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Genomics of Theobroma cacao, “the Food of the Gods”

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Genomics of Tropical Crop Plants

Part of the book series: Plant Genetics and Genomics: Crops and Models ((PGG,volume 1))

Abstract

Theobroma cacao, the chocolate tree, is an important tropical tree-crop that provides sustainable economic and environmental benefits to some of the poorest and most ecologically sensitive areas of the world. Recent progress in the development of genomics tools for cacao is reviewed. These include a reference molecular genetic map, simple sequence repeats and other molecular markers, two germplasm databases with microsatellite DNA fingerprints and other molecular data, many quantitative trait loci mapping projects which have identified disease resistance and yield component loci, several expressed sequence tag resources, a cacao microarray, bacterial artificial chromosome libraries, and a genetic transformation system. The evolutionary relatedness of cacao with other important crops and model plant systems positions cacao genomics to play a significant role in translational plant genomics. The future prospects for the contribution of cacao genomics to improvement of this crop for sustainable cacao production and as a tool for poverty alleviation and environmental stabilization are discussed.

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References

  • Aime MC, Phillips-Mora W (2005) The causal agents of witches' broom and frosty pod rot of cacao (chocolate, Theobroma cacao) form a new lineage of Marasmiaceae. Mycologia 97:1012–1022

    PubMed  CAS  Google Scholar 

  • Antúnez de Mayolo G (2003) Genetic Engineering Of Theobroma Cacao And Molecular Studies On Cacao Defense Responses, A Thesis in Integrative Biosciences. Ph.D. Thesis: The Pennsylvania State University, The Graduate School, Graduate Degree Program in Integrative Biosciences

    Google Scholar 

  • Antunez de Mayolo G, Maximova SN, Pishak S, Guiltinan MJ (2003) Moxalactam as a counter-selection antibiotic for Agrobacterium-mediated transformation and its positive effects on Theobroma cacao somatic embryogenesis. Plant Sci 164:607–615

    Article  CAS  Google Scholar 

  • Appiah AA, Flood J, Bridge PD, Archer SA (2003) Inter- and intraspecific morphometric variation and characterization of Phytophthora isolates from cocoa. Plant Pathol 52:168–180

    Article  Google Scholar 

  • Appiah AA, Flood J, Archer SA, Bridge PD (2004) Molecular analysis of the major Phytophthora species on cocoa. Plant Pathol 53:209–219

    Article  CAS  Google Scholar 

  • Bartley BGD (1994) A review of cacao improvement: fundamentals, methods and results. http://ingenic.cas.psu.edu/proceedings.htm. Proc Intl Workshop Cocoa Breeding Strategies. pp. 3–16

    Google Scholar 

  • Bartley BGD (2005) The Genetic Diversity of Cacao and its Utilization. (Wallingford, UK: CABI Publishing)

    Google Scholar 

  • Bennett AB (2003) Out of the Amazon: Theobroma cacao enters the genomic era. Trends Plant Sci 8:561–563

    Article  PubMed  CAS  Google Scholar 

  • Bhattacharjee R, Aikpokpodion P, Kolesnikova-Allen M, Badaru K, Schnell RJ (2004) West African Cocoa: A pilot study on DNA fingerprinting the germplasm from Cross River State of Nigeria. INGENIC Newslett 9:15–20

    Google Scholar 

  • Boccara M, Zhang D (2006) Progress in resolving identity issues among the Parinari accessions held in Trinidad: the contribution of the collaborative USDA/CRU project. CRU Ann Rpt 2005, Cacao Research Unit, The University of the West Indies, St. Augustine, Trinidad and Tobago

    Google Scholar 

  • Borrone JW, Kuhn DN and Schnell RJ. (2004) Isolation, characterization, and development of WRKY genes as useful genetic markers in Theobroma cacao. Theor Appl Genet 109: 495–507

    Article  PubMed  CAS  Google Scholar 

  • Borrone JW, Brown JS, Kuhn DN, Schnell RJ (2007) Microsatellite markers developed from Theobroma cacao L. expressed sequence tags. Mol Ecol Notes 7: 236–239

