Genetic variations on the Y chromosome in the Japanese population and implications for modern human Y chromosome lineage

A polymorphism in the coding sequence of the SRY gene was found by single-s trand conformation polymorphism (SSCP) and direct sequencing analysis. The new allele of the SRY gene, which is raised by a C-to-T transition in the 1 55th codon, was found in 24% of Honshu, 35% of Okinawan, and 51% of Korean males respectively, whereas it was not observed among 16 Caucasian and 18 N egroid males. A haplotype analysis of the Y chromosome was carried out in J apanese, Korean, Caucasian and Negroid populations, using a combination of the polymorphisms in SRY, DXYS5Y, DYS287, and DXYS241Y loci. The results in dicated that the Y chromosomes can be classified into seven haplotypes (Ia, Ib, Ic, IIa, IIb, III, IV). However, of these seven, only four (Ia, IIa, I II, IV) were observed in the Japanese population. Furthermore, the presumed haplotype C, Y1, YAP, (CA)(14), from which haplotype III was probably deri ved, was not found in any populations in this study. The regional distribut ion of each haplotype revealed that type III is more frequently observed in Okinawa (16%) and in Korea (21%) than in Honshu (4.4%). The haplotype anal ysis of the Y chromosome may contribute to the exploration of the origin of Japanese and the relationship between east Asian populations.