Research Article: Inner and inter population structure construction of Chinese Jiangsu Han population based on Y23 STR system

Date Published: July 13, 2017

Publisher: Public Library of Science

Author(s): Huipin Wang, Huajie Ba, Chun Yang, Jianqiu Zhang, Yunchun Tai, Tzen-Yuh Chiang.

http://doi.org/10.1371/journal.pone.0180921

Abstract

In this study, we analyzed the genetic polymorphisms of 23 Y-STR loci from PowerPlex® Y23 system in 916 unrelated healthy male individuals from Chinese Jiangsu Han, and observed 912 different haplotypes including 908 unique haplotypes and 4 duplicate haplotypes. The haplotype diversity reached 0.99999 and the discrimination capacity and match probability were 0.9956 and 0.0011, respectively. The gene diversity values ranged from 0.3942 at DYS438 to 0.9607 at DYS385a/b. Population differentiation within 10 Jiangsu Han subpopulations were evaluated by RST values and visualized in Neighbor-Joining trees and Multi-Dimensional Scaling plots as well as population relationships between the Jiangsu Han population and other 18 Eastern Asian populations. Such results indicated that the 23 Y-STR loci were highly polymorphic in Jiangsu Han population and played crucial roles in forensic application as well as population genetics. For the first time, we reported the genetic diversity of male lineages in Jiangsu Han population at a high-resolution level of 23 Y-STR set and consequently contributed to familial searching, offender tracking, and anthropology analysis of Jiangsu Han population.

Partial Text

Genetic markers derived from Y chromosome independent of recurrent mutations or recombination [1], play special roles in uncovering genetic structure [2,3] and inferring human dispersal and important migration time range [4,5]. In Y chromosomes, genetic variations are inherited from father to son paternally. Thus, Y chromosome could reflect the gene flows and genetic differentiation of male lineages [6]. In addition, genetic markers in Y chromosome have smaller effective population size compared to those in autosomes. The advancement of new sequencing technologies and more attention paid to human genome project provided abundant genetic markers in Y-DNA [3,7,8]. Among the various markers in Y chromosome, short tandem repeats (STRs), are widely employed due to their hypervariability and hypermutability, thus it is available to perform multiplex amplifications at Y-STRs. So far, several commercial kits have been developed, such as PowerPlex Y (Promega, USA) [9], Yfiler™ Plus (Thermo Fisher Scientific, USA) [10], and PowerPlex® Y23 [11]. The population data of Y-STRs now is being enriched to explore the genetic diversity of global male lineages [12–15]. Thus far, Y-STR Haplotype Reference Database (YHRD) has received a large-scale Y-STR data to generate reliable Y-STR haplotype frequencies for forensic purposes, as well as to assess male lineage stratification for population genetics studies (https://www.yhrd.org). In investigating authorities, Y-STR haplotype analysis serves to track male suspects in potential pedigrees sharing identical or highly similar Y-STR haplotypes to crime evidence [16].

As we have noted above, 916 unrelated healthy Han males from Jiangsu province were genotyped at 23 Y-STR loci. 912 different haplotypes, including 908 singletons (99.6%) and 4 duplicates (0.4%), were found in total comprising, revealing that the 23 Y-STRs contained in the PowerPlex® Y23 System were highly polymorphic (HD = 0.9999952) in Jiangsu Han population and were great valuable for forensic application (DC = 0.9956, MP = 0.0011). The highest GD value was 0.9607 at DYS385, and the lowest was 0.3942 at DYS438. Then, LD analysis elaborated the necessity of forming these markers into haplotype. Pairwise RST genetic distances and relevant significances among inner- and inter-population of Jiangsu Han, combined with N-J trees and MDS plots were conducted to illustrate the genetic background of Jiangsu Han population objectively. For the first time, we depicted the inner-population differentiation and genetic characteristics of Jiangsu Han population. Additionally, in the scale of East Asian, it indicated that the major male component of Han population in Jiangsu came from Northern Chinese Han.

 

Source:

http://doi.org/10.1371/journal.pone.0180921

 

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