with both the haplotype diversity and discrimination capacity being 1.000. The gene diversity (GD) of 39 Y-STR loci in the studied group ranged from 0.3956 (DYS588) to 0.9990 (DYF403S1). Population comparisons between the Henan Han and 24 reference groups were performed. Both multidimensional scaling plots and phylogenetic analysis demonstrated that significant genetic differences existed between Henan Han and reference ethnic minorities of China, particularly the Tibetan, Uighur, and Mongolian populations. Moreover, the results indicated that 39 Y-STRs included in the two fluorescent-multiplex amplification systems are highly polymorphic and informative in the studied populations and can be employed as complementary tools for forensic application and human genetics research.

     

Haplotype diversity of 17 Y-chromosome STR loci in Han population from different areas of Sichuan Province,Southwest China

The distribution of 17 Y-chromosome short tandem repeat (STR) loci, included in the AmpFlSTR®Yfiler™ amplification kit, were analyzed in six different samplings (N = 878) from Sichuan, China. Haplotype diversity and discrimination capacity (DC) values were calculated. Pairwise Rst values were evaluated in AMOVA analysis and visualized through multidimensional scaling (MDS). A total of 547 unique haplotypes were detected. The observed haplotype diversity and discrimination capacity were 0.9995 and 0.7745, respectively. The homogeneity of Sichuan Han population was detected when microareas were analyzed. This population exhibited no significant genetic difference to both of the minorities in reference databases, Mongolian and Manchu, which had been through mass ethnic amalgamation with Sichuan Han population in history.     

Analysis of 24 Y chromosomal STR haplotypes in a Chinese Han population sample from Henan Province,Central China

We analyzed haplotypes for 24 Y chromosomal STRs (Y-STRs), including 17 Yfiler loci (DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DY438, DYS439, DYS448, DYS456, DYS458, DYS635 and Y-GATA-H4) and 7 additional STRs (DYS388, DYS444, DYS447, DYS449, DYS522 and DYS527a/b) in 1100 unrelated Chinese Han individuals from Henan Province using AGCU Y24 STR kit systems. The calculated average gene diversity (GD) values ranged from 0.4105 to 0.9647 for the DYS388 and DYS385a/b loci, respectively. The discriminatory capacity (DC) was 72.91% with 802 observed haplotypes using 17 Yfiler loci, by the addition of 7 Y-STRs to the Yfiler system, the DC was increased to 79.09% while showing 870 observed haplotypes. Among the additional 7 Y-STRs, DYS449, DYS527a/b, DYS444 and DYS522 were major contributors to enhancing discrimination. In the analysis of molecular variance, the Henan Han population clustered with Han origin populations and showed significant differences from other Non-Han populations. In the present study, we report 24 Y-STR population data in Henan Han population, and we emphasize the need for adding additional markers to the commonly used 17 Yfiler loci to achieve more improved discriminatory capacity in a population with low genetic diversity.     

Investigation of extended Y chromosome STR haplotypes in Sardinia

Y-chromosomal variation of selected single nucleotide polymorphisms (SNPs) and 32 short tandem repeat (STR) loci was evaluated in Sardinia in three open population groups (Northern Sardinia, n = 40; Central Sardinia, n = 56; Southern Sardinia, n = 91) and three isolates (Desulo, n = 34; Benetutti, n = 45, Carloforte, n = 42). The tested Y-STRs consisted of Yfiler^® Plus markers and the seven rapidly mutating (RM) loci not included in the YFiler^® Plus kit (DYF399S1, DYF403S1ab, DYF404S1, DYS526ab, DYS547, DYS612, and DYS626).As expected, inclusion of additional Y-STR loci increased haplotype diversity (h), though complete differentiation of male lineages was impossible even by means of RM Y-STRs (h = 0.99997).Analysis of molecular variance indicated that the three open populations were fairly homogeneous, whereas signs of genetic heterogeneity could be detected when the three isolates were also included in the analysis.Multidimensional scaling analysis showed that, even for extended haplotypes including RM Y-STR markers, Sardinians were clearly differentiated from populations of the Italian peninsula and Sicily. The only exception was represented by the Carloforte sample that, in accordance with its peculiar population history, clustered with Northern/Central Italian populations.The introduction of extended forensic Y-STR panels, including highly variable RM Y-STR markers, is expected to reduce the impact of population structure on haplotype frequency estimations. However, our results show that the availability of geographically detailed reference databases is still important for the assessment of the evidential value of a Y-haplotype match.     

Population data for 17 Y-chromosome STRs in a sample from Apulia (Southern Italy)

The 17 Y-STR loci included in the AmpFLSTR Yfiler PCR Amplification Kit were analyzed in 98 unrelated healthy males from Apulia (Southern Italy). A total of 97 different haplotypes were identified, of which 96 haplotypes were unique and 1 occurred twice. Allele frequencies for each Y-STR locus in pooled sample and estimated value of gene diversity (GD) were evaluated. The lowest value of GD was observed for DYS392 (0.126) and the highest one (0.936) for DYS385. The HD (haplotype diversity) for the studied Y-STR set showed a value of 0.9994, with an HMP (haplotype match probability) value of 0.0006, while the overall DC was 98.98%. Microvariant alleles were found for the DYS458 and DYS385 markers and sequenced.Furthermore, Φ_st-based genetic distance computation and pair-wise analysis of molecular variance (AMOVA) test were carried out. When comparing our population with the Apulia sample previously investigated, the AMOVA analysis detected no evidence for significant differentiation. The comparison with all Italian populations submitted to the YHRD website showed no relevant differences with all Southern Italian populations (San Giorgio La Molara, Belvedere, Trapani and Catania) and significant genetic deviation with all Northern Italian populations (Udine, Biella, La Spezia, Modena, Ravenna, Marche and North Sardinia). Moreover, the other populations and meta-populations belonging to the whole Mediterranean area (Croatia, Macedonia, Albania, Greece, Turkey, Israel, Libya, Tunisia, Algeria, Morocco and Spain) were different from our Apulia sample. The data were submitted to YHRD.     

Population study and evaluation of 20 Y-chromosome STR loci in Germans

The nine European minimal haplotype (EMH) loci, the two SWGDAM loci and five further single-copy Y-chromosomal short tandem repeats (Y-STRs) DYS446, DYS447, DYS448, DYS449, DYS463, and the multicopy loci DYS464 were evaluated in the German population groups Dresden, Hamburg, Rostock, Munich, and the Sorbs who are a Slavic-speaking minority in Lusatia. Highest gene diversities in all populations were shown for DYS464, DYS385, and DYS449 (D=0.8559–0.9486). The haplotype diversity for the European minimal haplotype loci ranged between 0.9852 for Sorbs and 0.9983 for the Hamburg population showing that there is a significant portion of haplotypes which could not be resolved. Advanced typing using DYS446, DYS447, DYS448, DYS449, DYS463, and DYS464 discriminated all non-related individuals of the Dresden, Hamburg, and Rostock populations. Evaluation of the Y-STRs was accomplished by sequence analysis of all allelic fragments of the allelic ladders and microvariant alleles of DYS385 and the determination of the amounts of stutter products of the loci. Electronic Supplementary Material Supplementary material is available for this article at