Genetic Structural Differentiation Analyses of Intercontinental Populations and Ancestry Inference of the Chinese Hui Group Based on a Novel Developed Autosomal AIM-InDel Genotyping System

In the present study, we investigated the genetic polymorphisms of 39 ancestry informative marker-insertion/deletion (AIM-InDel) loci in the Chinese Hui group using a previously self-developed panel, further clarified the genetic relationships between the Hui group and other reference populations, and assessed the ancestry inference efficiency of the AIM-InDel panel based on the worldwide population data from 1000 Genomes Phase 3. The results of the locus-specific informativeness (I(n)) and pairwise fixation index (F(st)) values, multidimensional scaling analysis, and success ratio of estimation with cross-validation showed that the novel panel could well reveal the genetic structural differentiations of the East Asian, European, African, and South Asian populations. Besides, the biogeographical ancestry origin inference both at the individual and population levels was conducted on the Chinese Hui group by principal component analysis and STRUCTURE analysis, and the results revealed that the Hui group had the East Asian origin, and the East Asian component ratio of Hui group was approximately 88.87%. Furthermore, the population genetic analyses among the Hui group and reference populations were performed based on the insertion allele frequency heat map, population pairwise F(st) values and phylogenetic tree, and the results indicated that the Hui group was genetically closer to East Asian populations, especially two Chinese Han populations (CHS and CHB populations).