Genetic substructure and forensic characteristics of Chinese Hui populations using 157 Y-SNPs and 27 Y-STRs

The Hui group is the second largest ethnic minority and one of the most widespread ethnic groups in China. However, the genetic architecture of the Hui population remains largely unexplored, particularly with respect to the male-specific region of the Y chromosome. Here, we studied nine Hui populations (Xinjiang, Qinghai, Gansu, Ningxia, Shaanxi, Henan, Shandong, Sichuan, Yunnan) using 157 Y-chromosome single nucleotide polymorphisms (Y-SNPs) and 27 short tandem repeats (Y-STRs) to unravel their genetic substructure and forensic characteristics. A total of 650 unrelated male samples from the Hui populations were genotyped by SNaPshot^®, a single base extension (SBE) assay. Finally, 95 terminal haplogroups and high haplotype diversity (0.9999) were observed in Hui populations. Frequency heat map matrices, genetic distance (F_ST) and network analysis within Hui populations indicated that these nine Hui populations can be divided into three groups: Hui populations from the northwest (NWH), Hui populations from Sichuan and Shandong (SSH), and Hui populations from Yunnan (YNH). Our results suggested that we should use different databases for different Hui samples in forensic cases. Comparison with other populations that used different population genetic analysis revealed that the Hui populations had close relationships with East Asian populations, especially Chinese Han population. Overall, the high-resolution panel with Y-SNPs and Y-STRs gives new and complete insight into Hui populations, which can be used to interpret the genetic substructure of Hui populations and affect the utility of forensic databases.