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.

我们分析了从日本所有 47 个县招募的 11,069 名日本人的全基因组单核苷酸多态性数据，以阐明他们的遗传结构。地级主成分分析使我们能够研究地理位置与遗传分化之间的关系。结果表明，日本本土人在遗传上并不均一，其遗传结构主要可以用绳文血统的程度和地理位置来解释。有趣的发现之一是四国地区（即德岛县、香川县、爱媛县和高知县）的个体在基因上与汉族人接近。因此，弥生时代东亚大陆移民的遗传成分可能在四国得到了很好的保存。