    Article  CAS  Google Scholar 

  • Bowers JH, Bailey BA, Hebbar PK, Sanogo S, Lumsden RD (2001) The impact of plant diseases on worldwide chocolate production (APSNet; Plant Health Progress, http://www.plantmanagementnetwork.org/pub/php /review/cacao/)

    Google Scholar 

  • Brown JS, Kuhn DN, Lopez U, Schnell RJ (2005) Resistance gene mapping for witches' broom disease in Theobroma cacao L. in an F2 population using SSR markers and candidate genes. J Am Soc Hort Sci 130:366–373

    CAS  Google Scholar 

  • Brown J, Phillips W, Power E, Kroll C, Cervantes-Martinez C, et al. (2006) Preliminary QTL mapping for resistance to frosty pod in cacao (Theobroma cacao L.). Proc Intl Cocoa Res Conf 15: (in press)

    Google Scholar 

  • Buckler ES, Thornsberry J (2002) Plant molecular diversity and applications to genomics. Curr Opin Plant Biol 5:107–111

    Article  PubMed  CAS  Google Scholar 

  • Chowdappa P, Brayford D, Smith J, Flood J (2003) Molecular discrimination of Phytophthora isolates on cocoa and their relationship with coconut, black pepper and bell pepper isolates based on rDNA repeat and AFLP fingerprints. Curr Sci 84:1235–1237

    CAS  Google Scholar 

  • Christopher Y, Mooleedhar V, Bekele F, Hosein F (1999) Verification of accession in the ICG, T using botanical descriptors and RAPD analysis. Ann Rpt 1998. St. Augustine, Trinidad and Tobago: Cocoa Research Unit, The University of the West Indies. pp. 15–18

    Google Scholar 

  • Clément D, Risterucci AM, Lanaud C (2001) Analysis of QTL studies related to yield and vigour traits carried out with different cocoa genotypes. Proc Intl Workshop New Technol Cocoa Breeding (INGENIC). pp. 127–134

    Google Scholar 

  • Clement D, Risterucci AM, Motamayor JC, Ngoran J, Lanaud C (2003a) Mapping quantitative trait loci for bean traits and ovule number in Theobroma cacao L. Genome 46:103–111

    Article  CAS  Google Scholar 

  • Clement D, Risterucci AM, Motamayor JC, N'Goran J, Lanaud C (2003b) Mapping QTL for yield components, vigor, and resistance to Phytophthora palmivora in Theobroma cacao L. Genome 46:204–212

    Article  CAS  Google Scholar 

  • Clement D, Lanaud C, Sabau X, Fouet O, Le Cunff L, et al. (2004) Creation of BAC genomic resources for cocoa (Theobroma cacao L.) for physical mapping of RGA containing BAC clones. Theor App Genet 108:1627–1634

    Article  CAS  Google Scholar 

  • Couch JA, Zintel HA, Fritz PJ (1993) The genome of the tropical tree Theobroma cacao L. Mol Gen Genetics 237:123–128

    Article  CAS  Google Scholar 

  • Crouzillat D, Lerceteau E, Pétiard V, Morera J, Rodriguez H, et al. (1996) Theobroma cacao L: A genetic linkage map and quantitative trait loci analysis. Theor Appl Genet 93:205–214

    Article  CAS  Google Scholar 

  • Crouzillat D, Phillips W, Fritz PJ, Petiard V (2000a) Quantitative trait loci analysis in Theobroma cacao using molecular markers. Inheritance of polygenic resistance to Phytophthora palmivora in two related cacao populations. Euphytica 114:25–36

    CAS  Google Scholar 

  • Crouzillat D, Menard B, Mora A, Phillips W, Petiard V (2000b) Quantitative trait analysis in Theobroma cacao using molecular markers. Euphytica 114:13–23

    Article  CAS  Google Scholar 

  • Crouzillat D, Rigoreau M, Cabigliera M, Alvarez M, Bucheli P, Pétiard V (2001) QTL studies carried out for agronomic, technological and quality traits of cocoa in Ecuador. Proc Intl Workshop New Technol Cocoa Breeding (INGENIC). pp. 120–126

