Prefecture-level population structure of the Japanese based on SNP genotypes of 11,069 individuals

Abstract

We analyzed genome-wide single-nucleotide polymorphism data of 11,069 Japanese individuals recruited from all 47 prefectures of Japan to clarify their genetic structure. The principal component analysis at the prefectural level enabled us to study the relationship between geographical location and genetic differentiation. The results revealed that the mainland Japanese were not genetically homogeneous, and the genetic structure could be explained mainly by the degree of Jomon ancestry and the geographical location. One of the interesting findings was that individuals in the Shikoku region (i.e., Tokushima Prefecture, Kagawa Prefecture, Ehime Prefecture, and Kochi Prefecture) were genetically close to Han Chinese. Therefore, the genetic components of immigrants from continental East Asia in the Yayoi period may have been well maintained in Shikoku. The present results will be useful for understanding the peopling of Japan, and also provide suggestions for recruiting subjects in genetic association studies. Japanese who do not live in Okinawa Prefecture as mainland Japanese. There are three major models about the demographic history of the Japanese population (i.e., transformation, replacement, and hybridization models). Of these, the "dual-structure model," one of the hybridization models, is the most widely accepted. According to the dual-structure model, the present Japanese population was formed by admixture between indigenous Jomon people and immigrants from continental East Asia [1]. Previous studies on cranial morphology suggested that the Ainu and Ryukyuans were closer to Jomon people than the mainland Japanese were and, among the mainland Japanese, people in the Tohoku region were morphologically closer to Ainu [1, 2]. Genetic studies also corroborate the relatedness between Jomon people and the Ainu and Ryukyuans; the Ainu and Ryukyuans were likely to retain more Jomon ancestry in their genomes than the mainland Japanese were [3, 4]. Although several genetic studies have shown genetic differentiation between the mainland Japanese and Okinawa people [5-9], the genetic difference among prefectures in the mainland Japanese is not well understood. Yamaguchi-Kabata et al. [8], based on the genome-wide single-nucleotide polymorphism (SNP) data of 7003 Japanese patients treated at hospitals in seven geographic regions, found that Japanese are genetically differentiated.

Genome-wide SNP data of Izumo and Makurazaki populations support inner-dual structure model for origin of Yamato people

“…We also confirmed region specific characteristics discovered by Yamaguchi-Kabata et al [9] and later confirmed by Okada et al [31] in which Hokkaido, Kanto, and Tokai area individuals are more or less genetically similar, whereas Tohoku individuals are slightly differentiated from those three regions people based on PCA, network and f4 tests. We also confirm that Kinki people are the closest to continental Asians as reported by Yamaguchi-Kabata et al [9] and Watanabe et al [29]. Kinki area includes Nara and Kyoto, past capitals of Japan and thus has a history of human migration from the Asian continent.…”

“…However, f4 test showed that the Kinki population is the closest to continental Asians (f4(GBR, CHB; Okinawa, x)). This is supported by another study using genome-wide SNPs [29]. Interestingly, Izumo population has higher genetic affinity to Okinawa and Kyushu than to other populations in Honshu, as suggested by f4(GBR, x; Izumo, Kinki).…”

Role of an Atypical Cadherin Gene,Cdh23in Prepulse Inhibition and Implication ofCDH23in Schizophrenia

“…The samples were recruited from the Honshu region of Japan (the main island), where the population fall into a single genetic cluster. 17, 18 Additionally, we also used genetic data of 8,380 healthy Japanese controls from the Integrative Japanese Genome Variation Database (iJGVD) by Tohoku Medical Megabank Organization (ToMMo) (https://ijgvd.megabank.tohoku.ac.jp/) to compare the allele frequencies of the identified variant.…”

“…However, the enrichment did not persist when the samples from Honshu and Shikoku regions were analysed together (P = 0.27) (Supplementary Table 6). This could be due to the population genetic structure of the Shikoku region, which is distinct from the main island of Honshu, and is genetically closer to Han Chinese [39]. The pooled analysis of schizophrenia samples [Japanese + Schizophrenia exome meta-analysis consortium, (SCHEMA); https://schema.broadinstitute.org/] and all controls, also did not show any allelic association (P = 0.21) (Supplementary Table 6), which could be attributed to the rarity of variant allele A in other populations compared to the Japanese population.…”

Modern human DNA analyses with special reference to the inner dual-structure model of Yaponesian

“…Recently Watanabe et al (2020) reported analysis of ~140000 nuclear SNP data for 11069 individuals distributed in all the 47 prefectures. They also found a clear difference between Okinawa and the remaining 46 prefectures, and all seven prefectures in Kyushu are closest to Okinawa.…”