Genomics and Physiology: genetics

Right click and "Save As" to download these files to your hard drive.

• Detection and quantification of in vitro-culture induced chimerism using simple sequence repeat (SSR) analysis in Theobroma cacao (L.). Theoretical and applied genetics. Vol. 2, p. 157-166. 2004. by Rodriguez Lopez, C.M.; Wetten, A.C. and Wilkinson, M.J. [PDF: 415 kb]
• Genetic diversity and natural population structure of cacao (Theobroma cacao L.) from the Brazilian Amazon evaluated by microsatellite markers. ConservationGenetics.2006,vol. 7, p. 13-24. by Sereno, M.L.; Albuquerque, P.S.B.; Vencovsky, R.; Figueira, A.[PDF: 312KB]
• A computer simulation study on the number of loci and trees required to estimate genetic variability in cacao (Theobroma cacao L.). Tree Genetics & Genomics. 2006 by Cervantes-Martinez, C.; Brown, J.S.; Schnell, R.; Motamayor, J.C.; Meerow, A. W.; Zhang, D. [PDF: 482KB]
• Combining ability for disease resistance, yield, and horticultural traits of cacao (Theobroma cacao L.) clones J. American Soc. Horticultural Science, 2006, vol. 131, p. 231-241. by Cervantes-Martinez, C.; Brown, J.S.; Schnell, R.; Phillips-Mora, W.; Takrama, J.F.; Motamayor, J.C. [PDF: 463KB]
• Assessing the genetic diversity in the International Cocoa Genebank, Trinidad (ICG,T) using isozyme electrophoresis and RAPD by Sounigo et al. [PDF: 258 kb]
• Genetic Improvement and Cocoa Yields in Ghana, Expl Agric. (2005), volume 41, 2005 Cambridge University Press, by J. Edwin and W. A. Masters. [PDF: 108 kb]
• Developmental expression of stress response genes in Theobroma cacao leaves and their response to Nep1 treatment and a compatible infection by Phytophthora megakarya, Plant Physiology and Biochemistry, 2005 by B.A. Bailey, et. al. [PDF: 1.79 MB]
• Analysis of molecular diversity in Crinipellis perniciosa with AFLP markers, European Journal of Plant Pathology, 2005 by R. Ploetz, et. al. [PDF: 290 kb]
• Single-strand conformation polymorphism analysis of candidate genes for reliable identification of alleles by capillary array electrophoresis by David N. Kuhn, et al. [PDF: 460.69 kb]
• Characterisation of the cacao somatic embryogenesis receptor-like kinase (SERK) gene expressed during somatic embryogenesis by Marcelo de Oliveira Santos, et al. [PDF: 213.83 kb]
• Retrospective Determination of the Parental Population of Superior Cacao (Theobroma cacao L.) Seedlings and Association of Microsatellites Alleles with Productivity by R.J. Schnell, et al. [PDF: 5.48 MB]
• Detection and quantification of in vitro-culture induced chimerism using simple sequence repeat (SSR) analysis in Theobroma cacao (L.) by C.M. Rodriguez Lopez, et al. [PDF: 415.13 kb]
• An Improved Semiautomated Rapid Method of Extracting Genomic DNA for Molecular Marker Analysis in Cocoa, Theobroma cacao L. by R. Bhattacharjee, et al. [PDF: 126.73 kb]
• Rapid Isolation of DNA from Chocolate and Date Palm Tree Crops by K. M. Haymes, et al. [PDF: 3.93 MB]
• Selection of International Molecular Standards for DNA Fingerprinting of Theobroma cacao by J. A. Saunders, et al. [PDF: 3.94 MB]
• Variability in cacao accessions from the Brazilian, Ecuadorian, and Peruvian Amazons based on molecular markers by F. G. Faleiro, et al. [PDF: 850 kb]
• Stable transformation of Theobroma cacao L. and influence of matrix attachment regions on GFP expression by S. Maximova, et al. [PDF: 527 kb]
• A Haplotype-Based Method for QTL Mapping of F1 Populations in Outbred Plant Species by C. C-M and J.S. Brown [PDF: 211 kb]
