Population genetics of 24 Y-STR loci in Chinese Han population from Jilin Province, Northeast China.

BACKGROUND: It is meaningful to expand the available population information on forensic medicine and to investigate the genetic characteristics of Han population from Jilin Province, Northeast China.
METHODS: In this study, we investigated the genetic characteristics of 24 Y-chromosomal short tandem repeat (STR) loci in 1,088 unrelated Chinese Han male individuals from Jilin Province, using DNATyperTM Y24 amplification kit. Additionally, we performed the population comparison between the Jilin population and the other nine reported populations based on the Y-STR genotyping haplotypes.
RESULTS: A total of 1,067 different haplotypes were found from 1,088 unrelated individuals, of which 1,046 were unique and 21 were shared by two individuals. The gene diversity values of 22 loci ranged from 0.3870 (DYS391) to 0.9668 (DYS385ab). The random match probability was 0.0010 with the discrimination capacity of 0.9807. Population comparison showed that there were minor differences compared to Beijing Chinese Han, China Manchu, Gansu Chinese Han, and Jiangsu Chinese Han, but major differences with respect to the populations of Guangdong Chinese Han, Yunnan Chinese Han, China Hui, China Korean, and China Tibetan.
CONCLUSION: Our results showed that the 24 Y-STR loci in Jilin Han population are valuable for forensic application and human genetics.

BACKGROUND

Short tandem repeats (STRs) are being widely used in forensic DNA analysis, considering that they are diversely distributed in the human genome and present the high discrimination power among the individuals (Yao & Wang, 2016; Zhu et al., 2015). STR, as the common genetic markers in forensic DNA analysis, can provide a great powerful discrimination capability. Therefore, they can be usually utilized in the fields of personal identification and paternity testing (Chen et al., 2017; Guo, 2017; He, Wang, Liu, Hou, & Wang, 2018). Additionally, they are also used to uncover the population genetic backdrop and structure (Eaaswarkhanth et al., 2009; El Ossmani et al., 2010; Li et al., 2006; Lowery et al., 2011; Zhang et al., 2015). The STR loci are potentially related to the genetic geographic distribution and microevolutionary process of human population, which can reveal the different population genetic structure at the continental and sub‐continental scales (Verrier, Waite, Linney, Sutton, & Galgut, 1989).

The analysis of Y‐chromosomal short tandem repeat (Y‐STR) has been widely used in forensic investigation and paternity testing on account of its male‐specific characteristic and paternal genetic model (Ballantyne et al., 2014; Jobling, Pandya, & Tyler‐Smith, 1997). It can be applied for inferring the biological sex of a crime scene trace donor. Haplotypes composed of Y‐STRs are utilized to characterize paternal lineages of unknown male trace donors, especially available and useful in case that males and females have contributed to the same trace, such as in sexual assault cases. It can provide more information for identifying a male component in sexual assaults, where the very low amount of male DNA is mixed with the high amount of female DNA (Roewer, 2009).

DNATyperTM Y24 amplification kit (Physical evidence identification center, Ministry of Public Security) can co‐amplify one Amelogenin locus and 22 low mutating Y‐STR loci (DYS460, DYS389I, DYS390, DYS389II, DYS392, DYS458, DYS437, DYS385ab, GATA‐H4, DYS522, DYS456, DYS391, DYS447, DYS438, DYS448, DYS617, DYS393, DYS635, DYS439, DYS19, DYS444, and DYS527ab) with the five dye (Mo Xiaoting et al., 2017). For DYS385ab and DYS527ab loci, they contain two alleles. For the 24 Y‐STR, it is meaningful to expand the available population information on forensic medicine, for example, database construction and family investigation. Thus, we used the DNATyperTM Y24 kit to investigate the genetic characteristics of Han population from Jilin Province, Northeast China. Additionally, in order to better understand the genetic and structure and background of the Jilin Han population, we performed the population comparison with the other ethnic groups based on the genetic distances generated by the observed gene allelic frequencies.

METHODS

Ethical compliance

The research have been performed in accordance with the Declaration of Helsinki and the study was approved by the Ethics Committee of China Medical University. Informed consent regarding participating and publishing was obtained from all the participated subjects.

Study population

Blood‐stained filter papers were collected from 1,088 unrelated healthy male individuals living in Jilin Province, Northeast China after providing written informed consent to participate in the study (Figure 1).

Figure 1

In this study, Jilin Province was the area of sample collection

Data extraction, PCR amplification, and genotyping

Twenty‐four Y‐STR loci were amplified simultaneously using DNATyperTM Y24 amplification kit (Physical evidence identification center) in a GeneAmp® PCR 9700 (Life Technologies) thermal cycler, according to the manufacturer's recommendations. Subsequently, separation and detection were performed using an Applied Biosystems™ 3500 Series Genetic Analyzer (Life Technologies). Finally, the raw data were analyzed using GeneMapper ID v4.1 software (Life Technologies). We strictly followed the recommendations of the DNA Commission of the International Society of Forensic Genetics on the analysis of Y‐STRs (Gusmao et al., 2006).

