Comprehensive elucidation on the genetic profile of the Hezhou Han population via an efficient InDel panel

Abstract

The Han nationality is widely distributed in different regions, and it is one of the most populous nationalities in China. Compared with the ethnic minorities in Guangxi Zhuang Autonomous Region, there is relatively less research on Han individuals dwelled in Guangxi as a part of Chinese Han population. In this study, the genetic polymorphisms of 57 autosomal insertion/deletion (InDel) loci were explored in Hezhou Han (HZH) population. Forensic-related parameters revealed that these 57 InDel loci had high forensic validity and could be used in forensic practice application. In addition, the genetic relationships between the HZH population and 30 worldwide reference populations were explored using a variety of analytical methods, such as phylogenetic tree, principal component analysis, and genetic structure analysis. These results demonstrated that there were closer genetic relationships between the HZH and nine populations from East Asia (EAS). The prediction accuracy rates of five inter-continental cross-validation analyses for individuals from EAS was >0.9, and the prediction accuracy rates of three inter-continental cross-validation analyses for individuals from EAS, Europe, and Africa were all >0.95. In addition, 24 of the 57 InDel loci could be served as ancestral information inference loci, which could effectively distinguish individuals of EAS, Europe, and Africa. In conclusion, these InDel loci could be used not only as a good tool for individual identification and paternity testing in HZH population, but also as an auxiliary tool for ancestry information inference research.

Keywords: Hezhou Han population; InDel; ancestry information inference; cross-validation; genetic relationship.

Figure 1

Heatmaps of allelic frequencies and forensic parameters. (A) Insertion allelic frequencies of 57 InDel loci in 31 worldwide populations. (B) Forensic parameters of 57 InDel loci in Hezhou Han population.

Figure 2

Two phylogenetic trees of 31 different populations. (A) Neighbour-joining tree was performed by MEGA software based on pairwise D_A values among 31 populations. (B) Circular phylogenetic tree was constructed by iTOL online software on the basis of pairwise D_A values among 31 populations.

Figure 3

PCA analyses among 31 worldwide populations at population level and individual level. (A) PC1 and PC2 at population level. (B) PC1 and PC3 at population level. (C) PC1 and PC2 at individual level. (D) PC1 and PC3 at individual level.

Figure 4

The structure analyses (K=2–4) among 31 populations based on the raw genotyping data of 57 InDel loci.

Figure 5

Prediction matrix for different intercontinental populations based on 57 autosomal InDel genotyping data. (A) Cross-validation success rates of 4 224 individuals in five intercontinental populations. (B) Cross-validation success rates of 3 388 individuals in three intercontinental populations.

Figure 6

(A) In values of 57 InDel loci in Hezhou Han population. (B) Cos2 analyses of 57 InDel loci in Hezhou Han population.