• Isolation, characterization, and development of WRKY genes as useful genetic markers in Theobroma cacao by J. W. Borrone, D. N. Kuhn and R. J. Schnell [PDF: 363 kb]
• Genetic Variability and Host Specialization in the Latin American Clade of Ceratocystis fimbriata by C.J. Baker et al. [PDF: 241 kb]
• Creation of BAC genomic resources for cocoa (Theobroma cacao L.) for physical mapping of RGA containing BAC clones by D. Clement et al. [PDF: 307 kb]
• A new cacao linkage map based on codominant markers: development and integration of 201 new microsatellite markers by T. Pugh et al. [PDF: 439 kb]
• Out of the Amazon: Theobroma cacao enters the genomic era by A. B. Bennett [PDF: 559 kb]
• New Cacao Selections offer Sweet Relief to Chocolate Growers
• Food of the Gods: Cacao and Marker-Assisted Selection
• Yield efficiency in progeny trails with cocoa. Experimental Agriculture, vol. 42, p. 289-299. by J.T.Y. Pang [84 KB] posted Nov. 2 2006
• Gene expression in leaves of Theobroma cacao in response to mechanical wounding, ethylene and/or methyl jasmonate. Plant Sciences, vol. 168, p. 1247-1258, 2005. by B.A. Bailey, M.D Strem, H. Base G. Antunez de Mayolo, and M. Guiltinan. [PDF: 473 KB] posted Dec. 4 2006
• Over-expression of a cacao class I chitinase gene in Theobroma cacao L. enhances resistance against the pathogen, Colletotrichum gloeosporioides. Planta, vol. 224, p. 740-749, 2006. by S.N. Maximova, J.P. Marelli, A. Young, S. Pishak, J.A. Verica, and M.J. Guiltinan. [PDF: 407 KB] posted Dec. 4 2006
• Assessment of genetic diversity on a sample of cocoa accessions resistant to witches' broom disease based on RAPD and pedigree data. Bragantia, vol. 64 p. 361-368, 2005. by R.C. dos Santos, J.L. Pires, U.V. Lopes, K.P.G. Gramacho, A.B. Flores, R. de C.S. Bahia, H.C.C. Ramos, R.X. Correa, and D. Ahnert. [PDF: 173 KB] posted Dec. 5 2006
• Microsatellite loci transferability from Themobroma cacao to Theobroma Grandiflorum. Molecular Ecology Notes. Vol. 6, p. 1219-1221, 2006. by R. Alvez, A. Sebbenn, A. Artero, and A. Figueira [PDF: 76 KB] posted Jan. 2 2007
• Características de compatibilidad sexual de algunos clones de cacao y su aplicación en siembras comerciales. [in Spanish with English abstract] Compañia Nacional de Chocolates, Colombia, S.A. by S. Cadavid-Vélez. [PDF: 17 MB] posted Jan. 16 2007
• Mapping quantitative trait loci for bean traits and ovule number in Theobroma cacao L. Genome, vol. 46, p. 103-111, 2003. by D. Clement, A.M. Risterucci, J.C. Motamayor, J. N'Goran, and C. Lanaud [PDF: 643 KB] posted Jan. 17 2007
• Mapping QTL for yield components, vigor, and resistance to Phytophthora palmivora in Theobroma cacao L. Genome, vol. 46, p.204-212, 2003. by D.Clement, A.M. Kisterucci, J.C. Motamayor, J. N'Goran, and C. Lanaud [PDF: 312 KB] posted Jan. 17 2007
• Centres of crop diversity and/or origin, genetically modified crops and implications for plant genetic resources conservation. Genetic Resources and Crop Evolution, vol. 53, p.1675-1688, 2006. by J. M. M. Engels, A.W. Ebert, I. Thormann and M.C. de Vicente [PDF: 206 KB] posted Jan. 17 2007
• Allelic size standards and reference genotypes to unify international cocoa (Theobroma cacao L.) microsatellite data. Genetic Resources and Crop Evolution. Genetic Resources and Crop Evolution, vol. 53, p.1643-1652, 2006. by N.C. Cryer, M.G.E. Fenn, C.J. Turnbull and M.J. Wilkinson [PDF: 221 KB] posted Jan. 17 2007
