Chinese population genetic substructure using 23 Y-chromosomal STRs

China, as the largest national database within the YHRD (Y chromosome haplotype reference database), has repeatedly been a research hotspot in the field of genetics, archaeology and molecular anthropology. In the present study, 23 Y-STR loci were used to investigate genetic relationships among 29 Chinese populations (6029 individuals). Pairwise genetic distance (Rst value) was calculated based on haplotype frequency distributions by the Analysis of Molecular Variance. Multidimensional scaling (MDS) and phylogenetic analysis were performed on the online tool and Mega 6.0, respectively. Tibetans (Rst = 0.1601 ± 0.0421), Shuis (Rst = 0.0934 ± 0.0327), Uyghurs (Rst = 0.0791 ± 0.0459) and Zhuangs (Rst = 0.0790 ± 0.0404) showed the high genetic distance with other populations and kept relatively isolated with other reference populations in the MDS plots and Neighbor-Joining tree. Additionally, genetic distinction among same ethnicities (Han and Hui) distributed in different administrative divisions was also explored and no significant differences were identified.