Tree Genetics & Genomes

, Volume 8, Issue 1, pp 205–220 | Cite as

Diversity distribution and population structure of tea germplasms in China revealed by EST-SSR markers

  • Ming-Zhe Yao
  • Chun-Lei Ma
  • Ting-Ting Qiao
  • Ji-Qiang Jin
  • Liang ChenEmail author
Original Paper


Tea plant (Camellia sinensis (L.) O. Kuntze) originated from China, where distributed abundant genetic resources. It is of critical importance to well understanding of genetic diversity and population structure for effective collection, conservation, and utilization of tea germplasms. In this study, 96 new polymorphic EST-SSR markers were developed and used to analyze 450 tea accessions collected from 14 tea-producing regions across China. A total of 409 alleles were observed, and the gene diversity (H) and polymorphic information content (PIC) were estimated to be averagely 0.64 and 0.61, respectively, across all the tested samples. The higher level of genetic diversity was observed in original regions like Guangxi, Yunnan, and Guizhou provinces. The allele number, H, and PIC showed decreasing trend when the region was more and more away from origin center of tea plant, which gave us implications on the spreading route of tea plant in China. The clustering of 450 samples both showed a clear separation according to their geographic origin based on either model simulation or genetic distance. The genetic differentiation was further analyzed among five inferred populations represented different eco-geographic regions. The lowest F st and the closest relationship were revealed between proximal populations, which indicated that gene exchanges occurred frequently between nearby regions than distance ones. The majority of genetic variation resulted from differentiation within population (81.36%) rather than among inferred (13.6%) and regional (5.04%) populations based on analysis of molecular variance. Our study also revealed that the lower diversity and simpler population structure were found in improved cultivars than wild teas and landraces, which indicated that genetic base of developed cultivars became narrow because of long-standing domestication and artificial selection. So more attentions should be focused to conserve and utilize the beneficial genes in wild teas and landraces to broaden genetic variation of new cultivars in future breeding of the tea plant.


Camellia sinensis Genetic diversity Population structure EST-SSR 



The authors thank the associate editor Dr. Yoshihiko Tsumura and two anonymous reviewers for their valuable suggestions. This work was supported, in part, by the Earmarked Fund for China Agriculture Research System (CARS-023) to Liang Chen and the National Science Foundation of China (NSFC; no. 30901159) to Ji-Qiang Jin and Natural Science Foundation of Zhejiang province (no. Y3110260) to Ming-Zhe Yao.

Supplementary material

11295_2011_433_MOESM1_ESM.xls (87 kb)
ESM 1 (XLS 87 kb)