• Adding value to cocoa (Theobroma cacao L.) germplasm information with domestication history and admixture mapping. Theoretical Applied Genetics, 2007, vol. 114. by M. Marcano, T. Pugh, E. Cros, S. Morales, E.A. Portillo Paez, B. Courtois, J.C. Glazmann, J.M.M. Engels, W. Phillips, C. Astorga, A.M. Risterucci, O. Fouet, V. Gonzales, K. Rosenberg, I. Vallat, M. Dagert, and C. Lanaud. [PDF: 373 KB] posted Feb. 27 2007
• Genetic diversity in cocoa germplasm of southern Cameroon revelaed by simple sequences repeat (SSRS) markers. African Journal of Biotechnology, 2006, vol. 5, p. 1441-1449. by M.I.B. Efobagn, O. Sounigo, S. Nyasse, M. Manzanares-Dauleux, C. Cilas, M.A.B Eskes, and Kolesnikova-Allen. [PDF: 247 KB] posted Feb. 27 2007
• Final Report of the CFC/ICCO/IPGRI Project on "Cocoa Germplasm Utilization and Conservation: A Global Approach". CFC Technical Paper No. 50; ISBN-13: 978-92-9043-734-5, 224 pages with 25 contributed articles. Edited by A.B. Eskes and Y. Efron. [PDF: 31.4 MB] also available at http://www.cacaonet.org posted Mar. 30 2007
• Microsatellite markers developed from Theobroma cacao L. expressed sequence tag. Molecular Ecology Notes, Vol. 7, p. 236-239, 2007. by J.W. Borrone, J.S. Brown, D.N. Kuhn, J.C. Motamayor, and R.J. Schnell. [PDF: 93 KB] posted May 1 2007
• Development and characterization of a novel tetra-, tri- and di-nucleotide microsatellite markers in cacao (Theobroma cacao L.). Molecular breeding, vol. 20, p. 73-81, 2007. by A.C. Araujo, A.C. Intorne, M.G. Pereira, U.V. Lopes, G. de Souza Filho. [PDF: 229 KB] posted July 3 2007
• Field guide efficacy in the identification of reallocated clonally propagated accession of cacao (Theobroma cacao L.). Genetic Resources Crop Evolution, vol. 54, p. 1301-1313, 2007. by E.S. Johnson, A. Mora, and R.J. Schnell [PDF: 240 KB] posted Aug 1 2007
• Identificación de cultivares de cacao, Guía de Campo [in Spanish]. Universidad Nacional Agraria de la Selva, Tingo María, Peru. 2007 by L.F. García Carrion [PDF: 712 KB] posted September 5 2007
• The potential of the WRKY gene family for phylogenetic reconstruction: An example from the Malvaceae. Molecular Phylogenetics and Evolution, vol. 44, p. 1141-1154, 2007 by J.W. Borrone, A.W. Meerow, D.N. Kuhn, B.A. Whitlock, and R.J. Schnell [PDF: 306 KB] posted October 2 2007
• Mapping QTLs for resistance to frosty pod and black pod diseases and horticultural traits in Theobroma cacao L. Crop Science, vol. 47, p. 1851-1858, 2007 by J.S. Brown, W. Phillips-Mora, E.J. Power, C. Krol, C. Cervantes-Martinez, J.C. Motamayor and R.J. Schnell [PDF: 1 MB] posted October 2 2007
• Twenty years of agronomic evaluation of wild cocoa trees (Theobroma cacao L.) from French Guiana. Scientia Horticulturae, vol. 113, issue 4, p. 313-321 by P. Lachenaud, D. Paulin, M. Ducamp, J.M. Thevenin. [PDF: 167 KB] posted October 2 2007
• Marcadores microssatelites relacionados com a resistencia a vassoura-de-bruxa do cacauerio. [English abstract: Microsatellite markers related to resistance of cocoa tree against witches' broom]. Pesq. Agropec. Bras. Brasilia, vol. 42, p. 1137-1142, 2007. by R.M.G. Santos, U.V. Lopes, R. de C. Bahia, R.C.R. Machado, D. Ahnert, and R.X. Correa [PDF: 88 KB] posted October 31 2007
• High levels of genetic divergence and inbreeding in populations of cupuassu (Theobroma grandiflorum). Tree Genetics and Genomes, vol. 3, p. 289-298, 2007. by R.M. Alves, A. M. Sebbenn, A. S. Artero, C. Clement, A. Figueira [PDF: 315 KB] posted November 30 2007
• New sources of resistance to Phytophthora megakarya identified in wild cocoa tree populations of French Guiana. Crop Protection, vol. 27, p. 1143-1147, 2008 by D. Paulin, M. Duchamp, and P. Lachenaud. [PDF: 142 KB] posted June 3 2008
