RESEARCH ARTICLE Morphological and molecular genetics of ancient remains and modern rice (Oryza sativa) confirm diversity in ancient Japan Katsunori Tanaka . Nobuhiko Kamijo . Hiroaki Tabuchi . Kuniko Hanamori . Ryuji Matsuda . Junko Suginomori . Yo-Ichiro Sato . Tetsuro Udatsu . Ryuji Ishikawa Received: 16 September 2014 / Accepted: 5 May 2015 / Published online: 11 July 2015 Ó Springer Science+Business Media Dordrecht 2015 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 chloro- plast 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 Electronic supplementary material The online version of this article (doi:10.1007/s10722-015-0262-2) contains supple- mentary material, which is available to authorized users. K. Tanaka Á N. Kamijo Faculty of Humanities, Hirosaki University, 1 Bunkyo, Hirosaki, Aomori 036-8560, Japan H. Tabuchi Upland Farming Research Division, NARO Kyushu Okinawa Agricultural Research Center, 6651-2 Yokoichicho, Miyakonojo, Miyazaki 885-0091, Japan K. Hanamori Genetec Co. Ltd., Tokai University, 3-20-1 Orido, Shimizu, Shizuoka 424-8610, Japan R. Matsuda Paleoenvironment Research Institute Co. Ltd., 1795-24 Tsuchiya, Nishi, Saitama 331-0062, Japan J. Suginomori Aomori Prefectural Museum, 2-8-14 Honcho, Aomori 030-0802, Japan Y.-I. Sato 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 T. Udatsu Agricultural Museum, Faculty of Agriculture, Miyazaki University, 1-1 Gakuen-Kibanadai-nishi, Miyazaki 889-2192, Japan R. Ishikawa (&) Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan e-mail: ishikawa@hirosaki-u.ac.jp 123 Genet Resour Crop Evol (2016) 63:447–464 DOI 10.1007/s10722-015-0262-2