Skip to main content
SpringerLink
Log in

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

  • Research Article
  • Published:
Genetic Resources and Crop Evolution Aims and scope Submit manuscript

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Agricultural Industry Division, Department of Agriculture, Forestry and Fisheries, Kyoto Prefectural Office (2016) Statistical yearbook of the tea industry 2016 (Heisei 28 nendo chagyo tokei). Agricultural Industry Division, Department of Agriculture, Forestry and Fisheries, Kyoto Prefectural Office, Kyoto (in Japanese)

  • Andrews KR, Good JM, Miller MR, Luikart G, Hohenlohe PA (2016) Harnessing the power of RADseq for ecological and evolutionary genomics. Nat Rev Genet 17:81–92

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Mol Ecol 22:3124–3140

    Article  PubMed  PubMed Central  Google Scholar 

  • Chamber of Kyoto Prefecture Tea Association (1935) History of tea industry in Kyoto Prefecture (Kyoto-fu chagyo-shi). Chamber of Kyoto Prefecture Tea Association, Uji, pp 4–7 (in Japanese)

  • Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361

    Article  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Fuchinoue Y, Fuchinoue H (1999) Compendium of Japanese tea: from production to consumption (Nihon-cha zensho: seisan kara shomi made). Rural Culture Association Japan, Tokyo, pp 268–277 (in Japanese)

  • Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321

    Article  CAS  PubMed  Google Scholar 

  • Hanamori K, Ishikawa S, Saito H, Tanaka J, Sato Y, Okada Y (2012) Phylogenetic analysis of rpl16 and PS-ID region in tea (Camellia sinensis). DNA Polymorph 20:340–348 (in Japanese)

    Google Scholar 

  • Hashimoto M (2006) The studies of Japanese tea gardens in the medieval period. Nenpo Chuseishi Kenkyu 31:159–182 (in Japanese)

    Google Scholar 

  • Hasimoto M (1985) The origin of the tea plant. Jpn Agric Res Q 19:40–43

    Google Scholar 

  • Hubisz MJ, Falush D, Stephens M, Pritchard JK (2009) Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour 9:1322–1332

    Article  PubMed  PubMed Central  Google Scholar 

  • Katoh Y, Katoh M, Takeda Y, Omori M (2003) Genetic diversity within cultivated teas based on nucleotide sequence comparison of ribosomal RNA maturase in chloroplast DNA. Euphytica 134:287–295

    Article  CAS  Google Scholar 

  • Kopelman NM, Mayzel J, Jakobsson M, Rosenberg NA, Mayrose I (2015) CLUMPAK: a program for identifying clustering modes and packaging population structure inferences across K. Mol Ecol Resour 15:1179–1191

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kubo N, Hirai M, Kaneko A, Tanaka D, Kasumi K (2009) Development and characterization of simple sequence repeat (SSR) markers in the water lotus (Nelumbo nucifera). Aquat Bot 90:191–194

    Article  CAS  Google Scholar 

  • Kubo N, Douke A, Nishigaki T, Tsuji G (2017) Development and characterization of simple sequence repeat markers for genetic analyses of Sargassum horneri (Sargassaceae, Phaeophyta) populations in Kyoto, Japan. J Appl Phycol 29:1729–1733

    Article  CAS  Google Scholar 

  • Kyoto Prefectural Library and Archives (1991) Historic timeline of Kyoto Prefectural agriculture (Kyoto-fu Nogyo-shi Nenpyo) 1867–1965. Kyoto Prefectural Library and Archives, Kyoto, p 69 (in Japanese)

  • Langella O (2011) Populations 1.2.32: population genetic software (individuals or population distances, phylogenetic trees). http://www.bioinformatics.org/project/?group_id=84. Accessed July 12, 2018

  • Ma JQ, Zhou YH, Ma CL, Yao MZ, Jin JQ, Wang XC, Chen L (2010) Identification and characterization of 74 novel polymorphic EST-SSR markers in the tea plant, Camellia sinensis (Theaceae). Am J Bot 97:e153–e156

    Article  CAS  PubMed  Google Scholar 

  • Ma JQ, Ma CL, Yao MZ, Jin JQ, Wang ZL, Wang XC, Chen L (2012) Microsatellite markers from tea plant expressed sequence tags (ESTs) and their applicability for cross-species/genera amplification and genetic mapping. Sci Hortic (Amsterdam) 134:167–175

    Article  CAS  Google Scholar 

  • Matsumoto S, Kiriiwa Y, Takeda Y (2002) Differentiation of Japanese green tea cultivars as revealed by RFLP analysis of phenylalanine ammonia-lyase DNA. Theor Appl Genet 104:998–1002

    Article  CAS  PubMed  Google Scholar 

  • Matsumoto S, Kiriiwa Y, Yamaguchi S (2004) The Korean tea plant (Camellia sinensis): RFLP analysis of genetic diversity and relationship to Japanese tea. Breed Sci 54:231–237

