Genetic Resources and Crop Evolution

, Volume 66, Issue 2, pp 441–451 | Cite as

Classification of tea (Camellia sinensis) landraces and cultivars in Kyoto, Japan and other regions, based on simple sequence repeat markers and restriction site-associated DNA sequencing analysis

  • Nakao KuboEmail author
  • Yutaka Mimura
  • Tomohiro Matsuda
  • Atsushi J. Nagano
  • Nobuhiro Hirai
  • Shigekazu Higashimoto
  • Hiromi Yoshida
  • Norihiro Uemura
  • Takao Fujii
Research Article


The tea plant (Camellia sinensis (L.) Kuntze) of Japan is now thought to have originated in China. Actual cultivation of tea plants presumably started in Kyoto, and then spread to other regions of Japan. Tea gardens used to be composed of heterogenic, seed-derived populations—landraces—selected for climatic preferences and cultivation methods. Cultivars were bred from landraces in the modern era. A number of landraces remain in Kyoto Prefecture. However, little is known about their genetic characteristics compared with other landraces. We investigated the relationships of tea landraces and cultivars from Kyoto Prefecture and other regions. A neighbor-joining phylogram was constructed from 113 lines including 68 landraces, 44 cultivars, and one wild relative, based on simple sequence repeat markers. The lines could be classified into four groups (I–IV). In group I, most of the Kyoto landraces were close to other Japanese landraces, supporting the idea of the spread of tea plants from Kyoto to other regions in the country. The remaining lines were included into groups III and IV, apart from group II, which contained Shizuoka lines. Similar results were observed by restriction site-associated DNA sequencing analysis using 44 cultivars. Our data provide valuable information for the classification of tea lines, especially for the relationships of Kyoto lines among Japanese tea varieties.


Camellia sinensis Classification Cultivar Landrace Restriction site-associated DNA sequencing (RAD-seq) Simple sequence repeat (SSR) 



We thank the Institute of Fruit Tree and Tea Science, NARO, Maizuru Floral & Green Public Corporation, Mr. R. Mizuta and residents of Nakagawa area, Kita-ku, Kyoto for providing tea samples. We are grateful to Mr. K. Harada, Mr. H. Sawasaki, Ms. M. Kanda, Mr. T. Fujiwara, Mr. K. Okadome, Mr. T. Takemoto, Dr. S. Tokumaru, Mr. K. Yamashita, Ms. Y. Hotta, Drs. S. Sano, S. Morita, I. Ohshima, and students of Kyoto Prefectural Kizu High School for valuable comments and their kind help, Dr. A. Tezuka for the analysis of the RAD-seq data, and Ms. H. Kasaoka for technical assistance. This work was supported by Academic Contribution to Region (ACTR) grants (2014–2017) from Kyoto Prefectural University and a grant (2017) from Kyoto Institute, Library and Archives to N.K.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

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Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  1. 1.Graduate School of Life and Environmental SciencesKyoto Prefectural UniversitySakyo-kuJapan
  2. 2.Biotechnology Research DepartmentKyoto Prefectural Agriculture, Forestry and Fisheries Technology CenterSoraku-gunJapan
  3. 3.Tea Industry Research Division, Agriculture and Forestry Technology DepartmentKyoto Prefectural Agriculture, Forestry and Fisheries Technology CenterUjiJapan
  4. 4.Department of Agriculture, Forestry and FisheriesKyoto Prefectural OfficeKyotoJapan
  5. 5.Faculty of AgricultureRyukoku UniversityOhtsuJapan
  6. 6.Graduate School of AgricultureKyoto UniversityKyotoJapan
  7. 7.Rural Development DivisionSoraku-gun, KyotoJapan
  8. 8.Systematic Horticulture CourseKyoto Prefectural Kizu High SchoolKizugawaJapan
  9. 9.CHA Experience Park, Fukujuen Co., Ltd.KizugawaJapan
  10. 10.Faculty of Bioenvironmental ScienceKyoto Gakuen UniversityKameokaJapan

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