    Google Scholar 

  • Cryer NC, Fenn MGE, Turnbull CJ, Wilkinson MJ (2006a) Allelic size standards and reference genotypes to unify international cocoa (Theobroma cacao L.) microsatellite data. Genetic Res Crop Evol 53:1643–1652

    Article  CAS  Google Scholar 

  • Cryer NC, Fenn MGE, Turnbull CJ, Wilkinson MJ (2006b) Allelic size standards and reference genotypes to unify international cocoa (Theobroma cacao L.) microsatellite data. Genetic Res Crop Evol, http://dx.doi.org/10.1007 /s10722-005-1286-9

    Google Scholar 

  • Day RK (1984) Population dynamics of cocoa pod borer Acrocercops cramerella: Importance of host plant cropping cycle. Intl Conf Cocoa and Coconuts. pp. 1–9

    Google Scholar 

  • Dias LAS (2001) Genetic Improvement of Cacao. Editora Folha de Vicosa Ltda. xii + 578 pp. Translation (2005) by Cornelia Elisabeth Abreu-Reichart, Vicosa, M.G., Brazil; aided by the Editor and Peter Griffee of FAO and supported by FAO. Web version: http://ecoport.org/ep?SeachType=earticleView &earticleId=197

    Google Scholar 

  • Efombagn MIB, Marelli JP, Ducamp M, Cilas C, Nyasse S, et al. (2004) Effects of fruiting traits on the field resistance of cocoa (Theobroma cacao L.) clones to Phytophthora megakarya. Phytopathology 152:557–562

    Article  Google Scholar 

  • Efombagn MIB, Sounigo O, Nyass S, Manzanares-Dauleux M, Cilas CB, et al. (2006) Genetic diversity in cocoa germplasm of southern Cameroon revealed by simple sequences repeat (SSRs) markers. African J Biotech 5:1441–1449

    CAS  Google Scholar 

  • Engels J (1981) Genetic resources of cacao, A catalogue of the CATIE collection. (Turrialba, Costa Rica)

    Google Scholar 

  • Eskes A (2003) Proc Intl Workshop Cocoa Breeding for Improved Production Systems: INGENIC International Workshop on Cocoa Breeding. Bekele F, End M, Eskes A (eds) (Accra, Ghana: INGENIC and Ghana Cocoa Board 2005, http://ingenic.cas. psu.edu/proceedings.htm)

    Google Scholar 

  • Evans HC, Holmes KA, Reid AP (2003) Phylogeny of the frosty pod rot pathogen of cocoa. Plant Pathol 52:476–485

    Article  CAS  Google Scholar 

  • Faleiro FG, Yamada MM, Lopes UV, Pires JL, Faleiro ASG, et al. (2002) Genetic similarity of Theobroma cacao L. accessions mantained in duplicates in the Cacao Research Center germplasm collection, based on RAPD markers. Crop Breed Appl Biotechnol 2:439–444

    Google Scholar 

  • Faleiro FG, Lopes UV, Yamada MM, Melo GRP, Monteiro WR, et al. (2004) Genetic diversity of cacao accessions selected for resistance to witches' broom disease based on RAPD markers. Crop Breed Appl Biotechnol 4:12–17

    CAS  Google Scholar 

  • Faleiro F, Queiroz V, Lopes U, Guimarães C, Pires J, et al. (2006) Mapping QTLs for witches' broom (Crinipellis perniciosa) resistance in cacao (Theobroma cacao L.). Euphytica 149:227–235

    Article  CAS  Google Scholar 

  • Figueira A, Janick J, Goldsbrough P (1992) Genome size and DNA polymorphism in Theobroma cacao. J Am Soc Hort Sci 117:673–677

    CAS  Google Scholar 

  • Figueira A, Janick J, Levy M, Goldsbrough P (1994) Reexamining the classification of Theobroma cacao l. using molecular markers. J Am Soc Hort Sci 119:1073–1082

    CAS  Google Scholar 

  • Figueira A, Albuquerque P, Leal-Jr G (2006) Genetic mapping and differential gene expression of Brazilian alternative resistance sources to witches’ broom (causal agent Crinipellis perniciosa). Proc Intl Cocoa Res Conf 15: (in press)

