Brief CommunicationInvestigation of Japanese-specific alleles: Most are of Jomon lineage
Introduction
The focus of a recent field in forensic genetics has been on the differentiation of individuals using ancestry-informative markers (AIMs) [1], [2], [3]. Genetic markers with a geographically restricted distribution, or with marked differences in allele frequency between two regions, are useful to infer the ancestry of an individual and population to which an individual belongs, and to understand human migration and expansion in anthropology. Japanese-specific alleles are expected to be powerful for the characterization of a forensic sample as being of Japanese origin. Y chromosomal haplogroups C1 and D2 have been observed only in the Japanese Archipelago in large-scale investigations [4], [5]. In particular, haplogroup D2 was found at a frequency as high as 0.55 in the Ryukyuans, the Japanese in Okinawa, the southernmost part of the Japanese Archipelago, and 0.85 in the Ainu, the aboriginal people of Hokkaido, the northernmost part of the Japanese Archipelago. The Wajins, the mainland Japanese, had frequencies of 0.26–0.38 [6]. However, these two haplogroups were also observed in Koreans at low frequencies [6], [7], and haplogroup D2 was found in Chinese at a lower frequency [7]. Mitochondrial haplogroup M7a was not restricted to Japanese and Koreans, but showed higher frequencies in Japan than in mainlanders of East Asia [8], [9]. Thus, they can be regarded as fairly Japanese-specific. On autosomes, only a few Japanese-specific single nucleotide polymorphisms (SNPs) have been found to date. We previously reported that a derived allele of a SNP (rs3778922) in the GALNT11 gene was observed at frequencies of 0.076–0.153 in the Wajins and Ryukyuans, and 0.004–0.017 in two Korean populations [10]. A derived allele (rs76162918) of the H19 gene showed frequencies of 0.068–0.088 in four Wajin populations and 0–0.005 in two Korean populations [11]. These alleles were not found in several mainland populations of East Asia. They are not entirely Japanese-specific, but can be regarded as such because of the clearly low frequencies in the Korean populations. The HapMap database suggests the existence of a Japanese-specific allele (rs2285715) in the PLA2G12A gene, which is adjacent to the CFI gene with a nearly Japanese-specific allele [12]. In this study, we analyzed the frequencies of these three SNPs in the GALNT11, H19, and PLA2G12A genes in 25 global populations and Jomon skeletons, and investigated SNPs on autosomes to search for new Japanese-specific markers on autosomes, possibly permitting the differentiation between Japanese and mainlanders of East Asia.
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Materials and methods
For the three SNPs of GALNT11, H19, and PLA2G12A, a total of 2,396 unrelated individuals from 25 populations were investigated (Table 1). The geographical locations of 22 South and East Asian populations are shown in Fig. 1. To identify new Japanese-specific alleles, a total of 874 individuals from nine populations were investigated. Fifty-four DNA samples extracted from Jomon skeletons excavated from archaeological sites in Hokkaido [13] were also investigated. Simultaneous typing of the three
Typing of three SNPs
Fig. 2 shows the electrophoretic pattern of products obtained by the triplex APLP method. The nucleotide substitutions were clearly and unambiguously detected as bands with different sizes. Table 1 shows the frequencies of derived alleles of the three SNPs. The observed distribution was in good agreement with the Hardy–Weinberg law. The derived alleles of GALNT11 and PLA2G12A were restricted to the Japanese and Korean populations, suggestive of being nearly Japanese-specific. The H19 derived
Discussion
To explain the origins of modern Japanese, three main models have been proposed based on morphological studies. The transformation model claims that modern Japanese evolved solely from Jomon people, who spread to the Japanese Archipelago more than 15,000 years ago and developed the Jomon culture of hunter-gatherers. The replacement model contends that modern Japanese evolved solely from Yayoi people, who migrated to the Japanese Archipelago through the Korean Peninsula with wet rice agriculture
Acknowledgements
We would like to thank Prof. Naruya Saitou, National Institute of Genetics for his providing us with some Chinese DNA samples. This study was supported in part by Grants-in-Aid for Scientific Research (23590849 and 26460878 to IY and 264440257 to NA) from the Japan Society for the Promotion of Science, Japan.
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