메뉴 건너뛰기




Volumn 9, Issue 3, 2013, Pages 829-840

Complex origin of Trinitario-type Theobroma cacao (Malvaceae) from Trinidad and Tobago revealed using plastid genomics

Author keywords

Chloroplast; Microsatellites; Single nucleotide polymorphisms; Theobroma cacao; Trinitario

Indexed keywords

MALVACEAE; THEOBROMA CACAO;

EID: 84877713755     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-013-0601-4     Document Type: Article
Times cited : (24)

References (56)
  • 4
    • 84866455449 scopus 로고
    • The botanical programme of 1933
    • Government Printing Office, Port-of-Spain, Trinidad
    • Cheesman EE (1934) The botanical programme of 1933. In Third annual report on cacao research, 1933. Government Printing Office, Port-of-Spain, Trinidad, pp 1-2.
    • (1934) Third Annual Report On Cacao Research, 1933 , pp. 1-2
    • Cheesman, E.E.1
  • 5
    • 0000437961 scopus 로고
    • Notes on the nomenclature, classification and possible relationships of cocoa populations
    • Cheesman EE (1944) Notes on the nomenclature, classification and possible relationships of cocoa populations. Trop Agric 21: 144-159.
    • (1944) Trop Agric , vol.21 , pp. 144-159
    • Cheesman, E.E.1
  • 7
    • 0001635951 scopus 로고
    • Rapid screening method to detect potential biparental inheritance of plastid DNA and results for over 200 angiosperms
    • Corriveau JL, Coleman AW (1988) Rapid screening method to detect potential biparental inheritance of plastid DNA and results for over 200 angiosperms. Am J Bot 75: 1443-1458.
    • (1988) Am J Bot , vol.75 , pp. 1443-1458
    • Corriveau, J.L.1    Coleman, A.W.2
  • 8
    • 0037346501 scopus 로고    scopus 로고
    • Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets
    • Dieringer D, Schlötterer C (2003) Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Mol Ecol Notes 3: 167-169.
    • (2003) Mol Ecol Notes , vol.3 , pp. 167-169
    • Dieringer, D.1    Schlötterer, C.2
  • 10
    • 84959848780 scopus 로고
    • Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters
    • Felsenstein J (1973) Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Syst Zool 22: 240-249.
    • (1973) Syst Zool , vol.22 , pp. 240-249
    • Felsenstein, J.1
  • 11
    • 0000122573 scopus 로고
    • PHYLIP - phylogeny inference package (Version 3.2)
    • Felsenstein J (1989) PHYLIP - phylogeny inference package (Version 3. 2). Cladistics 5: 164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 13
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
    • (2003) Syst Biol , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 14
    • 0842269254 scopus 로고    scopus 로고
    • Causes of size homoplasy among chloroplast microsatellites in closely related Clusia species
    • Hale ML, Borland AM, Gustafsson MH, Wolff K (2004) Causes of size homoplasy among chloroplast microsatellites in closely related Clusia species. J Mol Evol 58: 182-190.
    • (2004) J Mol Evol , vol.58 , pp. 182-190
    • Hale, M.L.1    Borland, A.M.2    Gustafsson, M.H.3    Wolff, K.4
  • 15
    • 27244461126 scopus 로고    scopus 로고
    • Mutational decay and age of chloroplast and mitochondrial genomes transferred recently to angiosperm nuclear chromosomes
    • Huang CY, Grünheit N, Ahmadinejad N, Timmis JN, Martin W (2005) Mutational decay and age of chloroplast and mitochondrial genomes transferred recently to angiosperm nuclear chromosomes. Plant Physiol 138: 1723-33.
    • (2005) Plant Physiol , vol.138 , pp. 1723-1733
    • Huang, C.Y.1    Grünheit, N.2    Ahmadinejad, N.3    Timmis, J.N.4    Martin, W.5
  • 16
    • 77749277412 scopus 로고    scopus 로고
    • Microsatellite fingerprinting of the USDA-ARS tropical agriculture research station cacao (Theobroma cacao L.) germplasm collection
    • Irish BI, Goenaga R, Zhang D, Schnell R, Brown S, Motamayor JC (2010) Microsatellite fingerprinting of the USDA-ARS tropical agriculture research station cacao (Theobroma cacao L.) germplasm collection. Crop Sci 50: 656-667.