  1. Balasaravanan T, Pius PK, Kumar RR, Muraleedharan N, Shasany AK (2003) Genetic diversity among south Indian tea germplasm (Camellia sinensis, C. assamica and C. assamica spp. lasiocalyx) using AFLP markers. Plant Sci 165:365–372CrossRefGoogle Scholar
  2. Chang HT (1981) Thea—a section of beveragial tea trees of the genus Camellia. Acta Sci Natl Univer Sunyatseni 1:87–99Google Scholar
  3. Chen L, Yamaguchi S (2002) Genetic diversity and phylogeny of tea plant (Camellia sinensis) and its related species and varieties in the section Thea genus Camellia determined by randomly amplified polymorphic DNA analysis. J Hortic Sci Biotech 77:729–732Google Scholar
  4. Chen L, Zhou ZX (2005) Variations of main quality components of tea genetic resources preserved in China national germplasm tea repository. Plant Foods Hum Nutr 60:31–35PubMedCrossRefGoogle Scholar
  5. Chen L, Yu FL, Tong QQ (2000) Discussions on phylogenetic classification and evolution of Sect. Thea. J Tea Sci 20:89–94Google Scholar
  6. Chen J, Wang PS, Xia YM, Xu M, Pei SJ (2005a) Genetic diversity and differentiation of Camellia sinensis L. (cultivated tea) and its wild relatives in Yunnan province of China, revealed by morphology, biochemistry and allozyme studies. Genet Resour Crop Evol 52:41–52CrossRefGoogle Scholar
  7. Chen L, Zhao LP, Gao QK (2005b) Generation and analysis of expressed sequence tags from the tender shoots cDNA library of tea plant (Camellia sinensis). Plant Sci 168:359–363CrossRefGoogle Scholar
  8. Chen L, Zhou ZX, Yang YJ (2007) Genetic improvement and breeding of tea plant (Camellia sinensis) in China: from individual selection to hybridization and molecular breeding. Euphytica 154:239–248CrossRefGoogle Scholar
  9. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50Google Scholar
  10. Feng HS (2010) Both production and income of Chinese tea industry increased in 2009. China Tea 32:1Google Scholar
  11. Freeman S, West J, James C, Lea V, Mayes S (2004) Isolation and characterization of highly polymorphic microsatellites in tea (Camellia sinensis). Mol Ecol Notes 4:324–326CrossRefGoogle Scholar
  12. Gupta PK, Rustgi S, Kulwal PL (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Bio 57:461–485CrossRefGoogle Scholar
  13. Hashimoto M, Takasi S (1978) Morphological studies on the origin of the tea plant V, a proposal of one place of origin by cluster analysis. Jpn J Crop Agr 21:93–101Google Scholar
  14. Huang FP, Liang YR, Lu JL, Chen RB, Mamati G (2004) Evaluation of genetic diversity in Oolong tea germplasms by AFLP fingerprinting. J Tea Sci 24:183–189Google Scholar
  15. Hung CY, Wang KH, Huang CC, Gong X, Ge XJ, Chiang TY (2008) Isolation and characterization of 11 microsatellite loci from Camellia sinensis in Taiwan using PCR-based isolation of microsatellite arrays (PIMA). Conserv Genet 9:779–781CrossRefGoogle Scholar
  16. Jin JQ, Cui HR, Chen WY, Lu MZ, Yao YL, Xin Y, Gong XC (2006) Data mining for SSRs in ESTs and development of EST-SSR marker in tea plant (Camellia sinensis). J Tea Sci 26:17–23Google Scholar
  17. Kato F, Taniguchi F, Monobe M, Ema K, Hirono H, Maeda-Yamamoto M (2008) Identification of Japanese tea (Camellia sinensis) cultivars using SSR markers. Nippon shokuhin kagaku kogaku kaishi, 55:49–55Google Scholar
  18. 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 134:287–295CrossRefGoogle Scholar
  19. Kaundun SS, Matsumoto S (2002) Heterologous nuclear and chloroplast microsatellite amplification and variation in tea, Camellia sinensis. Genome 45:1041–1048PubMedCrossRefGoogle Scholar
  20. Kaundun SS, Matsumoto S (2003) Development of CAPS markers based on three key genes of the phenylpropanoid pathway in tea, Camellia sinensis (L.) O. Kuntze, and differentiation between assamica and sinensis varieties. Theor Appl Genet 106:375–383PubMedGoogle Scholar
  21. Kaundun SS, Zhyvoloup A, Park YG (2000) Evaluation of the genetic diversity among elite tea (Camellia sinensis var. sinensis) accessions using RAPD markers. Euphytica 115:7–16CrossRefGoogle Scholar
  22. Ladizinsky G (1999) Plant evolution under domestication. Kluwer Academic Publishers, LondonCrossRefGoogle Scholar
  23. Li YC, Korol AB, Fahima T, Nevo E (2004) Microsatellites within genes: structure, function and evolution. Mol Biol Evol 21:991–1007PubMedCrossRefGoogle Scholar
  24. Liu K, Muse SV (2005) PowerMarker: integrated analysis environment for genetic marker data. Bioinformatics 21:2128–2129PubMedCrossRefGoogle Scholar
  25. Liu Z, Wang XC, Zhao LP, Yao MZ, Wang PS, Xu M, Tang YC, Chen L (2008) Genetic diversity and relationship analysis of tea germplasms originated from southwestern China based on EST-SSR. Mol Plant Breed 6:100–110Google Scholar
  26. Luo JW, Shi ZP, Shen CW, Liu CL, Gong ZH, Huang YH (2002) Studies on genetic relationships of tea cultivars [Camellia sinensis (L.) O. Kuntze] by RAPD analysis. J Tea Sci 22:140–146Google Scholar
  27. 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(12):e153–e156PubMedCrossRefGoogle Scholar
  28. Mackay I, Powell W (2007) Methods for linkage disequilibrium mapping in crops. Trends Plant Sci 12:57–63PubMedCrossRefGoogle Scholar
