Skip to main content
SpringerLink
Log in

Nuclear microsatellites reveal the genetic architecture and breeding history of tea germplasm of East Africa

Tree Genetics & Genomes volume 12, Article number: 11 (2016) Cite this article

Abstract

Tea is the most popular non-alcoholic beverage worldwide and is one of the most important tree cash crops in East Africa. However, no comprehensive study has been carried out on the genetic structure and diversity of tea germplasm for this region to date. In the present study, 193 tea accessions held at the ex situ Germplasm Bank of the Tea Research Institute (TRI), Kenya, were analysed using genetic data from 23 polymorphic simple sequence repeat (SSR) loci. A total of 266 alleles were detected with the number of alleles per locus ranging from 4 to 19 with an average of 7.88. Genetic clustering by STRUCTURE was used to correct misidentified accessions based on morphological characters. After reassignment of the tea accessions, Camellia assamica exhibited the lowest genetic diversity (Hs = 0.648) despite being the most widely cultivated tea type in the East African region. C. assamica subsp. lasiocalyx showed the highest genetic diversity (Hs = 0.76), which supported its origin by hybridization among tea types. Tea cultivars cultivated across the region exhibited lower genetic diversity (Hs = 0.661) compared to material held at the ex situ Germplasm Bank of TRI. Tea accessions clustered in the neighbour-joining tree on the basis of geographical origin, pedigree and leaf pigmentation, indicating their common origin. Our results indicated further that East African tea germplasm has a complex breeding history with a majority of the hybrids being F2 generation and backcross plants. C. assamica contributed significantly more genetic materials in the tea breeding programmes in East Africa. This study highlights the importance of ex situ germplasm banks to conserve the highest genetic diversity, which is an important resource for future tea crop improvements in East Africa.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

39,95 €

Price includes VAT (Finland)

Fig. 1
Fig. 2
Fig. 3

References

  • Anderson EC, Thompson EA (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160:1217–1229

    PubMed Central  CAS  PubMed  Google Scholar 

  • Anon (1962) Historical notes on tea introduction in Africa. In: Wilson S (ed) Tea estates in Africa. Mabey & Fitzclarence, London, pp 6–9

    Google Scholar 

  • Bandyopadhyay T (2011) Molecular marker technology in genetic improvement of tea. Int J Plant Breed Gen 5:23–33

    Article  Google Scholar 

  • Beche E, Silva CL, Pagliosa ES, Capelin MA, Franke J, Matei G, Benin G (2013) Hybrid performance and heterosis in early segregant populations of Brazilian spring wheat. Aust J Crop Sci 7:51–57

    Google Scholar 

  • Bijlsma R, Loeschcke V (2012) Genetic erosion impedes adaptive responses to stressful environments. Evol Appl 5:117–129

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Castillo A, Dorado G, Feuillet C, Sourdille P, Hernandez P (2010) Genetic structure and ecogeographical adaptation in wild barley (Hordeum chilense Roemer et Schultes) as revealed by microsatellite markers. BMC Plant Biol 10:266

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Chang HT (1981) A taxonomy of the genus Camellia. Acta Sci Nat Univ Sunyatseni. Monogr Ser 1:1–180

    CAS  Google Scholar 

  • Chen J, Wang PS, Xia YM, Xu M, Pei SJ (2005) 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 Res Crop Evol 52:41–52

    Article  CAS  Google Scholar 

  • Chen X, Hao S, Wang L, Fang W, Wang Y, Li XH (2012) Late-acting self incompatibility in tea plant (Camellia sinensis). Biologia 67:347–351

    Google Scholar 

  • Cherotich L, Kamunya SM, Alakonya A, Msomba SW, Uwimana MA, Wanyoko JK, Owuor PO (2013) Variation in catechin composition of popularly cultivated tea clones in East Africa (Kenya). Am J Plant Sci 4:628–640

    Article  Google Scholar 

  • Davis MB, Shaw RG (2001) Range shifts and adaptive responses to quaternary climate changes. Science 292:673–679

    Article  CAS  PubMed  Google Scholar 

  • de Andrés MT, Benito A, Pérez-Rivera G, Ocete R, Lopez MA, Gaforio L, Muñoz G, Cabello F, Martínez-Zapater JM, Arroyo-García R (2012) Genetic diversity of wild grapevine populations in Spain and their genetic relationships with cultivated grapevines. Mol Ecol 21:800–816

