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


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.

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  1. 1.

    Hanihara K. Dual structure model for the population history of the Japanese. Jpn Rev. 1991;2:1–33.

    Google Scholar 

  2. 2.

    Hanihara K. Geographic variation of modern Japanese crania and its relationship to the origin of Japanese. Homo. 1985;36:1–10.

    Google Scholar 

  3. 3.

    Kanzawa-Kiriyama H, Kryukov K, Jinam AT, Hosomichi K, Saso A, Suwa G, et al. A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan. J Hum Genet. 2017;62:213–21.

    CAS  Article  Google Scholar 

  4. 4.

    Kanzawa-Kiriyama H, Jinam AT, Kawai Y, Sato T, Hosomichi K, Tajima A, et al. Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan. Anthropol Sci. 2019;1–26.

  5. 5.

    Hammer MF, Horai S. Y chromosomal DNA variation and the peopling of Japan. Am J Hum Genet. 1995;56:951–62.

    CAS  PubMed  PubMed Central  Google Scholar 

  6. 6.

    Horai S, Murayama K, Hayasaka K, Matsubayashi S, Hattori Y, Fucharoen G, et al. mtDNA polymorphism in East Asian populations, with special reference to the peopling of Japan. Am J Hum Genet. 1996;59:579–90.

    CAS  PubMed  PubMed Central  Google Scholar 

  7. 7.

    Hatta Y, Ohashi J, Imanishi T, Kamiyama H. HLA genes and haplotypes in Ryukyuans suggest recent gene flow to the Okinawa Islands. Hum Biol. 1999;71:353–65.

    CAS  PubMed  Google Scholar 

  8. 8.

    Yamaguchi-Kabata Y, Nakazono K, Takahashi A, Saito S, Hosono N, Kubo M, et al. Japanese population structure, based on SNP genotypes from 7003 individuals compared to other ethnic groups: effects on population-based association studies. Am J Hum Genet. 2008;83:445–56.

    CAS  Article  Google Scholar 

  9. 9.

    Japanese Archipelago Human Population Genetics Consortium. The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations. J Hum Genet. 2012;57:787–95.

    Article  Google Scholar 

  10. 10.

    Hellwege JN, Keaton J, Giri A, Gao X, Velez Edwards DR, Edwards TL. Population stratification in genetic association studies. Curr Protoc Hum Genet. 2017;95:1.22.1–23.

    Google Scholar 

  11. 11.

    Berg JJ, Harpak A, Sinnott-Armstrong N, Joergensen AM, Mostafavi H, Field Y, et al. Reduced signal for polygenic adaptation of height in UK biobank. Elife. 2019;8:1–47.

    Article  Google Scholar 

  12. 12.

    Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 2015;4.

  13. 13.

    1000 Genomes Project Consortium. A global reference for human genetic variation. Nature. 2015;526:68–74.

    Article  Google Scholar 

  14. 14.

    Wickham H. ggplot2: elegant graphics for data analysis. New York, NY: Springer; 2016.

    Book  Google Scholar 

  15. 15.

    Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009;19:1655–64.

    CAS  Article  Google Scholar 

  16. 16.

    Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406–25.

    CAS  PubMed  Google Scholar 

  17. 17.

    Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, et al. Ancient admixture in human history. Genetics. 2012;192:1065–93.

    Article  Google Scholar 

  18. 18.

    Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35:1547–9.

    CAS  Article  Google Scholar 

  19. 19.

    Jinam TA, Kanzawa-Kiriyama H, Inoue I, Tokunaga K, Omoto K, Saito N. Unique characteristics of the Ainu population in Northern Japan. J Hum Genet. 2015;60:565–71.

    Article  Google Scholar 

  20. 20.

    Koganebuchi K, Kimura R. Biomedical and genetic characteristics of the Ryukyuans: demographic history, diseases and physical and physiological traits. Ann Hum Biol. 2019;46:354–66.

    Article  Google Scholar 

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We are grateful to the individuals who participated in the study. We would like to express our deepest gratitude to Masahiro Inoue, Shota Arichi, and Akito Tabira who obtained the genotype data and provided the technical environment for analyzing them. We thank two anonymous reviewers for helpful suggestions. This study was partly supported by Grant-in-Aid for Scientific Research (B) (18H02514) and Grant-in-Aid for Scientific Research on Innovative Areas (19H05341) from the Ministry of Education, Culture, Sports, Science, and Technology of Japan, and supported by AMED under Grant Numbers JP19fk0310115 and JP20km0405211.

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Correspondence to Jun Ohashi.

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Watanabe, Y., Isshiki, M. & Ohashi, J. Prefecture-level population structure of the Japanese based on SNP genotypes of 11,069 individuals. J Hum Genet 66, 431–437 (2021).

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