    • (2010) Crop Sci , vol.50 , pp. 656-667
    • Irish, B.I.1    Goenaga, R.2    Zhang, D.3    Schnell, R.4    Brown, S.5    Motamayor, J.C.6
  • 17
    • 78650475518 scopus 로고    scopus 로고
    • Complete plastid genome sequences of three rosids (Castanea, Prunus, Theobroma): evidence for at least two independent transfers of rpl22 to the nucleus
    • Jansen RK, Saski C, Lee SB, Hansen AK, Daniell H (2011) Complete plastid genome sequences of three rosids (Castanea, Prunus, Theobroma): evidence for at least two independent transfers of rpl22 to the nucleus. Mol Biol Evol 28: 835-847.
    • (2011) Mol Biol Evol , vol.28 , pp. 835-847
    • Jansen, R.K.1    Saski, C.2    Lee, S.B.3    Hansen, A.K.4    Daniell, H.5
  • 18
    • 63149187142 scopus 로고    scopus 로고
    • Population structure and genetic diversity of the Trinitario cacao (Theobroma cacao L.) from Trinidad and Tobago
    • Johnson ES, Bekele FB, Brown SJ, Song Q, Zhang D, Meinhardt LW, Schnell RJ (2009) Population structure and genetic diversity of the Trinitario cacao (Theobroma cacao L.) from Trinidad and Tobago. Crop Sci 49: 564-572.
    • (2009) Crop Sci , vol.49 , pp. 564-572
    • Johnson, E.S.1    Bekele, F.B.2    Brown, S.J.3    Song, Q.4    Zhang, D.5    Meinhardt, L.W.6    Schnell, R.J.7
  • 19
    • 84863338497 scopus 로고    scopus 로고
    • Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA
    • Kane N, Sveinsson S, Dempewolf H, Yang JY, Zhang D, Engels JMM, Cronk Q (2012) Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA. Am J Bot 99: 320-329.
    • (2012) Am J Bot , vol.99 , pp. 320-329
    • Kane, N.1    Sveinsson, S.2    Dempewolf, H.3    Yang, J.Y.4    Zhang, D.5    Engels, J.M.M.6    Cronk, Q.7
  • 20
    • 67349123718 scopus 로고    scopus 로고
    • Identification of highly variable chloroplast sequences and development of cpDNA-based molecular markers that distinguish four cytoplasm types in radish (Raphanus sativus L.)
    • Kim S, Lee Y-P, Lim H, Ahn Y, Sung SK (2009) Identification of highly variable chloroplast sequences and development of cpDNA-based molecular markers that distinguish four cytoplasm types in radish (Raphanus sativus L.). Theor Appl Genet 119: 189-198.
    • (2009) Theor Appl Genet , vol.119 , pp. 189-198
    • Kim, S.1    Lee, Y.-P.2    Lim, H.3    Ahn, Y.4    Sung, S.K.5
  • 23
    • 0347927382 scopus 로고    scopus 로고
    • Chloroplast phylogeography and evolution of highly polymorphic microsatellites in lodgepole pine (Pinus contorta)
    • Marshall HD, Newton C, Ritland K (2002) Chloroplast phylogeography and evolution of highly polymorphic microsatellites in lodgepole pine (Pinus contorta). Theor Appl Genet 104: 367-378.
    • (2002) Theor Appl Genet , vol.104 , pp. 367-378
    • Marshall, H.D.1    Newton, C.2    Ritland, K.3
  • 24
    • 27244457663 scopus 로고    scopus 로고
    • The rice nuclear genome continuously integrates, shuffles, and eliminates the chloroplast genome to cause chloroplast-nuclear DNA flux
    • Matsuo M, Ito Y, Yamauchi R, Obokata J (2005) The rice nuclear genome continuously integrates, shuffles, and eliminates the chloroplast genome to cause chloroplast-nuclear DNA flux. The Plant Cell 17: 665-675.
