Genetic polymorphism and variability in the Guangdong Hakka, Teochew, and Cantonese groups: A comprehensive analysis of 19 X-STRs

BACKGROUND

X chromosomeshort tandem repeat (X-STR) loci are playing an increasingly important role inforensic work, identifying female traces in male contamination and explainingcomplex kinship analyses.

METHODS

In this study, we analyzed thegenetic polymorphism of 19 X-STR loci in the Guangdong Hakka, Teochew and Cantonese groups, respectively, aswell as in the Guangdong Hakka, Teochew andCantonese pooled Han. The genetic diversity and forensic characteristics of the19 X-STRs and 7 linkage groups were investigated, respectively.

RESULTS

The experiments showed that the genetic diversity (GD) and polymorphism information content (PIC) in the pooledGuangdong Han ranged from 0.5320 to 0.9234 and 0.4369 to 0.9171, respectively, and the cumulative power of discrimination for males (PDM), power of discrimination for females (PDF) and mean paternity exclusion chance (MEC) were higher than 0.9999999, indicating that the 19 X-STRs had high geneticpolymorphism and discriminatory power. Genetic differences among Chinese Hansubgroups and among different Chinese populations were investigated byphylogenetic reconstruction and principal component analysis (PCA), respectively. Genetic analyses based on neighbor-joining (NJ) tree and principal component analysis plot showed that Cantonese, Teochew and Hakka were closely genetically related, and different populations with closer linguistic components had more genetic affinity.

CONCLUSIONS

This study adds to the forensic X-STR database and demonstrates the forensic efficiency of 19 X-STRs for the Hakka, Teochewand Cantonese populations in Guangdong, and the pooled Han of Hakka, Teochewand Cantonese people in Guangdong.

Genetic polymorphisms of 19 X-STRs in populations of Hubei Han and Guangxi Zhuang and their comparisons with 13 other Chinese populations

BACKGROUND

A prerequisite for applying short tandem repeat (STR) kits is obtaining population allele and/or haplotype frequencies and forensic parameters.

AIM

Firstly, we aimed to investigate the population data of 19 X-chromosomal STRs (X-STRs) included in the AGCU X19 STR kit in the Han people residing in Hubei Province, Central China, and the Zhuang people residing in the Guangxi Zhuang Autonomous Region of South China. Furthermore, we compared these population data with those for other Chinese populations.

SUBJECTS AND METHODS

In total, 509 unrelated Han males and 266 unrelated Zhuang males were genotyped using the AGCU X19 STR kit. Allele frequencies, haplotype frequencies, and forensic parameters were computed, and genetic differences among 15 Chinese populations were analysed.

RESULTS

The 19 X-STRs showed a high power of discrimination and high mean chance of exclusion, whether calculated using allele or haplotype frequencies. Major differences were found between Han and Oroqen, Uyghur, Mongolian, Tibetan, Li, and Yi populations. Aberrant biallelic patterns at DXS10159, DXS10134, and DXS10079 and allelic dropouts at DXS10164 were observed.

CONCLUSION

The 19 X-STRs were highly polymorphic in the Hubei Han and Guangxi Zhuang populations, and the AGCU X19 STR kit was shown to be suitable for forensic casework.

Phylogenetic analyses of the 19 STR loci in X chromosome revealed discriminant forensic characteristics for Chinese Daur and Oroqen minorities

In respect of forensic genetics, X-STRs are widely applied for deficiency paternity cases. Given the popularization of AGCU-X19 STR Kit in China, there has been investigation conducted into the genetic data and forensic parameters of 19 X-STR loci in many of the Chinese ethnic groups, which makes it possible to perform nationwide phylogenetic comparation. To evaluate the allele and haplotype diversity of 19 X-STR loci and to explore their forensic efficiency in the Daur and Oroqen minorities, unrelated healthy Daur (n = 86) and Oroqen (n = 165) individuals were recruited from Heilongjiang province, so as to reveal the phylogenetic relationship between the two minorities and other Chinese ethnic groups. Of the Daur and Oroqen minorities, 172 and 183 alleles at the 19 X-STR loci were observed, respectively. Haplotype diversity exceeded 0.9 among all the linkage clusters. High cumulative value was observed for the power of discrimination, the probability of exclusion, and the mean exclusion chance for deficiency cases (normal trios and duo cases). As revealed by this study, the panel of 19 X-STR loci is an effective supplementary tool for the kinship test of the studied nationalities.