• Evaluation of phenotypic stability of resistance to Phytophthora spp. in cacao clones. Fitopatologia Brasileira, vol. 32, p. 453-457, 2007. by L.R.M. Pinto, S.D.V.M. Silva, and M.M. Yamada [PDF: 792 KB] posted June 28 2008
• Genetic diversity and structure of farm and GenBank accessions of cacao (Theobroma cacao L.) in Cameroon revealed by microsatellite markers. Tree Genetics & Genomes, vol. 4, p. 821-831 by I.B.M. Efombagn, J.C. Motamayor, O. Sounigo, A.B. Eskes, S. Nyasse, C. Cilas, R. Schnell, M.J. Dauleux, and M. Kolesnikova-Allen. [PDF: 381 KB] posted September 29 2008
• Genetic diversity among farm and germplasm bank accessions of cacao in Bahia, Brazil. <Original in Portuguese> Diversidade genetica entre acessos de cacau de fazendas e de banco de germoplasma na Bahia. Pesquisa Agropecuaria Brasileira, vol. 43, p. 851-858, 2008 by J.B. Leal, L.M. dos Santos, C.A.P. dos Santos, J.L. Pires, D. Ahnert and R.X. Correa. [PDF: 105 KB] posted October 31 2008
• A re-interpretation of hybrid vigour in cocoa. Experimental Agriculture, vol. 44, p. 329-338, 2008. Experimental Agriculture, vol. 44, p. 329-338, 2008 by J. T-Y Pang and G. Lockwood. [PDF: 80 KB] posted October 31 2008
• Increasing accuracy and throughput in large-scale microsatellite fingerprinting of cacao field germplasm collections. Tropical Plant Biology, DOI 10.1007/s12042-008-9016-z, 2008. by L. Motilal, D. Zhang, P. Umaharan, S. Mischke, M. Boccara, and Pinney Stephen. [PDF: 340 KB] posted October 31 2008
• Geographic and genetic population differentiation of the Amazonian chocolate tree (Theobromam cacao L.), Plos One, www.plosone.org, vol. 3 (10), p. 1-8, 2008 by J.C. Motomayor, P. Lachenaud, J. Wallace da Silva e Mota, R. Loor, D.N. Kuhn, S.B. Brown, and R.J. Schnell [PDF: 235 KB] posted October 31 2008
• Caracterización de genotipos superiores de cacao seleccionados por el programa de mejoramiento genético del CATIE por su rendimiento y Resistencia a Moniliasis. [Comprehensive characterization of superior cacao genotypes selected by CATIE's breeding program based on yield and/or moniliasis resistance.] In 15 International Cocoa Research Conference, Proceedings, Nigeria/COPAL Vol. I. p. 111-123. 2007. by A. Arciniegas, W. Phillips-Mora [PDF: 6.5 MB] posted December 19 2008
• Caracterización morfológica y molecular del cacao nacional boliviano y de selecciones élites del Alto Beni, Bolivia. [Morphologic and molecular characterization of the national bolivian and élite cacao selections in Alto Beni, Bolivia]. Spanish with English summary. Tesis Mag. Sc. Turrialba, Costa Rica, CATIE. 88p. by W. July Martínez [PDF: 1 MB] posted December 19 2008
• A large EST resource for Theobroma cacao including cDNAs isolated from various organs and under various biotic and abiotic stresses. [Un gran EST para el Theobroma cacao incluyendo cADN aislado de varios órganos y bajo varios estreses bióticos y abióticos]. In 15 International Cocoa Research Conference. Proccedings Nigeria, COPAL Vol. I p. 185-191. 2007. by C. Lanaud; O. Fouet; K. Gramacho; X. Argout; T. Legrave; X. Sabau; A.M. Risterucci; P. Wincker; C. Da Silva; G. Loor; V. Lopes; J. Cascardo; B. Courtois; D. Kuhn; R. Schnell; B. Bailey; R. Babin; O. Sounigo; M. Ducamp; D. Paulin; P. Deberdt; J. Verica; M. Guiltinan; L. Alemanno; R. Machado; W. Phillips; F. Micheli; A. Da Silva Gesteira; D. Clement; S. Maximova; D. Butler; E. Rosenquist and J.C. Gilmour Glaszmann [PDF: 3.5 MB] posted December 19 2008