    Google Scholar 

  • Flament MH (1998) Cartographie genetique de facteurs impliques dans la resistance du cacaoyer (Theobroma cacao L.) a Phytophthora megakarya et a Phytophthora palmivora (Montpellier, France: Ecole Nationale Supérieure Agronomique de Montpellier)

    Google Scholar 

  • Flament MH, Kebe I, Clement D, Pieretti I, Risterucci AM, et al. (2001) Genetic mapping of resistance factors to Phytophthora palmivora in cocoa. Genome 44:79–85

    Article  PubMed  CAS  Google Scholar 

  • George MLC, Li W, Moju C, Dahlan M, Pabendon M, et al. (2004) Molecular characterization of Asian maize inbred lines by multiple laboratories. Theor Appl Genet. 109:80–91

    Article  PubMed  CAS  Google Scholar 

  • Guiltinan M (2007) Cacao. In: Pua VE, Davey M (eds) Biotechnology in Agriculture and Forestry - Transgenic Crops. Berlin Heidelbelg: Springer-Verlag

    Google Scholar 

  • Guiltinan MJ, Li Z, Traore A, Maximova S, Pishak S (1998) High efficiency somatic embryogenesis and genetic transformation of cacao. Ingenic Newsl

    Google Scholar 

  • Guimarães CT, Queiros VT, Mota JWS, Pereira MG, Daher RF, et al. (2003) A cocoa genetic linkage map and QTL detection for witches' broom resistance. Plant Breeding 122: 268–272

    Article  Google Scholar 

  • Guyton B, Lumsden R, Matlick BK (2003) Strategic plan for sustainable cocoa production. Manufacturing Confectioner 83:55–60

    Google Scholar 

  • Hanna AD (1954) Application of a systemic insecticide by trunk implantation to control a mealybug vector of the cacao swollen shoot virus. Nature 173:730–731

    Article  PubMed  CAS  Google Scholar 

  • Hervé L, Djiekpor E, Jacquemond M (1991) Characterization of the genome of cacao swollen shoot virus. J Gen Virol 72:1735–1739

    Article  Google Scholar 

  • Hughes JA, Ollennu LAA (1994) Mild strain protection of cocoa in Ghana against cocoa swollen shoot virus-a review. Plant Pathol 43:442–457

    Article  Google Scholar 

  • Iwaro AD, Bekele FL, Butler DR (2003) Evaluation and utilization of cacao (Theobroma cacao L.) germplasm at the International Cocoa Genebank, Trinidad. Euphytica 130:207–221

    Article  CAS  Google Scholar 

  • Johnson L (2003) INGENIC Workshop, Cocoa genomics group. Gro Cocoa 4, 4–5 (http://www.cabi-commodities.org/Acc/ACCrc/PDFFiles/GROC/GROC.htm)

    Google Scholar 

  • Johnson SE, Mora A, Schnell RJ (2007 Johnson L (2003). INGENIC Workshop, Cocoa genomics group. Gro Cocoa 4, 4–5 (http://www.cabi-commodities.org/Acc/ACCrc/PDFFiles/GROC/GROC. htm )

    Google Scholar 

  • Johnson SE, Mora A, Schnell (2007) Field Guide efficacy in the identification of reallocated clonally propagated accessions of cacao. Genetic Res Crop Evol (in press)

    Google Scholar 

  • Jones PG, Allaway D, Gilmour DM, Harris C, Rankin D, et al. (2002) Gene discovery and microarray analysis of cacao (Theobroma cacao L.) varieties. Planta 216:255–264

    Article  PubMed  CAS  Google Scholar 

  • Keane PJ (1992) Diseases and pests of cocoa: An overview. Cocoa pest and disease management in Southeast Asia and Australasia, FAO Plant Production and Protection Paper 112:1–12

    Google Scholar 

  • Kuhn DN, Heath M, Wisser RJ, Meerow A, Brown JS, et al. (2003) Resistance gene homologues in Theobroma cacao as useful genetic markers. Theor Appl Genet 107:191–202