    Article  CAS  Google Scholar 

  • Merritt BJ, Culley TM, Avanesyan A, Stokes R, Brzyski J (2015) An empirical review: characteristics of plant microsatellite markers that confer higher levels of genetic variation. Appl Plant Sci 3:1500025

    Article  Google Scholar 

  • Nakamura Y (2014) A study of the folklore of Bancha (the course tea of the common people). Dissertation, Kanagawa University, pp 96–104 (in Japanese)

  • Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. J Mol Evol 19:153–170

    Article  CAS  PubMed  Google Scholar 

  • Ni S, Yao MZ, Chen L, Zhao LP, Wang XC (2012) Germplasm and breeding research of tea plant based on DNA marker approaches. In: Chen L, Apostolides Z, Chen ZM (eds) Global tea breeding: achievements, challenges and perspectives. Springer, Berlin, pp 361–376

    Chapter  Google Scholar 

  • Nishio Town Hall (1934) History of Nishio town, vol 2. In: Ozaki T, Aoyama Z (eds) Nishio Town Hall, Nishio, pp 218–221 (in Japanese)

  • Ohsako T, Ohgushi T, Motosugi H, Oka K (2008) Microsatellite variability within and among local landrace populations of tea, Camellia sinensis (L.) O. Kuntze, in Kyoto, Japan. Genet Resour Crop Evol 55:1047–1053

    Article  Google Scholar 

  • Oishi S (1983) Development of tea manufacture in Japan. Rural Culture Association Japan, Tokyo (in Japanese)

    Google Scholar 

  • Oshida K (1936) Cutting propagation and cultivation of tea plant (Chaju no sashiki hanshoku to ikubyo). In: Proceedings of the 50th anniversary of the Tea Industry Association, vol 1. Central Chamber of Tea Industry Association, Tokyo, pp 117–192 (in Japanese)

  • Penjor T, Mimura T, Kotoda N, Matsumoto R, Nagano AJ, Honjo MN, Kudoh H, Yamamoto M, Nagano Y (2016) RAD-seq analysis of typical and minor Citrus accessions, including Bhutanese varieties. Breed Sci 66:797–807

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • Sealy JR (1958) A revision of the genus Camellia. The Royal Horticultural Society, London, pp 111–113

    Google Scholar 

  • Sen S XV (1998) The Japanese way of tea: from its origins in China to Sen Rikyu. Morris VD (trans), University of Hawai’i Press, Honolulu

  • Sharma H, Kumar R, Sharma V, Kumar V, Bhardwaj P, Ahuja PS, Sharma RK (2011) Identification and cross-species transferability of 112 novel unigene-derived microsatellite markers in tea (Camellia sinensis). Am J Bot 98:e133–e138

    Article  CAS  PubMed  Google Scholar 

  • Takeda Y (2002) Studies on variations in genetic resources of tea in Japan and application to tea breeding. Bull Natl Inst Veg Tea Sci 1:97–180 (in Japanese with English summary)

    CAS  Google Scholar 

  • Tamaki I, Kuze T, Hirota K, Mizuno M (2016) Genetic variation and population demography of the landrace population of Camellia sinensis in Kasuga, Gifu Prefecture, Japan. Genet Resour Crop Evol 63:823–831

    Article  Google Scholar 

  • Tan LQ, Wang LY, Wei K, Zhang CC, Wu LY, Qi GN, Cheng H, Zhang Q, Cui QM, Liang JB (2013) Floral transcriptome sequencing for SSR marker development and linkage map construction in the tea plant (Camellia sinensis). PLoS ONE 8:e81611

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tanaka J (2012) Japanese tea breeding history and the future perspective. In: Chen L, Apostolides Z, Chen ZM (eds) Global tea breeding: achievements, challenges and perspectives. Springer, Berlin, pp 227–239

    Chapter  Google Scholar 

  • Taniguchi F, Furukawa K, Ota-Metoku S, Yamaguchi N, Ujihara T, Kono I, Fukuoka H, Tanaka J (2012) Construction of a high-density reference linkage map of tea (Camellia sinensis). Breed Sci 62:263–273

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Taniguchi F, Kimura K, Saba T, Ogino A, Yamaguchi S, Tanaka J (2014) Worldwide core collections of tea (Camellia sinensis) based on SSR markers. Tree Genet Genomes 10:1555–1565

    Article  Google Scholar 

  • Tea Research Station, Ministry of Agriculture and Forestry (1938) Report on achievement of services 1937, Tea Research Station (Showa 12 nendo Chagyo Shikenjo jigoseiseki hokokusho). Tea Research Station, Ministry of Agriculture and Forestry, Haibara, p 3 (in Japanese)