• Adding value to cocoa (Theobroma cacao L.) germplasm information with domestication history and admixture mapping. [Adicionando valor a la información sobre germoplasma de cacao (Theobroma cacao L.) con la historia de domesticación y mapeo de mezclas]. Theoretical Applied Genetics 114(5):877-884. 2007. by M. Marcano; T. Pugh; E. Cross; S. Morales; E.A. Portillo Paez; B. Courtois; J.C. Glaszmann; J.M.M. Engels; W. Phillips; C. Astorga; A.M. Risterucci; O. Fouet; V. Gonzales; K. Rosenberg; I. Vallat; M. Dagert and C. Lanaud [PDF: 373KB] posted December 29 2008
• Molecular characterization of an international cacao collection using microsatellite markers. Tree Genetics & Genomes, vol. 5, p. 1-10, 2009. by D. Zhang; S. Mischke; E.S. Johnson; W. Phillips-Mora and L. Meinhardt [PDF; 189KB] posted December 29 2008
• SSCP markers provide a useful alternative to microsatellites in genotyping and estimating genetic diversity in populations and germplast collections of plant specialty crops. By D.N. Kuhn; J.C. Motamayor; A.W. Meerow; J.W. Borrone; R.J. Schnell [PDF: 438KB] posted January 15 2009
• Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generate from various tissues and under various conditions. BMC Genomics, vol. 9, p. 512-531, 2008, by X. Argout, O. Fouet, P. Wincker, K. Gramacho, T.I. Legavre, X. Sabau, A.M. Risterucci, C. Da Silva, J. Cascardo, M. Allegre, D. Kuhn, J. Verica, B. Courtois, G. Loor, R. Babin, O. Sounigo, M. Ducamp, M.J. Guiltinan, M. Ruiz, L. Alemanno, R. Machado, W. Phillips, R. Schnell, M. Gilmour, E. Rosenquist, D. Butler, S. Maximova and C. Lanaud [PDF: 2.7MB] posted February 24 2009
• New tools for 21st century plant breeding, DNA markers: theory and applications, with examples from research on the chocolate tree, Theobroma cacao. English with Spanish summary. [Nuevas herramientas para el mejoramiento genético de plantas y marcadores ADN en el siglo 21: teoría y aplicaciones con ejemplos de investigación en cacao, Theobroma cacao]. CATIE, Turrialba, Costa Rica.  Technical Series. Technical Bulletin  N°. 251.  122 p., 1995 by P.J. Fritz, W. Phillips Mora and R.H. Rodríguez. [PDF:36.1MB] posted May 7 2009
• Study of the descendence of the interclonal cocoa cross Catongo x Pound-12 under conditions in Turrialba, Costa Rica. [Estudio de la descendencia del cruce interclonal de cacao catongo x pound-12 bajo las condiciones de Turrialba, Costa Rica]. Tesis Mag. Sc. Turrialba, Costa Rica, CATIE.  125 p., 1991 by J.R. Laínez Mejía. [PDF: 4.9MB] posted May 7 2009
• The dynamics of canopies of three leguminous shade tree species and their effects on the phenology of six interclonal crosses of cacao. Spanish with English summary.[Dinámica de doseles de tres especies de leguminosas de sombra y efectos sobre la fenología de seis cruces interclonales de cacao]. Tesis Mag. Sc. Turrialba, Costa Rica, CATIE. 101 p., 1992 by R. Luján Ferrer. [PDF: 3.4MB] posted May 7 2009
• Comparing 56 interclonal crosses of cocoa in Pococí, Costa Rica. Spanish. [Comparación de 56 cruces interclonales de cacao en Pococí, Costa Rica].   Turrialba (IICA). Vol. 41 (4) p. 578-582., 1991 by J. Morera and A. Mora. [PDF: 654KB] posted May 7 2009
• Inheritance of certain pod and tree characters of cocoa (Theobroma cacao L.). Herencia de ciertos caracteres de la mazorca y del árbol de cacao (Theobroma cacao L.). Tesis Mag. Sc. Turrialba, Costa Rica, CATIE. 82 p., 1987 by L.G. Ramírez Mora. [PDF: 3MB] posted May 7 2009