    Article  PubMed  CAS  Google Scholar 

  • Kuhn, DN, Borone J, Meerow A, Motamayor JC, Brown JS, et al. (2004) Single strand conformation polymorphism analysis of candidate genes for reliable identification of alleles by capillary array electrophoresis. Electrophoresis 26:112–115

    Article  CAS  Google Scholar 

  • Lachenaud P, Sounigo O, Oliver G (2004) Genetic structure of Guianan wild cocoa (Theobroma cacao L.) described using isozyme electrophoresis. Plant Genetic Res Newsl 139:24–30

    Google Scholar 

  • Lanaud C (1986) Genetic studies of Theobroma cacao L. with the help of enzymatic markers. I. Genetic control and linkage of nine enzymatic markers. Café Cacao Thé 30:259–270

    CAS  Google Scholar 

  • Lanaud C, Risterucci AM, N'Goran AKJ, Clement D, Flament MH, et al. (1995) A genetic linkage map of Theobroma cacao L. Theor Appl Genet 91:987–993

    Article  CAS  Google Scholar 

  • Lanaud C, Kebe I, Risterucci AM, Clement D, N'Goran JKA, et al. (1996) Mapping quantitative trait loci (QTL) for resistance to Phytophthora palmivora in T. cacao. Proc. Intl Cocoa Res Conf 12:99–105

    Google Scholar 

  • Lanaud C, Risterucci AM, Pieretti I, Falque M, Bouet A, et al. (1999) Isolation and characterization of microsatellites in Theobroma cacao L. Mol Ecol 8:2141–2143

    Article  PubMed  CAS  Google Scholar 

  • Lanaud C, Kébé I, Risterucci A, Clément D, N'Goran J, et al. (2000) Mapping quantitative trait loci (QTL) for resistance to Phytophthora palmivora in T. cacao. Proc Intl Cocoa Res Conf 12:99–105

    Google Scholar 

  • Lanaud C, Risterucci AM, Pieretti I, N'goran JAK, Fargeas D (2004) Characterisation and genetic mapping of resistance and defence gene analogs in cocoa (Theobroma cacao L.). Mol Breeding 13:211–227

    Article  CAS  Google Scholar 

  • Lanaud C, Boult E, Clapperton J, N'Goran J, Cros E, et al. (2005) Identification of QTLs related to fat content, seed size and sensorial traits of Theobroma cacao. Proc Intl Cocoa Res Conf 13:1119–1126

    Google Scholar 

  • Laurent V, Risterucci AM, Lanaud C (1994) Genetic diversity in cocoa revealed by cDNA probes. Theor Appl Genet 68:193–195

    Google Scholar 

  • Lerceteau E, Robert T Pétiard V, Crouzillat D (1997) Evaluation of the extent of genetic variability among Theobroma cacao accessions using RAPD and RFLP. Theor Appl Genet 95:10–19

    Article  CAS  Google Scholar 

  • Lockwood G, Gyamfi MMO (1979) The CRIG cocoa germplasm collection with notes on codes used in the breeding programme at Tafo and elsewhere (Ghana: Cocoa Research Institute). 62 pp

    Google Scholar 

  • Marcano M, Pugh T, Cros E, Morales S, Portillo Paez EA, et al. (2007) Adding value to cocoa (Theobroma cacao L.) germplasm information with domestication history and admixture mapping. Theor Appl Genet 114: 877–884

    Article  PubMed  Google Scholar 

  • Marita JM, Nienhuis J, Pires JL, Aitken WM (2001) Analysis of genetic diversity in Theobroma cacao with emphasis on withes' broom disease resistance. Crop Sci 41:1305–1316

    Article  Google Scholar 

  • Maximova S, Miller C, Antunez de Mayolo G, Pishak S, Young A, et al. (2003) Stable transformation of Theobroma cacao L. and influence of matrix attachment regions on GFP expression. Plant Cell Rep 21:872–883

    PubMed  CAS  Google Scholar 

  • Maximova SN, Marelli JP, Young A, Pishak S, Verica JA, et al. (2005) Over-expression of a cacao class I chitinase gene in Theobroma cacao L. enhances resistance against the pathogen, Colletotrichum gloeosporioides. Planta 224:740–749

