Genetic polymorphism and phylogenetic differentiation of the Huaxia Platinum System in three Chinese minority ethnicities

Abstract

Short tandem repeats (STRs) with features of high polymorphism and abundant evolution information play a significant role in genetic applications such as human forensics, anthropology and population genetics. The Huaxia Platinum System was specifically exploited to allow coamplification of all markers in the expanded Combined DNA Index System and the Chinese National Database. Herein, in continuation of our previous studies, 493 unrelated individuals were firstly genotyped to investigate the efficacy of this novel system in three minority ethnicities of China (Hui, Tibetan and Uygur). Additionally, genetic relationships among our three investigated populations and other previously published populations were analyzed using pairwise genetic distances, multidimensional scaling (MDS), principal component analysis (PCA), cladogram and STRUCTURE. The combined match probabilities (CMP) for the Hui, Tibetan and Uygur groups were 1.6894 × 10 −27 , 6.1666 × 10 −27 and 5.0655 × 10 −27 , respectively, and the combined powers of exclusion (CPE) were 0.999999999646627, 0.999999999304935 and 0.999999999433994. Population comparison analysis manifested that the Hui and Tibetan populations had genetic affinities with the Han, Yi and Korean populations, while the Uygur group had a close relationship with the Kazakh population. The aforementioned results suggested that the Huaxia Platinum System is a polymorphic and effective tool that is appropriate for personal identification and population genetics.

RETRACTED: Population genetic analysis of Shaanxi male Han Chinese population reveals genetic differentiation and homogenization of East Asians

“…We first merged our 630 raw genotypes of 20 overlapping STRs among different commercial STR amplification kits with 15,173 genotypes from 19 Eurasian populations (six Turkic‐speaking populations [Chen, Zou, Wang, Wang, & He, 2019; Chen, Zou, Wang, Gao, Su, et al, 2019; Jin et al, 2017; Liu et al, 2019]: Urumqi Uyghur, Hotan Uyghur, Kumul Uyghur1, Xinjiang Uyghur, Artux Uyghur, and Akto Kyrgyz; five Han Chinese populations [Chen, Zou, Wang, Gao, Su, et al, 2019; He, Wang, Liu, et al, 2018; He, Wang, Wang, Zou, et al, 2018; Liu et al, 2019; Wang et al, 2018]: Zhujiang Han, Shanxi Han, Chengdu Han, Wuzhong Hui, and Hainan Han; four Tibeto‐Burman‐speaking populations [Liu et al, 2019; Wang et al, 2018]: Liangshan Tibetan, Chengdu Tibetan, Tibet Tibetan, and Liangshan Yi; four western Eurasian populations [Alsafiah, Goodwin, Hadi, Alshaikhi, & Wepeba, 2017; Chen, Adnan, Rakha, et al, 2019; Ossowski et al, 2017; Sadam et al, 2015]: Quetta Hazara, Estonian, Poland, and Saudi Arabian). We referred to this dataset as the raw‐genotype dataset.…”

“…This system is a six‐dye, 25‐locus, multiplex assay that allows co‐amplification and fluorescent detection of the 23 autosomal STRs (D1S1656, D2S1338, D2S441, D3S1358, D5S818, D7S820, D8S1179, D10S1248, D12S391, D13S317, D16S539, D18S51, D19S433, D21S11, D22S1045, D6S1043, CSF1PO, FGA, TH01, TPOX, VWA, Penta D and Penta E) and Amelogenin as well as Y‐InDel (rs2032678) for sex determination. However, previous Huaxia Platinum System‐based studies have focused almost exclusively on ethnic groups (Liu, Wang, He, Wang, & Hou, 2019; Wang et al, 2016b, 2018).…”

Population Genetic Analysis of Modern and Ancient DNA Variations Yields New Insights Into the Formation, Genetic Structure, and Phylogenetic Relationship of Northern Han Chinese

“…To comprehensively dissect the genetic background of Shanxi northern-Han Chinese, we first integrated our raw genotyping data (23 STRs) with previously published genotype data from 11 Chinese populations from five Chinese ethnic groups (Han, Hui, Tibetan, Yi, and Uyghur) (He et al, 2018b; Wang et al, 2018a; Chen et al, 2019; Liu et al, 2019). To further explore the genetic relationship of Shanxi Han in the context of the genetic variations from the worldwide or nationwide populations, we subsequently combined our allele frequency of 20 STRs with publicly obtained data from 52 worldwide populations (Westen et al, 2012; Gaviria et al, 2013; Park et al, 2013; Fujii et al, 2014; Almeida et al, 2015; Parolin et al, 2015; Aguilar-Velazquez et al, 2016; Hossain et al, 2016; Ng et al, 2016; Park et al, 2016; Ramos-Gonzalez et al, 2016; Ristow et al, 2016; Vullo et al, 2016; Wang, 2016; Zhang et al, 2016a; Zhang et al, 2016b; Choi et al, 2017; Guerreiro et al, 2017; Jin et al, 2017; Liu et al, 2017; Moyses et al, 2017; Ossowski et al, 2017; Singh and Nandineni, 2017; Taylor et al, 2017; Wu et al, 2017; Yang et al, 2017a; He et al, 2018b; He et al, 2018e; Wang et al, 2018a; Liu et al, 2019) and allele frequency of 19 STRs with previously investigated the allele frequency distribution from 60 Chinese populations (Zhang et al, 2011; Zhang, 2012; Liu et al, 2013; Shen, 2013; Zhang, 2013; Wang, 2014; Wang et al, 2014; Xie, 2014; Hu et al, 2015; Li, 2015; Ruan, 2015; Shen et al, 2015; Wang, 2015; Yin, 2015; Zhang and Chen, 2015; Zhao et al, 2015a; Huang, 2016; Meng, 2016; Wang, 2016; Xiang, 2016; Xiao et al, 2016; Zhao, 2016; Chen et al, 2017; Fu et al, 2017; He et al, 2017a; He et al, 2017c; Jin et al, 2017; Liu, 2017; Lu et al, 2017;…”

A Tibetan group from Ngawa Tibetan and Qiang Autonomous Prefecture, southwest China, is rich in genetic polymorphisms at 36 autosomal STR loci and shares a complex genetic structure with other Chinese populations

“…We also collected the allele frequencies of autosomal STR from 26 relevant Chinese populations in previously published studies on PubMed, including 14 Han populations [ [26] , [27] , [28] , [29] , [30] , [31] , [32] , [33] , [34] , [35] , [36] , [37] , [38] , [39] ], five Tibetan [ [40] , [41] , [42] , [43] ], two Yi [ 44 , 45 ], one Li [ 46 ], one She [ 47 ], one Uyghur [ 48 ], one Xibe [ 49 ], and one Hui [ 43 ]. The approximate geographic locations of the Ngawa Tibetan population and the other 26 populations were depicted on a map created using the R project software on the website https://www.r-project.org/ (version 4.0.5).…”