Genetic investigation and phylogenetic analysis of three Chinese ethnic groups using 16 X chromosome STR loci

Background: The value of using X-chromosomal short tandem repeats (X-STRs) as genetic markers in human genetics has been widely recognised. However, the 16 X-STRs in the Goldeneye^® DNA ID System 17X kit have not been thoroughly applied.Aim: To investigate the genetic polymorphisms of 16 X-STRs in three main ethnic minorities (Tibetan, Mongolian and Kazakh) in China and to reveal the phylogenetic relationships of different populations.Subjects and methods: A total of 245 Tibetan, 168 Mongolian and 105 Kazakh individuals were genotyped using this 17X kit. The allelic frequencies and other parameters were calculated. An additional eight Chinese populations and nine global populations were included in genetic comparisons based on 16 or 8 overlapped X-STRs.Results: A total of 147 alleles were observed from 16 X-STRs with allelic frequencies ranging from 0.0024 to 0.7952 in the three studied groups. Based on 16 X-STRs, Tibetans, Kazakhs and Mongolians showed more similarity to each other and were genetically distinct from the Shanghai Han group; based on 8 X-STRs, only the genetic relationships between different nations could be clarified.Conclusions: Our study presents an extensive report on a novel X-STR assay in three Chinese ethnic groups and a comprehensive genetic comparison between different populations based on these X-STRs.

Genetic polymorphisms in 16 X-STR loci analyzed in the She population from Zhejiang Province, China

Allele frequencies for 16 X-chromosomal STR (X-STR) loci (DXS6795, DXS9902, DXS8378, HPRTB, GATA165B12, DXS7132, DXS7424, DXS6807, DXS6803, GATA172D05, DXS6800, DXS10134, GATA31E08, DXS6810, DXS6789, and DXS10159) were obtained from a sample set of 296 unrelated individuals from the Zhejiang She population in China. We observed a total of 117 alleles in the group, with allele frequencies ranging from 0.0022 to 0.8143. The most informative marker for the studied population was DXS10134, with a polymorphism information content (PIC) of 0.8547, and the least polymorphic locus was DXS6800 (PIC = 0.3071). The power of discrimination (PD) varied from 0.3244 (DXS6800) to 0.8680 (DXS10134) in males and from 0.5263 (DXS6800) to 0.9693 (DXS10134) in females. The combined PD_M and PD_F was 0.999999996987156 and 0.999999999999993, respectively. The combined MEC_D and MEC_T was 0.999993100252466 and 0.999999973583357, respectively. In the population comparisons, a close relationship between the Zhejiang She and Eastern Han populations was observed. In general, the present findings indicate that the 16 X-STR loci examined are highly genetically polymorphic in the She population of Zhejiang, providing useful information on She for forensic science and population genetic studies.

Population genetic analysis of Chinese Zhuang and Mulao minorities using AGCU-X19 STR kit

To investigate the genetic variation and forensic efficiency of 19 X-STR loci in the Zhuang and Mulao minorities, we calculated allele frequencies, forensic parameters, and haplotype frequencies of 405 Zhuang and 234 Mulao unrelated healthy individuals from Guangxi Zhuang Autonomous Region of China. Furthermore, we analyzed the population genetic differentiations between the two minorities and other reported Chinese populations.

Forensic characteristics and phylogenetic analyses of the Chinese Yi population via 19 X-chromosomal STR loci

The demographic characteristics and genetic polymorphism data of 56 Chinese nationalities or 31 administrative divisions in Chinese mainland have repeatedly been the genetic research hotspots. While most genetic studies focused on some particular Chinese populations based on autosomal or Y-chromosomal genetic markers, the forensic characteristics and phylogenetic analyses of the seventh largest Chinese population (Yi ethnicity) on the X-chromosomal genetic markers are scarce. Here, allele frequencies and forensic statistical parameters for 19 X-chromosomal short tandem repeat loci (DXS7424-DXS101, DXS6789-DXS6809, DXS7423-DXS10134, DXS10103-HPRTB-DXS10101, DXS10159-DXS10162-DXS10164, DXS10148-DXS10135-DXS8378, and DXS7132-DXS10079-DXS10074-DXS10075) of 331 Chinese Yi individuals were obtained. All 19 X-chromosomal short tandem repeat (STR) loci in females were consistent with the Hardy-Weinberg equilibrium test. A total of 214 alleles were identified with the corresponding allele frequencies spanned from 0.0019 to 0.6106. The combined PE, PDF, and PDM were 0.9999999214, 0.9999999999999999999993, and 0.9999999999998, respectively. The high combined MEC_Krüger, MEC_Kishida, MEC_Desmarais, and MEC_{Desmarais Duo} were achieved as 0.9999999617638, 0.9999999999971, 0.9999999999971, and 0.9999999931538, respectively. The findings suggested that the panel of 19 X-STR loci is highly polymorphic and informative in the Yi ethnic population and can be considered to be a powerful tool in forensic complex kinship identification. Population differentiation analyses among 12 populations indicated that significant differences in genetic structure were observed in between the Yi ethnicity and the Chinese Uyghur as well as Kazakh, and genetic homogeneity existed in similar ethno-origin or geographic origin populations.