• Usage of molecular markers for the construction of a linkage map in cocoa Theobroma cacao L..  Spanish with English summary. [ Uso de marcadores moleculares para la construcción de un mapa de ligamiento genético en cacao Theobroma cacao L.]. Tesis Mag. Sc. Turrialba, Costa Rica, CATIE.  84 p., 1992 by H. Rodríguez Rodríguez. [PDF: 4.2MB] posted May 7 2009
• Population Structure and Genetic Diversity of the Trinitario Cacao (Theobroma cacao L.) from Trinidad and Tobago. Crop Science, Vol. 49, p. 564-572, 2009 by E.S. Johnson, F.L. Bekele, S.J. Brown, Q. Song, D. Zhang, L.W. Meinhardt and R.J. Schnell. [PDF: 1057KB] posted June 9 2009
• Mapping of quantitative trait loci for butter content and hardness in cocoa beans (Theobroma cacao L.).  Plant Molecular Biology Reporter, vol. 27, p.177-183, 2009 by I.S. Araujo, F. de Souza, A. Goncalo, M.G. Pereira, F.G. Faleiro, V.T. de Queiroz, C.T. Guimaraes, M.A. Moreira, E.G. deBarros, R.C.R. Machado, J.L. Pires, R. Schnell and U.V. Lopes. [PDF: 249KB] posted July 31 2009
• Parentage analysis and outcrossing patterns in cacao (Theobroma cacao L.) farms in Cameroon. Heredity, vol. 103, p. 46-53, 2009 by M.I.B. Efombagn, O. Sounigo, A.B. Eskes, J.C. Motamayor, M.J. Manzanares-Dauleux, R. Schnell and S. Nyasse. [PDF: 112KB] posted July 31 2009
• Tracing the native ancestors of the modern Theobroma cacao L. population in Ecuador. Tree Genetics & Genomes, vol. 5. p. 421-433, 2009 by R.G. Loor, A.M. Risterucci, B. Courtois, O. Fouet, M. Jeanneau, E. Rosenquist, F. Amores, A. Vasco, M. Medina and C. Lanaud. [PDF: 520KB] posted July 31 2009
• Microsatellite diversityheteroqygosity of parents of a cocoa breeding population. Crop Breeding and Applied Biotechnology, vol.9, p. 17-22, 2009 by M.M. Yamada, F.G. Faleiro, A.B. Flores, U.V. Lopes, J.L. Pires, R.X. Correa and R.F. Santos. [PDF: 344KB] posted August 31 2009
• Single nucleotide polymorphisms from Theobroma cacao expressedsequence tags associated with witches' broom disease in cacao. Genetics and Molecular Research, vol. 8, p. 799-808, 2009 by S.L. Lima, K.P. Gramacho, N. Carels, R. Novais, F.A. Gaiotto, U.V. Lopes, A.S. Gesteira,H.A. Zaidan, J.C.M. Cascardo, J.L. Pires and F. Micheli [PDF: 348KB] posted September 22 2009
• Mining of expressed sequence tag libraries of cacao for microsatellite markers using five computational tools. Journal of Genetics, vol. 88, p. 217-225, 2009 by A. Riju, M.K. Rajesh, P.T.P.F. Sherin, A. Chandrasekar, S.E. Apshara, and V. Arunachalam [PDF: 209KB] posted September 22 2009
• Identification of cacao genetic resistance to black pod disease. Portuguese. Identificacao de resistencia genetica do cacaueiro a podridao-parda. Embrapa Informacao Tecnologica, vol. 44, p. 413-416, 2009 by E.S.L. dos Santos, C.B.M. Cerqueira-Silva, D.P.L. Clement and E.D.M.N. Luz [PDF: 237KB] posted September 22 2009
• Molecular characterization of an earliest cacao (Theobroma cacao L.) collection from Upper Amazon using microsatellite DNA markers.  Tree Genetics & Genomes, vol. 5, p. 595-607, 2009 by D. Z hang, M. Boccara, L. Motilal, S. Mischke, E.S. Johnson, D.R. Butler, B. Bailey, and L. Meinhardt [PDF:344KB] posted September 22 2009
• Relations between several traits linked to sexual plant reproduction in Theobroma cacao L.: number of ovules per ovary, number of seeds per pod, and seed weight.  Tree Genetics and Genomes, pp. 1-8, 2009 by C. Cilas, R. Machado and J-C Motamayor, J.-C [PDF: 223KB] posted November 9 2009
• A meta-QTL analysis of disease resistance traits of Theobroma cacao L. Molecular Breeding,  vol. 24 (4), p. 361-374, 2009 by C. Lanaud, O. Fouet, D. Clément, M. Boccara, A. M. Risterucci, S. Surujdeo-Maharaj, T. Legavre and X. Argout [PDF: 765KB] posted December 22 2009