  29. 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 104:998–1002PubMedCrossRefGoogle Scholar
  30. Ming TL (1992) A revision of Camellia sect. Thea. Acta Bot Yunnanica 14:115–132Google Scholar
  31. Nei M, Tajima FA, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. J Mol Evol 19:153–170PubMedCrossRefGoogle Scholar
  32. Ni S, Yao MZ, Chen L, Zhao LP, Wang XC (2008) Germplasm and breeding research of tea plant based on DNA marker approaches. Front Agric China 2:200–207CrossRefGoogle Scholar
  33. Park JS, Kim JB, Hahn BS, Kim KH, Ha SH, Kim YH (2004) EST analysis of genes involved in secondary metabolism in Camellia sinensis (tea), using suppression subtractive hybridization. Plant Sci 166:953–961CrossRefGoogle Scholar
  34. Paul S, Wachira FN, Powell W, Waugh R (1997) Diversity and genetic differentiation among populations of Indian and Kenyan tea (Camellia sinensis (L.) O. Kuntze) revealed by AFLP markers. Theor Appl Genet 94:255–263CrossRefGoogle Scholar
  35. Pritchard JK, Wen W (2004) Documentation for STRUCTURE software. The University of Chicago Press, ChicagoGoogle Scholar
  36. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  37. Qiao TT, Ma CL, Zhou YH, Yao MZ, Liu R, Chen L (2010) EST-SSR Genetic diversity and population structure of tea landraces and developed cultivars (lines) in Zhejiang Province, China. Acta Agr Sinica 36:744–753CrossRefGoogle Scholar
  38. Sealy JR (1958) A revision of genus Camellia. The Royal Horticultural Society, London, pp 111–131Google Scholar
  39. Sharma RK, Bhardwaj P, Negi R, Mohapatra T, Ahuja PS (2009) Identification, characterization and utilization of unigene derived microsatellite markers in tea (Camellia sinensis L.). BMC Plant Biol 9:53PubMedCrossRefGoogle Scholar
  40. Shen CW, Huang YH, Huang JA, Luo JW, Liu CL, Liu DH (2007) RAPD analysis for genetic diversity of typical tea populations in Hunan province. J Agr Biotech 15:855–860Google Scholar
  41. Shi CY, Yang H, Wei CL, Yu O, Zhang ZZ, Jiang CJ, Sun J, Li YY, Chen Q, Xia T, Wan XC (2011) Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. BMC Genomics 12:131PubMedCrossRefGoogle Scholar
  42. Takeo T, You XQ, Wang HF, Kinukasa H, Li MJ, Chen QK, Wang HS (1992) One speculation on the origin and dispersion of tea plant in China. J Tea Sci 12:81–86Google Scholar
  43. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599PubMedCrossRefGoogle Scholar
  44. Tanaka J, Taniguchi F, Hirai N, Yamaguchi S (2006) Estimation of the genome size of tea (Camellia sinensis), camellia (C. japonica), and their interspecific hybrids by flow cytometry. Tea Res J 101:1–7CrossRefGoogle Scholar
  45. Temnykh S, Declerck G, Lukashova A, Lipovich L, Cartinhour S, Mccouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452PubMedCrossRefGoogle Scholar
  46. Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotech 23:48–55CrossRefGoogle Scholar
  47. Wachira FN, Waugh R, Hackett CA, Powell W (1995) Detection of genetic diversity in tea (Camellia sinensis) using RAPD markers. Genome 38:201–210PubMedCrossRefGoogle Scholar
  48. 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 Biotech 76:557–563Google Scholar
  49. Yamanishi T (1995) Food Reviews International: Special Issue on Tea 11(3):371–546Google Scholar
  50. Yang YJ, Yu FL, Chen L et al (2003) Elite germplasm evaluation and genetic stability of tea plants. J Tea Sci 23(S):1–8Google Scholar
  51. Yao MZ, Chen L, Wang XC, Zhao LP, Yang YJ (2007) Genetic diversity and relationship of clonal tea cultivars in China revealed by ISSR markers. Acta Agr Sinica 33:598–604Google Scholar
  52. 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 programs. Plant Breeding 127:166–172CrossRefGoogle Scholar
  53. Yu FL (1986) Discussion on the originating place and the originating center of tea plants. J Tea Sci 6:1–8Google Scholar
  54. Yu FL, Wang HS, Han ZF (1991) The characterization on agronomic traits, quality and cold tolerance of tea germplasm. In: Tea Research Institute Chinese Academy of Agricultural Sciences (ed) Tea Science Research Proceedings. Shanghai Scientific and Technical Press, Shanghai, pp 29–34Google Scholar
  55. Yu FL, Chen SR, Chen L (1997) Evaluation on morphological character, made-tea quality and cold resistance of tea germplasm resources. In: Tea Research Institute Chinese Academy of Agricultural Sciences (ed) Tea Science Research Proceedings. Shanghai Scientific and Technical Press, Shanghai, pp 1–7Google Scholar
  56. Zhao LP, Liu Z, Chen L, Yao MZ, Wang XC (2008a) 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 9:1327–1331CrossRefGoogle Scholar
  57. Zhao LP, Ma CL, Chen L (2008b) Construction and expressed sequence tags analysis of young roots cDNA library of tea plant. Mol Plant Breed 6:893–898Google Scholar

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Ming-Zhe Yao
    • 1
  • Chun-Lei Ma
    • 1
  • Ting-Ting Qiao
    • 1
  • Ji-Qiang Jin
    • 1
  • Liang Chen
    • 1
    Email author
  1. 1.National Center for Tea ImprovementTea Research Institute of the Chinese Academy of Agricultural SciencesHangzhouChina

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