    Article  PubMed  CAS  Google Scholar 

  • Maximova, SN, Tan CL, Guiltinan MJ (2007) Cocoa In: Kole C, Hall TC (eds) A Compendium of Transgenic Crop Plants. Volume 7. Blackwell Publishing, Malden, MA, USA: In Press

    Google Scholar 

  • Morais RC (2005) The Genomes of cocoa. In Forbes,(March 14) pp. 110–112

    Google Scholar 

  • Motamayor JC, Lopez PA, Ortiz CF, Moreno A, Lanaud C (2002) Cacao domestication. I. The origin of the cacao cultivated by the Mayas. Heredity 89:380–386

    CAS  Google Scholar 

  • Motamayor JC, Risterucci AM, Heath M, Lanaud C (2003) Cacao domestication. II. Progenitor germplasm of the Trinitario cacao cultivar. Heredity 91:322–330

    Article  PubMed  CAS  Google Scholar 

  • Motilal L, Butler D (2003) Verification of identities in global cacao germplasm collections. Genetic Res Crop Evol 50:799–807

    Article  Google Scholar 

  • Motilal L, Sounigo O, Thévenin J, Risterucci A, Pieretti I, et al. (2002). Theobroma cacao L.: genome map and QTLs for Phytophthora palmivora resistance. Proc Intl Cocoa Res Conf 13 Kota Kinabalu, Malaysia, 2000. Cocoa Producer's Alliance, Lagos, Nigeria, pp. 111–118

    Google Scholar 

  • Muller E, Sackey S (2005) Molecular variability analysis of five new complete cacao swollen shoot virus genomic sequences. Arch Virol 150:53–66

    Article  PubMed  CAS  Google Scholar 

  • N’Goran JAK, Laurent V, Risterucci AM, Lanaud C (1994) Comparative genetic diversity studies of Theobroma cacao using RFLP and RAPD markers. Heredity 73:589–597

    Google Scholar 

  • Nyasse S, Despreaux D, Cilas C (2002) Validity of a leaf inoculation test to assess the resistance to Phytophthora megakarya in a cocoa (Theobroma cacao L.) diallel mating design. Euphytica 123:395–399

    Article  Google Scholar 

  • Opoku IY, Akrofi AY, Appiah AA (2002) Shade trees are alternative hosts of the cocoa pathogen Phytophthora megakarya. Crop Protection 21:629–634

    Article  Google Scholar 

  • Opoku IY, Bhattacharjee R, Kolesnikova-Allen M, Enu-Kwesi L, Asante E, et al. (2005) Impact of Breeders' Collection on Cocoa Plantings of Ghana: Assessment by Molecular Marker Analysis and Farmers' Field Survey. A paper presented in First COCOBOD Conference and Promotion of Local Consumption of Cocoa Products and 24 th Biennial Conference of The Ghana Science Association. Accra Ghana . 1–4 August 2005

    Google Scholar 

  • Pereira JL, Ram A, Defigueiredo JM, Dealmeida LCC (1990) First occurrence of witches' broom disease in the principal cocoa-growing region of Brazil. Trop Agric 67:188–189

    Google Scholar 

  • Perry MD, Davey MR, Power JB, Lowe KC, Bligh HFJ, et al. (1998) DNA isolation and AFLP genetic fingerprinting of Theobroma cacao (L.). Plant Mol Biol Rep 16:49–59

    Article  CAS  Google Scholar 

  • Presson A, Sobel E, Lange K, Papp J (2006) Merging microsatellite data. J Comput Biol 13:1131–1147

    Article  PubMed  CAS  Google Scholar 

  • Piasentin F, Klare-Repnik L (2004) Biodiversity conservation and cocoa agroforests. Gro Cocoa 5:7–8

    Google Scholar 

  • Piry S, Alapetite A, Cornuet J-M, Paetkau D, Baudouin L, et al. (2004) Geneclass2: A Software for Genetic Assignment and First-Generation Migrant Detection. J Heredity 95:536–539

    Article  CAS  Google Scholar 

  • Pound FJ (1940) Witches' broom resistance in cacao. Trop Agric 17:6–8

    Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Pugh T, Fouet O, Risterucci AM, Brottier P, Abouladze M, et al. (2004) A new cacao linkage map based on codominant markers: development and integration of 201 new microsatellite markers. Theor Appl Genet 108:1151–1161