    • (2005) The Plant Cell , vol.17 , pp. 665-675
    • Matsuo, M.1    Ito, Y.2    Yamauchi, R.3    Obokata, J.4
  • 25
    • 0030042907 scopus 로고    scopus 로고
    • The hows and whys of cytoplasmic inheritance in seed plants
    • Mogensen HL (1996) The hows and whys of cytoplasmic inheritance in seed plants. Am J Bot 83: 383-404.
    • (1996) Am J Bot , vol.83 , pp. 383-404
    • Mogensen, H.L.1
  • 27
    • 0141454836 scopus 로고    scopus 로고
    • Cacao domestication: II Progenitor germplasm of the Trinitario cacao cultivar
    • Motamayor JC, Risterucci AM, Heath M, Lanaud C (2003) Cacao domestication: II Progenitor germplasm of the Trinitario cacao cultivar. Heredity 91: 322-330.
    • (2003) Heredity , vol.91 , pp. 322-330
    • Motamayor, J.C.1    Risterucci, A.M.2    Heath, M.3    Lanaud, C.4
  • 28
    • 65249160575 scopus 로고    scopus 로고
    • Increasing accuracy and throughput in large scale microsatellite fingerprinting of cacao field germplasm collections
    • Motilal LA, Zhang D, Umaharan P, Mischke S, Boccara M, Pinney S (2009) Increasing accuracy and throughput in large scale microsatellite fingerprinting of cacao field germplasm collections. Trop Plant Biol 2: 23-37.
    • (2009) Trop Plant Biol , vol.2 , pp. 23-37
    • Motilal, L.A.1    Zhang, D.2    Umaharan, P.3    Mischke, S.4    Boccara, M.5    Pinney, S.6
  • 29
    • 77957348317 scopus 로고    scopus 로고
    • The relic Criollo cacao in Belize - genetic diversity and relationship with Trinitario and other cacao clones held in the International Cocoa Genebank Trinidad
    • Motilal LA, Zhang D, Umaharan P, Mischke S, Mooleedhar V, Meinhardt LW (2010) The relic Criollo cacao in Belize - genetic diversity and relationship with Trinitario and other cacao clones held in the International Cocoa Genebank Trinidad. Plant Genet Resource 8: 106-115.
    • (2010) Plant Genet Resource , vol.8 , pp. 106-115
    • Motilal, L.A.1    Zhang, D.2    Umaharan, P.3    Mischke, S.4    Mooleedhar, V.5    Meinhardt, L.W.6
  • 30
    • 79960119466 scopus 로고    scopus 로고
    • Microsatellite fingerprinting in the International Cocoa Genebank, Trinidad: accession and plot homogeneity information for germplasm management
    • Motilal LA, Zhang D, Umaharan P, Mischke S, Pinney S, Meinhardt LW (2011) Microsatellite fingerprinting in the International Cocoa Genebank, Trinidad: accession and plot homogeneity information for germplasm management. Plant Genet Resource 9: 430-438.
    • (2011) Plant Genet Resource , vol.9 , pp. 430-438
    • Motilal, L.A.1    Zhang, D.2    Umaharan, P.3    Mischke, S.4    Pinney, S.5    Meinhardt, L.W.6
  • 31
    • 0020965531 scopus 로고
    • Accuracy of estimated phylogenetic trees from molecular data
    • Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. J Mol Evol 19: 153-170.
    • (1983) J Mol Evol , vol.19 , pp. 153-170
    • Nei, M.1    Tajima, F.2    Tateno, Y.3
  • 32
    • 84920093347 scopus 로고    scopus 로고
    • Plant phylogeography based on organelle genes: an introduction
    • S. Weiss and N. Ferrand (Eds.), Dordrecht, Netherlands: Springer
    • Petit RJ, Vendramin GG (2007) Plant phylogeography based on organelle genes: an introduction. In: Weiss S, Ferrand N (eds) Phylogeography of Southern European refugia. Springer, Dordrecht, Netherlands, pp 23-97.