    Article  PubMed  Google Scholar 

  • Dieringer D, Schlötterer C (2003) Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Mol Ecol Notes 3:167–169

    Article  CAS  Google Scholar 

  • Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15

    Google Scholar 

  • Earl DA, von Holdt 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 

  • Fang W, Cheng H, Duan Y, Jiang X, Li X (2012) Genetic diversity and relationship of clonal tea (Camellia sinensis) cultivars in China as revealed by SSR markers. Plant Syst Evol 298:469–483

    Article  Google Scholar 

  • Fang PW, Meinhardt WL, Tan HW, Zhou L, Mischke S, Zhang D (2014) Varietal identification of tea (Camellia sinensis) using nanofluidic array of single nucleotide polymorphism (SNP) markers. Hortic Res. doi:10.1038/hortres.2014.35

    PubMed Central  PubMed  Google Scholar 

  • FAOSTAT (2015) FAO database. Food Agric Organ United Nations. URL http://faostat3.fao.org/download/Q/QC/E(2015). Accessed 19 November 2015

  • Felsenstein J (2004) PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle

  • Franks SJ, Hoffmann AA (2012) Genetics of climate change adaptation. Annu Rev Genet 46:185–208

    Article  CAS  PubMed  Google Scholar 

  • 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 4:324–326

    Article  CAS  Google Scholar 

  • Fu YB, Somers DJ (2009) Genome-wide reduction of genetic diversity in wheat breeding. Crop Sci 49:161–168

    Article  Google Scholar 

  • Goudet J (2002) FSTAT: a program to estimate and test gene diversities and fixation index. Version 2.9.3.2 http://www2.unil.ch/popgen/softwares/fstat.htm

  • Hyten DL, Song QJ, Zhu YL, Choi IY, Nelson RL, Costa JM, Spetch JE, Shoemaker RC, Cregan PB (2006) Impacts of genetic bottlenecks on soybean genome diversity. Proc Natl Acad Sci U S A 103:16666–16671

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Innan H, Kim Y (2004) Pattern of polymorphism after strong artificial selection in a domestication event. Proc Natl Acad Sci U S A 101:10667–10672

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kamunya SM, Wachira FN, Nyabundi KW, Kerio L, Chalo RM (2009) The Tea Research Foundation of Kenya pre-releases purple tea variety for processing health tea product. Tea 30:3–10

    Google Scholar 

  • Karunakaran G, Ravishankar H, Dinesh MR (2010) Genetical studies in papaya (Carica papaya L). Acta Hortic 851:103–108

    Article  Google Scholar 

  • Kaundun SS, Matsumoto S (2002) Heterologous nuclear and chloroplast microsatellite amplification and variation in tea, Camellia sinensis. Genome 45:1041–1048

    Article  CAS  PubMed  Google Scholar 

  • Kelly JD, Kolkman JM, Schneider K (1998) Breeding for yield in dry bean (Phaseolus vulgaris L.). Euphytica 102:348–356

    Article  Google Scholar 

  • Kerio LC, Wachira FN, Wanyoko JK, Rotich MK (2012) Characterization of anthocyanins in Kenya teas: extraction and identification. Food Chem 131:31–38

    Article  CAS  Google Scholar 

  • Li MM, Meegahakumbura MK, Yan LJ, Liu J, Gao LM (2015) Genetic involvement of Camellia taliensis in the domestication of Camellia sinensis var. assamica (Assamica tea) revealed by nuclear microsatellite markers. Plant Divers Resour 37:29–37

    Google Scholar 

  • Liu K, Muse SV (2005) PowerMaker: integrated analysis environment for genetic marker data. Bioinformatics 21:2128–2129

    Article  CAS  PubMed  Google Scholar 

  • Lopes MS, El-Basyoni I, Baenziger PS, Singh S, Royo C, Ozbek K, Aktas H, Ozer E, Ozdemir F, Manickavelu A, Ban T, Vikram P (2015) Exploiting genetic diversity from landraces in wheat breeding for adaptation to climate change. J Exp Bot. doi:10.1093/jxb/erv122

    PubMed  Google Scholar 

  • Ma YP, Milne RI, Zhang CQ, Yang JB (2010) Unusual patterns of hybridization involving a narrow endemic Rhododendron species (Ericaceae) in Yunnan, China. Am J Bot 97:1749–1757

