Genetic diversity of 71 Y-chromosomal biallelic markers in the Han population living in Southern China

Abstract

Polymorphic markers located on Y chromosome represent an important complement for special kinship cases. We analyzed 71 Y-chromosomal biallelic markers including 65 SNPs and 6 insertion/deletion events in a sample of 201 unrelated Han males living in Southern China. Genomic DNA was extracted from blood samples. Typing of 71 biallelic markers was performed using the MassARRAY MALDI-TOF MS platform (Agena Inc.). Allelic frequencies, gene diversities (GD) and haplotype diversity (HD) was calculated. Comparisons were then carried on with our previous data from Northwestern Han populations. Out of the 71 markers, five loci were not polymorphic (GD=0), 29 loci were found to be low informative (0.01<GD<0.2), 18 loci were found to be medium informative (0.2≤GD<0.3), 19 loci were found to be high informative (GD≥0.3). A total of 67 haplotypes were identified, of which 37 haplotypes were unique, 30 haplotypes were found more than once. The haplotype diversity was estimated to be 0.9535. Significant differences were found between Southern and Northwestern Han population at 36 loci. The results showed that joint usage of multiplex amplification and MALDI-TOF-MS could have advantages in screening and genotyping biallelic markers. In addition, the panel could provide Supplementary information for forensic identification, but the significant differences observed within Han populations should be taken into account.