  • Toyao T, Takeda Y, Matsushita S, Kayumi S, Kondo S (1996) Geographical variation and adaptability of Japanese local populations of tea plants. Bull Natl Res Inst Veg Ornam Plants Tea Jpn Ser B 9:1–29 (in Japanese with English summary)

    Google Scholar 

  • Ujihara T, Ohta R, Hayashi N, Kohata K, Tanaka J (2009) Identification of Japanese and Chinese green tea cultivars by using simple sequence repeat markers to encourage proper labeling. Biosci Biotechnol Biochem 73:15–20

    Article  CAS  PubMed  Google Scholar 

  • Wachira F, Tanaka J, Takeda Y (2001) Genetic variation and differentiation in tea (Camellia sinensis) germplasm revealed by RAPD and AFLP variation. J Hortic Sci Biotechnol 76:557–563

    CAS  Google Scholar 

  • Wang RJ, Gao XF, Kong XR, Yang J (2016) An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers. SpringerPlus 5:1152

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wei C, Yang H, Wang S, Zhao J, Liu C, Gao L, Xia E, Lu Y, Tai Y, She G et al (2018) Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality. Proc Natl Acad Sci USA 115:E4151–E4158

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu H, Chen D, Li J, Yu B, Qiao X, Huang H, He M (2012) De novo characterization of leaf transcriptome using 454 sequencing and development of EST-SSR markers in tea (Camellia sinensis). Plant Mol Biol Rep 31:524–538

    Article  CAS  Google Scholar 

  • Xia EH, Zhang HB, Sheng J, Li K, Zhang QJ, Kim C, Zhang Y, Liu Y, Zhu T, Li W et al (2017) The tea tree genome provides insights into tea flavor and independent evolution of caffeine biosynthesis. Mol Plant 10:866–877

    Article  CAS  PubMed  Google Scholar 

  • Yao MZ, Chen L, Liang YR (2008) Genetic diversity among tea cultivars from China, Japan and Kenya revealed by ISSR markers and its implication for parental selection in tea breeding programmes. Plant Breed 127:166–172

    Article  CAS  Google Scholar 

  • Yao MZ, Ma CL, Qiao TT, Jin JQ, Chen L (2012) Diversity distribution and population structure of tea germplasms in China revealed by EST–SSR markers. Tree Genet Genomes 8:205–220

    Article  Google Scholar 

  • Zhao LP, Liu Z, Chen L, Yao MZ, Wang XC (2008) Generation and characterization of 24 novel EST derived microsatellites from tea plant (Camellia sinensis) and cross-species amplification in its closely related species and varieties. Conserv Genet 9:1327–1331

    Article  CAS  Google Scholar 

Download references

Acknowledgements

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.

Author information

Author notes

  1. Tomohiro Matsuda

    Present address: Department of Agriculture, Forestry and Fisheries, Kyoto Prefectural Office, Kamigyo-ku, Kyoto, 602-8570, Japan

Authors and Affiliations

  1. Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, 606-8522, Japan

    Nakao Kubo

  2. Biotechnology Research Department, Kyoto Prefectural Agriculture, Forestry and Fisheries Technology Center, Soraku-gun, Kyoto, 619-0244, Japan

    Nakao Kubo & Yutaka Mimura

  3. Tea Industry Research Division, Agriculture and Forestry Technology Department, Kyoto Prefectural Agriculture, Forestry and Fisheries Technology Center, Uji, Kyoto, 611-0022, Japan

    Tomohiro Matsuda

  4. Faculty of Agriculture, Ryukoku University, Ohtsu, Shiga, 520-2194, Japan

    Atsushi J. Nagano

  5. Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan

    Nobuhiro Hirai

  6. Rural Development Division, Wazuka Town Hall, Soraku-gun, Kyoto, 619-1295, Japan

    Shigekazu Higashimoto

  7. Systematic Horticulture Course, Kyoto Prefectural Kizu High School, Kizugawa, Kyoto, 619-0214, Japan

    Hiromi Yoshida

  8. CHA Experience Park, Fukujuen Co., Ltd., Kizugawa, Kyoto, 619-0223, Japan

    Norihiro Uemura

  9. Faculty of Bioenvironmental Science, Kyoto Gakuen University, Kameoka, Kyoto, 621-8555, Japan

    Takao Fujii

Authors
  1. Nakao Kubo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yutaka Mimura
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Tomohiro Matsuda
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Atsushi J. Nagano
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Nobuhiro Hirai
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Shigekazu Higashimoto
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Hiromi Yoshida
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Norihiro Uemura
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Takao Fujii
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Nakao Kubo.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kubo, N., Mimura, Y., Matsuda, T. et al. 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. Genet Resour Crop Evol 66, 441–451 (2019). https://doi.org/10.1007/s10722-018-0722-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-018-0722-6

Keywords

Search

Navigation