Genetic distribution and forensic evaluation of multiplex autosomal short tandem repeats in the Chinese Xinjiang Mongolian group^,

Abstract

To further enrich the genetic data of the Chinese xinjiang Mongolian group, the genetic distribution and forensic parameters of 19 autosomal short tandem repeats (STRs) were investigated. Altogether, 249 alleles were observed in these 19 STRs. The mean values of the polymorphism information content (PIC), match probability (MP), discrimination power (DP), and probability of exclusion (PE) for these 19 STRs were 0.7775, 0.0699, 0.9301, and 0.6085, respectively. Additionally, the cumulative DP and PE values obtained in the Mongolian group were 0.999 999 999 999 999 999 999 995 67 and 0.999 999 992 163, respectively. Furthermore, population genetic analysis of the Mongolian group and 20 published populations was conducted based on the population data of 15 overlapping STRs. Genetic distances indicated that the Mongolian group had closer genetic similarities with the Uyghur, Xibe, and other Chinese populations rather than the other continental populations. Multidimensional scaling analysis further revealed that the Mongolian group possessed similar genetic distributions as most Chinese populations. To sum it all up, these STRs could be used as an extremely efficient tool for forensic applications in the xinjiang Mongolian group.

To further enrich the genetic data of the Chinese Xinjiang Mongolian group, the genetic distribution and forensic parameters of 19 autosomal short tandem repeats (STRs) were investigated. Altogether, 249 alleles were observed in these 19 STRs. The mean values of the polymorphism information content (PIC), match probability (MP), discrimination power (DP), and probability of exclusion (PE) for these 19 STRs were 0.7775, 0.0699, 0.9301, and 0.6085, respectively. Additionally, the cumulative DP and PE values obtained in the Mongolian group were 0.999 999 999 999 999 999 999 995 67 and 0.999 999 992 163, respectively. Furthermore, population genetic analysis of the Mongolian group and 20 published populations was conducted based on the population data of 15 overlapping STRs. Genetic distances indicated that the Mongolian group had closer genetic similarities with the Uyghur, Xibe, and other Chinese populations rather than the other continental populations. Multidimensional scaling analysis further revealed that the Mongolian group possessed similar genetic distributions as most Chinese populations. To sum it all up, these STRs could be used as an extremely efficient tool for forensic applications in the Xinjiang Mongolian group.

STRs, with repeat units of 2–6 bp, are abundant in the human genome. The high polymorphism of STRs makes them potential genetic markers for forensic applications (Ruitberg et al., 2001). Since genetic differences existed in different populations (Rosenberg et al., 2003; Xin et al., 2008), it was imperative to obtain the population genetic data of the STR loci before these markers were used for forensic applications in certain populations.

Mongolian, the ninth minority group in China, mainly lives in the Inner Mongolia and the Xinjiang Uygur Autonomous Regions, the Gansu and Qinghai Provinces, China. Most Mongolians believe in Lama Buddhism and still maintain a semi-nomadic lifestyle (http://www.paulnoll.com/China/Minorities/min-Mongolian.html). To date, genetic polymorphism analyses of 21 non-CODIS STR (Zha et al., 2014), X-STR (Hou et al., 2007), and Y-STR (Guo, 2015) loci have been reported in the Mongolian group from the Inner Mongolia autonomous region; however, few genetic analyses have been conducted for autosomal STRs in the Xinjiang Mongolian group.

Twenty genetic markers, i.e., D3S1358, D13S317, D7S820, D16S539, Penta E, TPOX, TH01, D2S1338, CSF1PO, Penta D, D19S433, vWA, D21S11, D18S51, D6S1043, D8S1179, D5S818, D12S391, FGA, and Amelogenin loci, were simultaneously amplified using the 5-dye fluorescence system based on the AGCU EX20 kit (AGCU ScienTech, Jiangsu, China), which could be used to establish the forensic DNA database in China. In the current study, we investigated allele distributions of these markers and evaluated their forensic values in the Xinjiang Mongolian group based on the aforementioned STR panel. Moreover, the genetic distances (D_A), fixation indexes (F_ST), and multidimensional scaling (MDS) analyses were conducted among the 21 populations using the genetic data of 15 available STR loci (excluding Penta D, D12S391, D6S1043, and Penta E). Compared populations and their corresponding references were given in Table S1. Materials and methods involved in this study were given in Data S1.

Results of the Hardy-Weinberg equilibrium (HWE) tests for 19 STR loci are shown in Table S2. No deviations from the HWE were observed at these 19 STRs since their P-values for the HWE tests were greater than the significant level (0.05), implying that these loci conformed to the HWE in the studied Mongolian group.

As shown in Fig. S1, the coefficients of linkage disequilibrium (Lewontin’s D') of the pairwise loci were observed to be less than 0.2, which demonstrated the relatively weak correlations of these pairwise loci. Consequently, these STRs could be viewed as independent loci in the Xinjiang Mongolian group.