    Article  PubMed  Google Scholar 

  • Macfarlane A, Macfarlane I (2004) The Empire of Tea. The Overlook Press, New York, p 32

    Google Scholar 

  • Matheson JK, Bovill EW (1950) Tea. East African Agriculture: A short survey of the agriculture of Kenya, Uganda, Tanganyika, and Zanzibar and of its principal products. Oxford University Press, London, pp 198–206

    Google Scholar 

  • Ming TL (1992) A revision of Camellia Sect. Thea. Acta Bot Yunnanica 14:115–132

    Google Scholar 

  • Ming TL (2000) Monograph of the Genus Camellia. Yunnan Science and Technology Press, Kunming

    Google Scholar 

  • Ming TL, Bartholomew B (2007) Theaceae. In: Wu ZY, Raven PH, Hong DY (eds) Flora of China (Hippocastanaceae through Theaceae), vol 12. Science Press, Beijing and Missouri Botanical Garden Press, St. Louis, pp 366–478

    Google Scholar 

  • Morgante M, Olivieri AM (1993) PCR-amplified microsatellites as markers in plant genetics. Plant J 3:175–182

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • 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 Res Crop Evol 55:1047–1053

    Article  Google Scholar 

  • 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 94:255–263

    Article  CAS  Google Scholar 

  • Peakall R, Smouse P (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research - an update. Bioinformatics 82:2537–2539

    Article  Google Scholar 

  • Perdereau AC, Kelleher CT, Douglas GC, Hodkinson TR (2014) High levels of gene flow and genetic diversity in Irish populations of Salix caprea L. inferred from chloroplast and nuclear SSR markers. BMC Plant Biol 14:120. doi:10.1186/s12870-014-0202-x

    Article  Google Scholar 

  • Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238

    Article  CAS  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    PubMed Central  CAS  PubMed  Google Scholar 

  • Qian W, Ge S, Hong DY (2001) Genetic variation within and among populations of a wild rice Oryza granulate from China detected by RAPD and ISSR. Theor Appl Genet 102:440–449

    Article  CAS  Google Scholar 

  • Rao VR, Hodgkin T (2002) Genetic diversity and conservation and utilization of plant genetic resources. Plant Cell Tissue Organ Cult 68:1–19

    Article  Google Scholar 

  • Riley L, McGlaughlin ME, Helenurm K (2010) Genetic diversity following demographic recovery in the insular endemic plant Galium catalinense subsp. acrispum. Conserv Genet 11:2015–2025

    Article  Google Scholar 

  • Rong J, Lammers Y, Strasburg JL, Schidlo NS, Ariyurek Y, Jong TJ, Klinkhamer PGL, Smulders MJM, Vrieling K (2014) New insights into domestication of carrot from root transcriptome analyses. BMC Genomics 15:589

    Article  Google Scholar 

  • Schmutz J, McClean PE, Mamidi S et al (2014) A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet 46:707–713

    Article  CAS  PubMed  Google Scholar 

  • Sealy JR (1958) A revision of genus Camellia. Royal Horticultural Society, London

    Google Scholar 

  • Seurei P (1996) Tea improvement in Kenya: a review. Tea 17:76–81

    Google Scholar 

  • Smulders MJM, Beringen R, Volosyanchuk R, Broeck VA, van der Schoot J, Arens P, Vosman B (2008) Natural hybridisation between Populusnigra L. and P. x canadensis Moench. Hybrid offspring competes for niches along the Rhine river in the Netherlands. Tree Genet Genome 4:663–675

    Article  Google Scholar 

  • Talve T, McGlaughlin ME, Helenurm K, Wallace LE, Oja T (2013) Population genetic diversity and species relationships in the genus Rhinanthus L. based on microsatellite markers. Plant Biol 16:495–502

    Article  PubMed  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 Genome 10:1555–1565

    Article  Google Scholar 

  • Tanksley SD, Mccough SR (1997) Seedbanks and molecular maps: unlocking genetic potential from the wild. Science 277:1063–1066

    Article  CAS  PubMed  Google Scholar 

  • Tea Board of Kenya (TBK) (2013) Annual Report and Accounts 2012/2013. TBK, Nairobi

  • vanOosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538

    Article  CAS  Google Scholar 

  • Vigouroux Y, Glaubitz JC, Matsuoka Y, Major M, Doebley J (2008) Population structure and genetic diversity of the new world maize races assessed by microsatellites. Am J Bot 95:1240–1253