    Article  PubMed  CAS  Google Scholar 

  • Queiroz VT, Guimaraes CT, Anhert D, Schuster I, Daher RT, et al. (2003) Identification of a major QTL in cocoa (Theobroma cacao L.) associated with resistance to witches’ broom disease. Plant Breed 122:268–272

    Article  CAS  Google Scholar 

  • Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100

    Article  PubMed  CAS  Google Scholar 

  • Rice RA, Greenberg R (2003) The Chocolate Tree: Growing cacao in the forest. Natural History 112:36–43

    Google Scholar 

  • Risterucci AM, Grivet L, Ngoran JA, Pieretti I, Flamen, MH, et al. (2000) A high-density linkage map of Theobroma cacao L. Theor Appl Genet 101:948–955

    Article  CAS  Google Scholar 

  • Risterucci AM, Paulin D, Ducamp M, N'Goran JAK, Lanaud C (2003) Identification of QTLs related to cocoa resistance to three species of Phytophthora. Theor Appl Genet 108:168–174

    Article  PubMed  CAS  Google Scholar 

  • Ronning CM, Schnell RJ (1994) Allozyme Diversity in a Germplasm Collection of Theobroma cacao L. J. Heredity 85:291–295

    Google Scholar 

  • Rodriguez LCM, Wetten AC, Wilkinson MJ (2004) Detection and quantification of in vitro-culture induced chimerism using simple sequence repeat (SSR) analysis in Theobroma cacao (L.). Theor Appl Genet 110:157–166

    Article  CAS  Google Scholar 

  • Ruf F, Zadi H (2003) Cocoa: From deforestation to reforestation (Migratory Bird Center: Smithsonian National Zoological Park, (http://nationalzoo.si.edu/ConservtionAndScience/MigratoryBirds/Research/Cacao/ruf.cfm))

    Google Scholar 

  • Russell JR, Hosein F, Johnson E, Waugh R, Powell W (1993) Genetic differentiation of cocoa (Theobroma cacao L.) populations revealed by RAPD analysis. Mol Ecol 2:89–97

    PubMed  CAS  Google Scholar 

  • Santoso D, Chaidamsari T, Wiryadiputra S, de Maagd RA (2004) Activity of Bacillus thuringiensis toxins against cocoa pod borer larvae. Pest Management Sci 60:735–738

    Article  CAS  Google Scholar 

  • Sampaio P, Gusm˜o L, Alves C, Pina-Vaz C, Amorim A, Pais C (2003). Highly polymorphic microsatellite for identification of Candida albicans strains. J Clin Microbiol 41:552–557

    Article  PubMed  CAS  Google Scholar 

  • Saunders JA, Hemeida AA, Mischke S (2001) USDA DNA fingerprinting programme for identification of Theobroma cacao accessions. p. 108–114. In F Bekele et al (ed) Proc Intl Workshop New Technol Cocoa Breeding 2000. INGENIC Press, London

    Google Scholar 

  • Sereno ML Albuquerque PSB, Vencovsky R, Figueira A (2006) Genetic diversity and natural population structure of cacao (Theobroma cacao L.) from the Brazilian Amazon evaluated by microsatellite markers. Conservation Genetics 7:13–24

    Article  CAS  Google Scholar 

  • Schnell RJ, Olano CT, Brown JS, Meerow AW, Cervantes-Martinez C, et al. (2005) Retrospective determination of the parental population of superior cacao (Theobroma cacao L.) seedlings and association of microsatellite alleles with productivity. J Am Soc Hort Sci 130:181–190

    CAS  Google Scholar 

  • Silva CRS, Figueira A (2005) Phylogenetic analysis of Theobroma (Sterculiaceae) based on Kunitz-like trypsin inhibitor sequences. Plant Syst Evol 250:93–104

    Article  CAS  Google Scholar 

  • Sounigo O, Umaharan R, Christopher Y , Sankar A, Ramdahin S (2005) Assessing the genetic diversity in the International Cocoa Genebank, Trinidad (ICG,T) using isozyme electrophoresis and RAPD. Genetic Res Crop Evol 52:1111–1120