Allele frequencies of the 19 STR loci are given in Table S2. Out of the 19 STR loci, 7 to 22 alleles could be observed. The lowest number of alleles was observed at the TH01 and TPOX loci, whereas the highest number of alleles was found at the Penta E locus. Furthermore, the minimum frequency value (0.0004) was observed in several alleles of different STR loci e.g., alleles 7 and 9 at the D8S1179 locus, whereas the maximum frequency value (0.4797) was observed at allele 8 of the TPOX locus. Forensic parameters of the 19 STRs in the Mongolian group showed that the obtained MP, DP, PE, PIC, observed heterozygosity (H_o), and expected heterozygosity (H_e) values ranged from 0.0115 to 0.1751, 0.8249 to 0.9885, 0.3820 to 0.8412, 0.5996 to 0.9191, 0.6690 to 0.9223, and 0.6562 to 0.9251, respectively. Among these STRs, the TPOX locus possessed the least DP, PIC, PE, H_o, and H_e values, while the Penta E locus had the highest DP, PIC, PE, H_o, and H_e values. A previous study suggested that a locus with a PIC value more than 0.5 was highly informative (Botstein et al., 1980). Therefore, these 19 STRs could be treated as highly informative markers for the Mongolian group. Based on the results shown in Fig. S1, the multiplication law was used to calculate the cumulative DP and PE values in the Mongolian group, which were 0.999 999 999 999 999 999 999 995 67 and 0.999 999 992 163, respectively, indicating that these 19 STRs could be used for individual identification and paternity analysis in the Xinjiang Mongolian group.

The D_A heatmap of pairwise populations is shown in Fig. 1, and their corresponding values are shown in Table S3. Different colors denote different D_A value levels: cyan for low values, pink for intermediate values, and green for large values. Compared to 20 reference populations, the studied Mongolian group showed the lowest genetic distance to the Uyghur group (0.0074), followed by the Xibe (0.0097), Henan Han (0.0101), Tibetan (0.0105), Sichuan Han (0.0106), and other Chinese populations; whereas larger genetic distances were observed when compared to the African American (0.0539), Caucasian American (0.0329), Portuguese (0.0305), Mexican (0.0296), and Hispanic American (0.0231) populations. The pairwise F_ST values of these 21 populations (Table S4) also showed that the Mongolian group had lower F_ST values when paired with the Uyghur, Xibe, and Uzbek groups. The present results revealed close genetic relationships between the Mongolian group and the Uyghur, Xibe, and other Chinese populations.

Fig. 1.

Heatmap of the genetic distances (D_A) among 21 populations

Different colors indicate different levels of D_A values: cyan for low values, pink for intermediate values, and green for large values

MDS was plotted using SPSS software v18.0 based on the pairwise F_ST values of the 21 populations (Fig. 2). In Dimension 1, most Chinese populations were distinguishable from other populations, and two Central Asian groups (Uyghur and Uzbek) were located between the Chinese and other continental populations. In Dimension 2, the Mexican and African American populations, located in the upper right and lower right parts of the graph, respectively, were distinguishable from the other populations. The studied Mongolian group was located closer to the Chinese populations and farther from the other continental populations, highlighting the similar genetic distributions between Mongolian and other Chinese populations.

Fig. 2.

Multidimensional scaling analysis between the Mongolian group and other compared populations

Based on the 15 shared STR data, we found that close relationships existed between the Mongolian group and the Uyghur, Xibe, and other Chinese populations. According to Chinese historical records, the Donghu, a nomadic group living in eastern Mongolian and northeast Chinese regions, might be proto-Mongols of the present Mongolian group. In the 13th century, Genghis Khan unified an army of Mongolian tribes, and he along with his Mongolian soldiers expanded westward and soon occupied almost all Eurasiatic regions. After the fall of the Mongolian empire, these dispersed Mongolian individuals were gradually assimilated by the surrounding people and became a part of the Uyghur, Xibe, and other tribes (https://en.wikipedia.org/wiki/Mongols). Findley (2005) suggested that the modern Uyghurs probably possessed admixture genetic information of Mongolian and Caucasian people, resulting in close genetic relationships between the Mongolian and Uyghur groups. Another study also revealed that the Xibe had an intimate relationship with the Mongolian group. For instance, the phylogenetic tree constructed using 17 Y-STR loci haplotypes showed the Xibe forming a branch with the Mongolian group firstly, followed by other populations (Zheng et al., 2009). More importantly, the Xibe people are descendants of the ancient Xianbei tribes, who are a branch of the ancient Donghu group (Wu, 2002). Thus, the common ancestral origins of the Mongolian and Xibe groups likely contributed to their close ties.

In brief, allele frequencies and forensic statistical parameters were obtained for 19 autosomal STRs in the Xinjiang Mongolian group, and these results laid the foundation for the STR database spanning different Chinese ethnic groups. The cumulative DP and PE values indicated that the multiplex STR system exhibited exceedingly high values for forensic applications in the Xinjiang Mongolian group. Moreover, the results of genetic distances and MDS analysis between the studied Mongolian group and other reference populations revealed that the Mongolian group had close genetic relationships with the Uyghur, Xibe, and other Chinese populations.

List of electronic supplementary materials

Data S1

Materials and methods

Fig. S1

Reverse triangular plot of the Lewontin’s D' values for 19 pairwise STRs in the Mongolian group

Table S1

Populations used as compared populations and their corresponding references

Table S2

Allele frequencies and forensic statistical parameters of 19 STRs in the Mongolian group

Table S3

Genetic distances (D_A) among 21 populations based on the allele frequencies of 15 STRs

Table S4

Fixation index (F_ST) and their corresponding P-values of the pairwise populations