    • (2007) Phylogeography of Southern European Refugia , pp. 23-97
    • Petit, R.J.1    Vendramin, G.G.2
  • 33
    • 45849154165 scopus 로고    scopus 로고
    • jModelTest: phylogenetic model averaging
    • Posada D (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 25: 1253-1256.
    • (2008) Mol Biol Evol , vol.25 , pp. 1253-1256
    • Posada, D.1
  • 39
    • 0029792620 scopus 로고    scopus 로고
    • Genepool variation in genus Glycine subgenus Soja revealed by polymorphic nuclear and chloroplast microsatellites
    • Powell W, Morgante M, Doyle JJ, McNicol JW, Tingey SV, Rafalski AJ (1996) Genepool variation in genus Glycine subgenus Soja revealed by polymorphic nuclear and chloroplast microsatellites. Genetics 144: 793-803.
    • (1996) Genetics , vol.144 , pp. 793-803
    • Powell, W.1    Morgante, M.2    Doyle, J.J.3    McNicol, J.W.4    Tingey, S.V.5    Rafalski, A.J.6
  • 40
    • 0031062349 scopus 로고    scopus 로고
    • Chloroplast DNA variability in wild and cultivated rice (Oryza spp.) revealed by polymorphic chloroplast simple sequence repeats
    • Provan J, Corbett G, McNicol JW, Powell W (1997) Chloroplast DNA variability in wild and cultivated rice (Oryza spp.) revealed by polymorphic chloroplast simple sequence repeats. Genome 40: 104-110.
    • (1997) Genome , vol.40 , pp. 104-110
    • Provan, J.1    Corbett, G.2    McNicol, J.W.3    Powell, W.4
  • 41
    • 0032907656 scopus 로고    scopus 로고
    • Polymorphic chloroplast simple sequence repeat primers for systematic and population studies in the genus Hordeum
    • Provan J, Russell JR, Booth A, Powell W (1999) Polymorphic chloroplast simple sequence repeat primers for systematic and population studies in the genus Hordeum. Mol Ecol 8: 505-511.
    • (1999) Mol Ecol , vol.8 , pp. 505-511
    • Provan, J.1    Russell, J.R.2    Booth, A.3    Powell, W.4
  • 42
    • 0035283384 scopus 로고    scopus 로고
    • Chloroplast microsatellites: new tools for studies in plant ecology and evolution
    • Provan J, Powell W, Hollingsworth PM (2001) Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends Ecol Evol 16: 142-147.
    • (2001) Trends Ecol Evol , vol.16 , pp. 142-147
    • Provan, J.1    Powell, W.2    Hollingsworth, P.M.3
  • 43
    • 84877724075 scopus 로고    scopus 로고
    • FigTree
    • Institute of Evolutionary Biology, University of Edinburgh, UK
    • Rambaut A (2006-2009) FigTree. Tree figure drawing tool v. 1. 3. 1, Institute of Evolutionary Biology, University of Edinburgh, UK.
    • (2006) Tree Figure Drawing Tool V. 1. 3. 1
    • Rambaut, A.1
  • 44
    • 0033990048 scopus 로고    scopus 로고
    • Primer3 on the WWW for general users and for biologist programmers
    • S. Krawetz and S. Misener (Eds.), New Jersey, USA: Humana Press
    • Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, New Jersey, USA, pp 365-386.
    • (2000) Bioinformatics Methods and Protocols: Methods in Molecular Biology , pp. 365-386
    • Rozen, S.1    Skaletsky, H.J.2
  • 46
    • 79956370841 scopus 로고    scopus 로고
    • Understanding the genetic diversity, spatial genetic structure and mating system at the hierarchical levels of fruits and individuals of a continuous Theobroma cacao population from the Brazilian Amazon
    • Silva CRS, Albuquerque PSB, Ervedosa FR, Mota JWS, Figueira A, Sebbenn AM (2010) Understanding the genetic diversity, spatial genetic structure and mating system at the hierarchical levels of fruits and individuals of a continuous Theobroma cacao population from the Brazilian Amazon. Heredity 106: 973-985.
