Genetic characteristics and phylogenetic analysis of three Chinese ethnic groups using the Huaxia Platinum System

Abstract

Short tandem repeats (STRs) are attractive to genetic applications like forensic, anthropological and population genetics studies. The Huaxia Platinum System was specifically developed to allow co-amplification and detection of all markers in the expanded CODIS core loci and the Chinese National Database. In this study, in continuation to our previous validation study, 568 unrelated individuals were firstly genotyped to investigate the effectiveness of this novel assay in 3 main ethnic groups of China (Han, Tibetan and Yi). The combined power of discrimination (CPD) were 0.9999999999999999999999999992, 0.999999999999999999999999992, 0.999999999999999999999999998, respectively, and the combined power of exclusion (CPE) were 0.9999999999, 0.999999995, 0.999999998, respectively. Next, genetic relationships along administrative and ethnic divisions were analyzed using pairwise genetic distances, multidimensional scaling (MDS), principal component analysis (PCA) and phylogenetic analysis. The Han ethnicity showed a high genetic homogeneity all across China, and significant genetic differences existed between Han groups and some minority groups, most prominently for the Tibetans, the Uyghurs, the Kazakhs, the Miaos, the Zhuangs and the Dais. Aforementioned results suggested that the Huaxia Platinum System is polymorphic and informative, which provides an efficient tool not only for human forensics, but also for population genetics studies.

Figure 1

Principal component analysis based on 19 overlapped STR loci of our studied populations (bold and red) and 46 reference Chinese Han populations.

Figure 2

Multidimensional Scaling plots (MDS) constructed based on Nei’s genetic distances calculated by allele frequency distributions of 19 overlapped autosomal STRs. (A) MDS of our studied populations (bold and blue) and 40 reference Chinese Han populations (the information of abbreviations are presented in Supplementary Table 12). (B) MDS of our studied populations (bold and blue) and 16 reference ethnic minorities (the information of abbreviations are presented in Supplementary Table 12).

Figure 3

Phylogenetic tree among three studied populations (red and bold) and 56 reference populations. Phylogenetic tree was constructed by the Neighbor-Joining method based on 19 overlapped STR loci in the Mega 7.0 software.