    Article  PubMed  Google Scholar 

  • Wachira FN (2002) Detection of genetic diversity and characterization of Kenyan tea germplasm. A Tea Genetic Diversity (TGD) project. TGD final project Document, Kericho, Kenya

  • Wachira FN, Waugh R, Hackett CA, Powell W (1995) Detection of genetic diversity in tea (Camellia sinensis) using RAPD markers. Genome 38:201–210

    Article  CAS  PubMed  Google Scholar 

  • Wachira FN, Powell W, Waugh R (1997) An assessment of genetic diversity among Camellia sinensis L. (cultivated tea) and its wild relatives based on randomly amplified polymorphic DNA and organelle-specific STS. Heredity 78:603–611

    Article  CAS  Google Scholar 

  • Wickramaratne MR, Tand VSI (1985) Insect pollination of tea (Camellia sinensis L.) in Sri Lanka. Trop Agric 62:243–247

    Google Scholar 

  • Wight W (1962) Tea Classification Revised. Curr Sci 31:298–299

    Google Scholar 

  • Wood DJ, Barua PK (1958) Species Hybrids of Tea. Nature 181:1674–1675

    Article  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 programs. 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 Genome 8:205–220

    Article  Google Scholar 

  • Zhao DW, Yang JB, Yang SX, Kato K, Lu JP (2014) Genetic diversity and domestication origin of tea plant Camelliata liensis (Theaceae) as revealed by microsatellite markers. BMC Plant Biol 14:14. doi:10.1186/1471-2229-14-14

    Article  PubMed Central  PubMed  Google Scholar 

Download references

Acknowledgments

We are grateful to Miaomiao Li, Junbo Yang, Hong-Tao Li, Jing Yang and Zhi-Rong Zhang for their help with data analysis or lab work. We thank Dr. Michael Möller from Royal Botanic Garden Edinburgh for his constructive comments on the manuscript. We also thank the Tea Research Institute Kenya for providing the tea samples conserved at the TRFK ex situ germplasm bank. This work was funded by the National Natural Science Foundation of China (31161140350). Laboratory work was performed at the Laboratory of Molecular Biology at the Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences.

Data archiving statement

We are in the process of archiving our genotype data on an online resource. We will provide details as soon as the process is completed.

Author information

Authors and Affiliations

  1. Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China

    M. C. Wambulwa, M. K. Meegahakumbura, J. Liu, D. Z. Li & L. M. Gao

  2. University of Chinese Academy of Sciences, Beijing, 100049, China

    M. C. Wambulwa, M. K. Meegahakumbura & D. Z. Li

  3. Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China

    M. C. Wambulwa, M. K. Meegahakumbura & D. Z. Li

  4. World Agroforestry Centre, 30677, Nairobi, Kenya

    M. C. Wambulwa & A. Muchugi

  5. Coconut Research Institute, Lunuwila, Sri Lanka

    M. K. Meegahakumbura

  6. Kenya Agricultural and Livestock Research Organization, Tea Research Institute (KALRO-TRI), 820, Kericho, Kenya

    R. Chalo & S. Kamunya

  7. World Agroforestry Centre, China and East Asia Node, Kunming, China

    J. C. Xu

Authors
  1. M. C. Wambulwa
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. M. K. Meegahakumbura
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. R. Chalo
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. S. Kamunya
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. A. Muchugi
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. J. C. Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. J. Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. D. Z. Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. L. M. Gao
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to D. Z. Li or L. M. Gao.

Additional information

Communicated by W. Ratnam

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(DOCX 33 kb)

ESM 2

(PDF 402 kb)

ESM 3

(PDF 278 kb)

ESM 4

(XLS 53 kb)

ESM 5

(DOCX 21.7 kb)

ESM 6

(DOCX 16 kb)

ESM 7

(DOCX 15 kb)

Rights and permissions

Reprints and Permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wambulwa, M.C., Meegahakumbura, M.K., Chalo, R. et al. Nuclear microsatellites reveal the genetic architecture and breeding history of tea germplasm of East Africa. Tree Genetics & Genomes 12, 11 (2016). https://doi.org/10.1007/s11295-015-0963-x

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11295-015-0963-x

Keywords

  • Camellia sinensis
  • East Africa
  • Genetic diversity
  • Nuclear microsatellites
  • Tea breeding

Search

Navigation