    Article  CAS  Google Scholar 

  • Takrama JF, Cervantes-Martinez CT, Phillips-Mora W, Brown JS, Motamayor JC, et al. (2005) Determination of off-types in a cacao breeding program using microsatellites. INGENIC Newsl 10:2–8

    Google Scholar 

  • Toxopeus H (1969) Cacao (Theobroma cacao). pp 79–109. In: Fewerda FP (ed) Outlines of perennial crop breeding in the tropics, (Landbouwhogesschool Wageningen, The Netherlands)

    Google Scholar 

  • Turnbull CJ, Butler DR, Cryer NC, Zhang D, Lanaud C, et al. (2004) Tackling mislabelling in cocoa germplasm collections. INGENIC Newsl 9:8–11

    Google Scholar 

  • Verica JA, Maximova SN, Strem MD, Carlson JE, Bailey BA, et al. (2004) Isolation of ESTs from cacao (Theobroma cacao L.) leaves treated with inducers of the defense response. Plant Cell Rep 23:404–413

    Article  PubMed  CAS  Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M, Van de Lee T, et al. (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414

    Article  PubMed  CAS  Google Scholar 

  • Warren J (1994) Isozyme variation in a number of populations of Theobroma cacao obtained through various sampling regimes. Euphytica 72:121–126

    Article  Google Scholar 

  • Whitkus R, De La Cruz M, Mota-Bravo L, Gomez-Pompa A (1998) Genetic diversity and relationships of cacao (Theobroma cacao L.) in southern Mexico. Theor Appl Genet 96:621–627

    Article  Google Scholar 

  • Wilde J, Waugh R, Powell W (1992) Genetic fingerprinting of Theobroma clones using randomly amplified polymorphic DNA markers. Theor Appl Genet 83:871–877

    Article  CAS  Google Scholar 

  • Wood GAR, Lass RA (1985) Cocoa. (New York: Longman Scientific & Technical)

    Google Scholar 

  • Yamada MM, Faleiro FG, Lopes UV, Bahia RCS, Pires JL, et al. (2001) Genetic variability in cultivated cacao populations in Bahia, Brazil, using isozymes and RAPD markers. Crop Breed Appl Biotechnol 1:377–384

    Google Scholar 

  • Zhang D-X, Hewitt GM (2003) Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Mol Ecol 12:563–584

    Article  PubMed  CAS  Google Scholar 

  • Zhang D, Mischke S, Goenaga R, Hemeida AA, Saunders JA (2006a) Accuracy and reliability of high-throughput microsatellite genotyping for cacao clone identification. Crop Sci 46:2084–2092

    Article  CAS  Google Scholar 

  • Zhang D, Arevalo-Gardini E, Mischke S, Zúñiga-Cernades L, Barreto-Chavez A, et al. (2006b) Genetic diversity and structure of managed and semi-natural populations of cacao (Theobroma cacao) in the Huallaga and Ucayali valleys of Peru. Ann Bot 98:647–655

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Horticulture, Life Sciences Building, The Pennsylvania State University, University Park, PA 16802-5807, USA

    Mark J. Guiltinan

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  1. Mark J. Guiltinan
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  2. Joseph Verica
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  3. Dapeng Zhang
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  4. Antonio Figueira
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  1. USDA-ARS, PBARC Hawaii Agriculture Research Center, 99-193 Aiea Heights Drive, Aiea 96701

    Paul H. Moore

  2. Department of Plant Biology, University of lllinois at Urbana-Champaign, 1201 W. Gregory Drive Urbana 61801 288 ERML, MC-051, Champaign, IL, USA

    Ray Ming

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Guiltinan, M.J., Verica, J., Zhang, D., Figueira, A. (2008). Genomics of Theobroma cacao, “the Food of the Gods”. In: Moore, P.H., Ming, R. (eds) Genomics of Tropical Crop Plants. Plant Genetics and Genomics: Crops and Models, vol 1. Springer, New York, NY. https://doi.org/10.1007/978-0-387-71219-2_6

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