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Morphological and molecular genetics of ancient remains and modern rice (Oryza sativa) confirm diversity in ancient Japan

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Abstract

Rice was introduced to northern Japan in the prehistoric era, when the local climate was relatively cool for rice cultivation. Ancient strains of rice could potentially be productive in unfavorable conditions for cultivation; modern strains sharing genetic traits with ancient rice may contribute useful genetic diversity. To understand the variation in Japanese rice, a comparison of seed sizes and chloroplast and nuclear DNA sequences was conducted, on modern rice accessions from diverse geographical areas, and eleven populations with seven reference populations of rice seed remains from 800 BC to 1500 AD. The populations of rice seed remains shared short grain shape and a specific chloroplast genotype with modern Japanese and worldwide rice accessions. This morphology and genotype may have been introduced to Japan along with farming techniques. Variability of seed shape and diversity of the nuclear genome both reduced through time, indicating genetic erosion in Japanese rice. Greater diversity in the populations of rice seed remains, taken together with archaeological and historical evidence, suggests that older rice populations had genetic traits that could adapt to unfavorable conditions of cultivation, such as flooding and low temperatures. Modern landraces share a genome structure with rice seed remains populations, which suggests that the modern landraces may have useful breeding traits such as tolerance of flooding and low temperatures.

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Acknowledgments

We thank Ms. Tamami Tanaka, Aomori Prefectural Board of Education, Japan, for supplying seeds of rice remains; and Mr. Yoshihiko Takeda, Inakadate Village Board of Education, Japan, and Dr. Nori Kurata, National Institute of Genetics, Japan, for kindly supplying seeds of modern rice and DNA of wild rice; Miho Tanaka, Nara University, Japan, for assistance in the laboratory; and the Research Institute for Humanity and Nature, Japan, for lending instruments for DNA analysis. This work was supported by the Special Research Fund of Hirosaki University entitled “Research Project for Promoting the Utilization of Archaeological Remains”, and a JSPS Grant-in-Aid for Challenging Exploratory Research (No. 25560137).

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The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Faculty of Humanities, Hirosaki University, 1 Bunkyo, Hirosaki, Aomori, 036-8560, Japan

    Katsunori Tanaka & Nobuhiko Kamijo

  2. Upland Farming Research Division, NARO Kyushu Okinawa Agricultural Research Center, 6651-2 Yokoichicho, Miyakonojo, Miyazaki, 885-0091, Japan

    Hiroaki Tabuchi

  3. Genetec Co. Ltd., Tokai University, 3-20-1 Orido, Shimizu, Shizuoka, 424-8610, Japan

    Kuniko Hanamori

  4. Paleoenvironment Research Institute Co. Ltd., 1795-24 Tsuchiya, Nishi, Saitama, 331-0062, Japan

    Ryuji Matsuda

  5. Aomori Prefectural Museum, 2-8-14 Honcho, Aomori, 030-0802, Japan

    Junko Suginomori

  6. National Institutes for the Humanities, Inter-University Research Institute Corporation, 2nd Floor, Hulic Kamiyacho Bldg., 4-3-13 Toranomon, Minato-ku, Tokyo, 105-0001, Japan

    Yo-Ichiro Sato

  7. Agricultural Museum, Faculty of Agriculture, Miyazaki University, 1-1 Gakuen-Kibanadai-nishi, Miyazaki, 889-2192, Japan

    Tetsuro Udatsu

  8. Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan

    Ryuji Ishikawa

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  1. Katsunori Tanaka
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Correspondence to Ryuji Ishikawa.

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Tanaka, K., Kamijo, N., Tabuchi, H. et al. Morphological and molecular genetics of ancient remains and modern rice (Oryza sativa) confirm diversity in ancient Japan. Genet Resour Crop Evol 63, 447–464 (2016). https://doi.org/10.1007/s10722-015-0262-2

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