• Recurrent selection of cocoa populations in Côte d'Ivoire: Comparative genetic diversity between the first and second cycles.  Plant Breeding, vol. 128 (5), p. 514-520, 2009 by N.D. Pokou, J.A.K. N'Goran, Ph. Lachenaud, A.B. Eskes, A.B., J.C. Motamayor, R. Schnell, M. Kolesnikova-Allen, D. Clément, D., and A. Sangaré [PDF: 246KB] posted December 22 2009
• The relic Criollo cacao in Belize - genetic diversity and relationship with Trinitario and other cacao clones held in the International Cocoa Genebank, Trinidad.  Plant Genetic Resources: Characterisation and Utilisation, pp. 1-10. Article in Press, 2010 ISSN:1479-2621 by L.A. Motilal, D. Zhang, P. Umaharan, S. Mischke, V. Mooleedhar, L.W. Meinhardt. [PDF: 762KB] posted March 1, 2010
• Accessing genetic diversity for crop improvement [including cacao]. Current Opinion in Plant Biology, 13, pp. 1-7, 2010 by J.C. Glaszmann, B. Kilian, H.D. Upadhyaya, R.K. Varshney [PDF:467KB]  posted April 2, 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 Genetic Resources: Characterisation and Utilisation, pp. 1-10. Article in Press, 2010 ISSN:1479-2621 by L.A. Motilal, D. Zhang, P. Umaharan, S. Mischke, V. Mooleedhar, L.W. Meinhardt  [PDF: 762KB] posted April 2, 2010
• Microsatellite fingerprinting of the USDA-ARS tropical agriculture research station cacao (Theobroma cacao L.) Germplasm collection. Crop Science, vol. 50 (2), pp. 656-667, 2010 by B.M. Irish, R. Goenaga, D. Zhang, R. Schnell, J.S. Brown, J.C. Motamayor  [PDF: 1MB] posted April 27, 2010  
• Development of single nucleotide polymorphism markers in Theobroma cacao and comparison to simple sequence repeat markers for genotyping of Cameroon clones.  Molecular Breeding, 2010 by D.S. Livingstone III, J.C. Motamayor, R.J. Schnell, K. Cariaga, B. Freeman, A.W. Meerow, J.S. Brown, D.N. Kuhn [PDF: 451KB] posted April 27, 2010

• Origin and Domestication of Native Amazonian Crops. Diversity, vol. 2, p.72-106, 2010 by C.R. Clement, M. de Cristo-Araújo, G. Coppens d’Eeckenbrugge, A. Alves Pereira, D. Picanço-Rodrigues. [PDF: 678 KB] posted July 7, 2010

• Improvement of High-throughput Genotype Analysis after Implementation of a Dual-curve Sybr Green I-based Quantification and Normalization Procedure. HortScience, vol. 44, p. 1228-1232, 2009 by D. Livingstone, B. Freeman, C.L. Tondo, K.A. Cariaga, N.H. Oleas, A.W. Meerow, R.J. Schnell, D.N. Kuhn. . [PDF: 2.29 MB] posted July 7, 2010 

• Genomics of Theobroma cacao, "the Food of the Gods." Genomics of tropical crops plants / foreword by Deborah Delmer ; Paul H. Moore, Ray Ming, editors. New York, N.Y. : Springer Science + Business Media, 2008., p. 145-170 by M.J. Guiltinan, J. Verica, D. Zhang, and A. Figueira. [PDF: 13.7MB]  posted August 9, 2010
• Microsatellite variation and population structure in the "Refractario" cacao of Ecuador. Conserv. Genet., vol. 9 :327-337, 2008 by D. Zhang, M. Boccara, L. Motilal, D.R. Butler, P. Umaharan, S. Mischke, and L. Meinhardt. [PDF: 255KB]  posted August 9, 2010
• Current challenges of tropical tree crop improvement: integrating genomics into an applied cacao breeding program. Acta Horticulturae, Proc. Biotechnol. Temp. Fruit Crops & Trop. Species, March, no. 738, p. 129-144, 2007 by R.J. Schnell, J.S. Brown, D.N. Kuhn, C. Cervantes-Martinez, J.W. Borrone, C.T. Olano, J.C. Motamayor, U. Lopes, W. Phillips, E. Johnson. [PDF: 6MB] posted September 7, 2010
• Genetic mapping of Theobroma cacao (Malvaceae) seedlings of the Parinari series, carriers of the lethal gene Luteus-Pa. Genetic Molecular Research, vol. 8, p. 1775-1784, 2010 by B.C. Reheem, A.A. Almeida, R.X. Corrêa, A.S. Gesteira, M.M. Yamada, R.R. Valle. [PDF: 562KB] posted October 8, 2010 