Analysis of the data

PowerMarker v3.25 was used to calculate the allele frequencies and gene diversity of the 24 Y‐STR loci (Gusmao et al., 2006). For DYS385ab and DYS527ab, the haplotype frequencies were calculated on account of their two alleles. The haplotype frequencies composed of the 24 Y‐STR loci and the random match probability (sum of squares) was calculated using the Arlequin Software v3.5 (Gusmao et al., 2006). The discrimination capacity was determined as the proportion of different haplotypes in the sample. Genetic distance (Rst statistics) between our data and the other published groups was generated by the analysis of molecular variance (AMOVA) and was visualized in two multidimensional scaling (MDS) plots of Rst using the YHRD online tools (http://www.yhrd.org/Analyse/AMOVA).

RESULTS AND DISCUSSION

A total of 1,067 different haplotypes were found from 1,088 unrelated individuals, of which 1,046 were unique and 21 were shared by two individuals (see Table S1). Null alleles were observed in 12 individuals at DYS460, four at DYS389I, five at DYS390, nine at DYS389II, six at DYS458, six at DYS437, two at YGATAH4, 33 at DYS522, 14 at DYS456, four at DYS391, four at DYS447, nine at DYS438, 11 at DYS448, 92 at DYS617, 30 at DYS393, 13 at DYS635, six at DYS439, six at DYS19, 23 at DYS444, one at DYS385ab, and 36 individual at DYS527, respectively. The gene diversity values of 22 loci ranged from 0.3870 (DYS391) to 0.9668 (DYS385ab; see Table S2). The random match probability was 0.0010 with the discrimination capacity of 0.9807. The results showed that the 24 Y‐STR loci exhibited the good polymorphic distributions and personal identification capability, which can be applied in the forensic field. Our haplotype data were compared with the nine populations submitted to the YHRD database (Release 55) including Beijing Chinese Han (Nothnagel et al., 2017), Gansu Chinese Han (Yao et al., 2016), Guangdong Chinese Han (Wang et al., 2016), Jiangsu Chinese Han (Li, Yu, Li, Jin, & Yan, 2016), Yunnan Chinese Han (Yanmei et al., 2010), Ningxia Chinese Han (Zhu et al., 2006), China Korean (YA004289), China Manchu (He & Guo, 2013), and China Tibetan (Zhu et al., 2008). Rst values for genetic distance showed that haplotypes of Jilin Han population had significant differences from those of the other nine populations (all p < .05, see Table 1). As shown in the MDS plot (Figure 2), there were minor differences compared to Beijing Chinese Han, China Manchu, Gansu Chinese Han, and Jiangsu Chinese Han, but major differences with respect to the populations of Guangdong Chinese Han, Yunnan Chinese Han, China Hui, China Korean, and China Tibetan. The populations' distribution in the MDS plot corresponded to their ethnogeographic origins. The results showed that the Jilin Han population owned its distinguished structure, which was similar with its surrounding populations in the adjacent geographic distribution.

Table 1

Rst values of pairwise comparisons between populations

Population	Jilin, China [Han]		Beijing, China [Han]	Gansu, China [Han]	Guangdong, China [Han]	Jiangsu, China [Han]	Yunnan, China [Han]	Ningxia, China [Hui]	Yanbian, China [Korean]	Liaoning, China [manchu]	Qinghai, China [Tibetan]
Jilin, China [Han]	—	0.1895		0.0085	0.0001	0.0591	0.0006	0.0000	0.0000	0.1585	0.0000
Beijing, China [Han]	0.0004	—		0.0473	0.0000	0.0261	0.0699	0.0002	0.0000	0.2942	0.0000
Gansu, China [Han]	0.0028	0.0016		—	0.0000	0.0002	0.0537	0.0003	0.0000	0.0130	0.0000
Guangdong, China [Han]	0.0075	0.0088		0.0148	—	0.0000	0.0451	0.0000	0.0000	0.0000	0.0000
Jiangsu, China [Han]	0.0038	0.0016		0.0051	0.0094	—	0.0327	0.0001	0.0000	0.0003	0.0000
Yunnan, China [Han]	0.0094	0.0084		0.0096	0.0113	0.0128	—	0.0605	0.0000	0.0553	0.0000
Ningxia, China [Hui]	0.0347	0.0283		0.0247	0.0524	0.0298	0.0137	—	0.0000	0.0000	0.0000
Yanbian, China [Korean]	0.0447	0.0526		0.0496	0.0654	0.0644	0.0859	0.1155	—	0.0000	0.0000
Liaoning, China [manchu]	0.0005	0.0002		0.0026	0.0115	0.0051	0.0095	0.0292	0.0445	—	0.0000
Qinghai, China [Tibetan]	0.2415	0.2317		0.1997	0.2680	0.2366	0.2018	0.1381	0.2878	0.2309	—

p values were above diagonal and Rst values were below diagonal.

Figure 2

Multidimensional scaling (MDS) plot based on the Rst between Jilin Han population and nine reference populations in the YHRD database (Jilin Han population marked with yellow)

CONCLUSION

We reported the 24 Y‐STR loci allelic frequencies, haplotype distribution of Jilin Han population, which exhibited the powerful discrimination capability and could be applied in forensic medicine. Additionally, the population comparison showed that Jilin Han population owned its unique structure, which could be used in ethnic tracing. In conclusion, the data provided a reference for Y‐STR database of Jilin Province and might be valuable for human genetics.

CONFLICT OF INTEREST

None declared.

AUTHOR CONTRIBUTIONS

XMX and JLZ participated in the design of the study and performed the statistical analysis. BJW and JY carried out the studies and drafted the manuscript. JY conceived the study and participated in its design and coordination. All authors contributed toward the drafting and revising of the final manuscript.

Click here for additional data file.

Click here for additional data file.