Evolution of the Japanese Y chromosome by analysis of the haplogroups and the deletion of the gene in the AZFc region.

The Y chromosome is classified into haplogroups based on its nucleotide polymorphisms. There are multiple amplicon genes in the azoospermia factor c (AZFc) region of the Y chromosome, and combinations of copy numbers of these genes diversify the Y chromosome structure. In this study, we investigated the evolution of the Y chromosome in a Japanese population based on the relationship between the Y chromosome haplogroup and the deletion patterns of genes in the AZFc region. Haplogroup branch markers were determined by PCR, PCR restriction fragment length polymorphism (PCR–RFLP), Sanger sequencing, and TaqMan PCR in 2,157 Japanese men. Single nucleotide variants (SNVs) on DAZ, BPY2, CDY1, TTTY4, and GOLGA2P2Y gene copies were analyzed for deletions by PCR–RFLP. Haplogroups D1a2a1a, D1a2a1c, and D1a2a2 showed the same AZFc deletion patterns. Haplogroups C and O1b2a showed a common AZFc deletion, with some exceptions. Therefore, it is possible that they diverged into subgroups following the occurrence of a common AZFc deletion pattern. Haplogroups O2a2 and O2a1b showed a common AZFc deletion pattern with some exceptions; however, after dividing into their respective downstream haplogroups, they showed several more deletion patterns. Thus, several additional deletion patterns may have occurred because of the divergence of downstream haplogroups. Haplogroups O1a and O1b1a1a exhibited several AZFc deletion patterns. Thus, each haplogroup may have originated from a different ancestor. This study provides further insights into the relationship between Y chromosome haplogroups and the deletion patterns of genes in the AZFc region, which is important for understanding the evolution of the Y chromosome.