Nuclear microsatellites reveal the genetic architecture and breeding history of tea germplasm of East Africa (original) (raw)
Anderson EC, Thompson EA (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160:1217–1229 PubMed CentralCASPubMed 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
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 ArticlePubMed CentralCASPubMed 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 ArticleCAS 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 ArticleCASPubMed 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 ArticlePubMed 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 ArticleCAS 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 CentralPubMed Google Scholar
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 ArticleCASPubMed 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 ArticleCAS Google Scholar
Fu YB, Somers DJ (2009) Genome-wide reduction of genetic diversity in wheat breeding. Crop Sci 49:161–168 Article Google Scholar
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 ArticlePubMed CentralCASPubMed 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 ArticlePubMed CentralCASPubMed 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 ArticleCASPubMed 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 ArticleCAS 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 ArticleCASPubMed 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 ArticlePubMed 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 ArticleCASPubMed Google Scholar
Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. J Mol Evol 19:153–170 ArticleCASPubMed 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 ArticleCAS 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 ArticleCAS Google Scholar
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959 PubMed CentralCASPubMed 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 ArticleCAS 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 ArticleCASPubMed 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 ArticlePubMed 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 ArticleCASPubMed 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 ArticleCAS 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 ArticlePubMed 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 ArticleCASPubMed 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 ArticleCAS 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 ArticleCAS 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 ArticlePubMed CentralPubMed Google Scholar