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Seed size and chloroplast DNA of modern and ancient seeds explain the establishment of Japanese cultivated melon (Cucumis melo L.) by introduction and selection

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Abstract

Melon is a fruit/vegetable that has been grown in Japan for at least 2000 years. To obtain a better understanding of melon crop evolution in this island country, we measured the seed size and determined the cytoplasmic genotype of 135 modern melon accessions and 12 populations of ancient melon seed remains from archaeological sites for a 2000-year period in Japan. Based on differences in seed length, populations of melon seed remains at the Shikata site (Okayama Prefecture, Japan) consisted of seed types corresponding to those of modern East and South Asian melon. Although several types of melon seeds were found in and around the Shikata site, only Agrestis-type seeds, <6.1 mm in length, were found in melon populations from 1 CE. Intra-population length variation was higher in 1050 CE than in 1530–1680 CE. Ancient DNA from archaeological melon was analysed for SNPs in the chloroplast genome. These revealed that cytoplasm type was heterogeneous and consisted of Ia and Ib types in melon populations prior to ca. 1600 CE, and thereafter becoming homogenous by genetic erosion of Ib, which is absent in modern endemic Japanese melon accessions. The decrease in variation of both seed length and cytoplasm type together with historical records indicates that artificial selection in the Japanese melons for desired fruit traits intensified in the past 1000 years.

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Acknowledgments

We thank Dr. Kathleen R. Reitsma, Iowa State University, USA and Dr. Yoshiteru Sakata, NARO Institute of Vegetable and Tea Science, Japan, for kindly supplying seeds of modern melon; Dr. Noriyuki Fujishita, the former Osaka Prefecture University, Japan, for instruction in classification of modern and ancient melon seed remains; Dr. Yo-Ichiro Sato, National Insititutes for the Humanities, Japan, for instruction in ancient DNA analysis; 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 Sasakawa Scientific Research Grant from the Japan Science Society (17-218), the Japan Society for the Promotion of Science (JSPS) Asian CORE Program entitled “Cooperative Research and Educational Center for Important Plant Genetic Resources in East Asia”, the Special Research of Hirosaki University entitled “Research Project for Promoting the Utilization of Archaeological Remains”, and the JSPS Grant-in-Aid for Scientific Research (A) (23255007), JSPS Grant-in-Aid for Young Scientists (B) (23701015) and JSPS Grant-in-Aid for Scientific Research (C) (15K01130). Current research by CS and DQF on comparing domestications and domestication rates is supported by the European Research Council Grant “Comparative Pathways to Agriculture” (no. 323842).

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Authors and Affiliations

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

    Katsunori Tanaka

  2. Institute of Archaeology, University College London, London, WC1H 0PY, United Kingdom

    Chris J. Stevens & Dorian Q. Fuller

  3. Archaeological Research Center, Okayama University, 3-1-1 Tsushima-Naka, Kita, Okayama, Okayama, 700-8530, Japan

    Shiho Iwasaki & Etsuyo Yamamoto

  4. Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita, Okayama, Okayama, 700-8530, Japan

    Yukari Akashi, Tran Phuong Dung, Hidetaka Nishida & Kenji Kato

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  1. Katsunori Tanaka
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Tanaka, K., Stevens, C.J., Iwasaki, S. et al. Seed size and chloroplast DNA of modern and ancient seeds explain the establishment of Japanese cultivated melon (Cucumis melo L.) by introduction and selection. Genet Resour Crop Evol 63, 1237–1254 (2016). https://doi.org/10.1007/s10722-015-0314-7

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