    • (2010) Heredity , vol.106 , pp. 973-985
    • Silva, C.R.S.1    Albuquerque, P.S.B.2    Ervedosa, F.R.3    Mota, J.W.S.4    Figueira, A.5    Sebbenn, A.M.6
  • 47
    • 0032229478 scopus 로고    scopus 로고
    • The tortoise and the hare: choosing between noncoding plastome and nuclear ADH sequences for phylogeny reconstruction of a recently diverged plant group
    • Small RL, Ryburn JA, Cronn RC, Seelanan T, Wendel JF (1998) The tortoise and the hare: choosing between noncoding plastome and nuclear ADH sequences for phylogeny reconstruction of a recently diverged plant group. Am J Bot 85: 1301-1315.
    • (1998) Am J Bot , vol.85 , pp. 1301-1315
    • Small, R.L.1    Ryburn, J.A.2    Cronn, R.C.3    Seelanan, T.4    Wendel, J.F.5
  • 48
    • 77954202497 scopus 로고    scopus 로고
    • DendroPy: a Python library for phylogenetic computing
    • Sukumaran J, Holder MT (2010) DendroPy: a Python library for phylogenetic computing. Bioinformatics 26: 1569-1571.
    • (2010) Bioinformatics , vol.26 , pp. 1569-1571
    • Sukumaran, J.1    Holder, M.T.2
  • 50
    • 33747074315 scopus 로고    scopus 로고
    • Phylogeography and genetic structure of Hibiscus tiliaceus - speciation of a pantropical plant with sea-drifted seeds
    • Takayama K, Kajita T, Murata J, Yoichi T (2006) Phylogeography and genetic structure of Hibiscus tiliaceus - speciation of a pantropical plant with sea-drifted seeds. Mol Ecol 15: 2871-2881.
    • (2006) Mol Ecol , vol.15 , pp. 2871-2881
    • Takayama, K.1    Kajita, T.2    Murata, J.3    Yoichi, T.4
  • 51
    • 0029786076 scopus 로고    scopus 로고
    • Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA
    • Takezaki N, Nei M (1996) Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics 144: 389-399.
    • (1996) Genetics , vol.144 , pp. 389-399
    • Takezaki, N.1    Nei, M.2
  • 52
    • 0002042093 scopus 로고
    • Botany, types and populations
    • 4th edn., G. A. R. Wood and R. A. Lass (Eds.), London: Longman
    • Toxopeus H (1985) Botany, types and populations. In: Wood GAR, Lass RA (eds) Cocoa, 4th edn. Longman, London, pp 11-37.
    • (1985) Cocoa , pp. 11-37
    • Toxopeus, H.1
  • 53
    • 0001632947 scopus 로고
    • New World tetraploid cottons contain Old World cytoplasm
    • Wendel JF (1989) New World tetraploid cottons contain Old World cytoplasm. Proc Natl Acad Sci 86: 4132-4136.
    • (1989) Proc Natl Acad Sci , vol.86 , pp. 4132-4136
    • Wendel, J.F.1
  • 54
    • 0006062877 scopus 로고
    • History and development
    • 4th edn., G. A. R. Wood and R. A. Lass (Eds.), London: Longman
    • Wood GAR (1985) History and development. In: Wood GAR, Lass RA (eds) Cocoa, 4th edn. Longman, London, pp 1-10.
    • (1985) Cocoa , pp. 1-10
    • Wood, G.A.R.1
  • 55
    • 84863385319 scopus 로고    scopus 로고
    • Chloroplast microsatellite primers for cacao (Theobroma cacao) and other Malvaceae
    • Yang JY, Motilal LA, Dempewolf H, Maharaj K, Cronk QC (2011) Chloroplast microsatellite primers for cacao (Theobroma cacao) and other Malvaceae. Am J Bot 98: e372-374.
    • (2011) Am J Bot , vol.98
    • Yang, J.Y.1    Motilal, L.A.2    Dempewolf, H.3    Maharaj, K.4    Cronk, Q.C.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.