• Genetic diversity in cocoa (Theobroma cacao L.) germplasm collection from Ghana. Journal of Crop Improvement, vol. 20, p. 73-87, 2007 by S.Y. Opoku, R. Bhattacharjee, M. Kolesnikova-Allen, J.C. Motamayor, R. Schnell, I. Ingelbrecht, L. Enu-Kwesi, Y. Adu-Ampomah.  [PDF: 10.3MB]posted October 8, 2010
• Clonal selection in cacao based on early yield performance of grafted trees. Journal of agriculture University Puerto Rico, vol. 84, p. 153-163, 2000 by H. Irizarry, R. Goenaga. [PDF: 706KB] posted October 8, 2010

• Evaluating Theobroma grandiflorum for comparative genomic studies with Theobroma cacao.  Tree Genetics & Genomes, vol. 6, p. 783-792, 2010 by D.N. Kuhn, A. Figueira, U. Lopes, J.C. Motamayor, A.W. Meerow , K. Cariaga, B. Freeman, D.S. Livingstone, R.J. Schnell.  [PDF: 181KB] posted October 25, 2010  

• Functional Analysis of the Theobroma cacao NPR1 Gene in Arabidopsis. BMC Plant Biology, 10:248, 2010 by Z. Shi, S. Maximova, Y. Lui, J. Verica, and M. Guiltinan.  [PDF: 3.3MB] posted December 2, 2010
• Nitrogen use efficiency in cacao genotypes. Journal Plant Nutrition, vol. 31, p.239-249, 2008 by M.A.Q. Ribeiro, J.O. Da Silva, W.M. Aitken, R.C. Machado, V.C. Baligar. [PDF: 134KB] posted December 22, 2010
• The genome of Theobroma cacao.  Nature Genetics, December 26, 2010 by X. Argout, J. Salse, J.M. Aury, M.J. Guiltinan, G. Droc, J. Gouzy, M. Allegre, C. Chaparro, T. Legavre, S.N. Maximova, M. Abrouk, F. Murat, O. Fouet, J. Poulain, M. Ruiz, Y. Roguet, M. Rodier-Goud, J.F. Barbosa-Neto, F. Sabot, D. Kudrna, J.S. Ammiraju, S.C. Schuster, J.E. Carlson, E. Sallet, T. Schiex, A. Dievart, M. Kramer, L. Gelley, Z. Shi, A. Bérard, C. Viot, M. Boccara, A.M. Risterucci, V. Guignon, X. Sabau, M.J. Axtell, Z. Ma, Y. Zhang, S. Brown, M. Bourge, W. Golser, X. Song, D. Clement, R. Rivallan, R. Tahi,  J.M., Akaza, B. Pitollat, K. Gramacho, A.  D'Hont, D. Brunel, D. Infante, I. Kebe, P. Costet, R. Wing, W.R. McCombie, E. Guiderdoni, F. Quetier, O. Panaud, P. Wincker, S. Bocs, C. Lanaud.. [Epub ahead of print] [PDF: 1.2 MB] posted January 25, 2011
• The genome of Theobroma cacao, Supplementary Information. Nature Genetics, December 26, 2010 by X. Argout, et al. Supplement. [PDF: 6 MB] posted January 25, 2011

• Genetic population structure of cacao plantings within a young production area in Nicaragua. PLoS One, vol. 6, no. 1, e16056, 2011 by B. Trognitz. X. Scheldeman, K. Hansel-Hohl, A. Kuant, H. Grebe, M. Hermann. [PDF: 1.3MB] posted February 25, 2011

• Introdução de genes em segmentos foliares de cupuaçu (Theobroma grandiflorum schumm.) usando biobalística.  Ciência Rural, vol. 34, no. 1, p. 265-279, 2004 by M. Ferreira, C. Carvalho, A.A. Carneiro, F.E.N. Cárdenas. [PDF: 126KB] posted April 4, 2011.
• Genetic distance and its association with heterosis in cacao. Brazilian Archives of Biology and Technology, vol. 46, p. 339-348, 2003 by L.A.S. Dias, J. Marita, C.D. Cruz, E.G. Barros, T.M.F. Salomão. [PDF: 104KB] posted April 4, 2011.
• Caracterización molecular de un banco de germoplasma del género Theobroma mediante la técnica RAPD*  Revista Colombiana de Biotecnología, vol. 6, p. 15-24, 2004 by Y. Moreno, M. Melgarejo Luz, M.S. Hernández, L. Quintero, G. Vargas. [PDF: KB] posted April 4, 2011.
• Dissecting genetic structure in farmer selections of Theobroma cacao in the Peruvian Amazon. Tropical Plant Biology DOI 10.1007/s12042-010-9064-z, 2011 by D. Zhang, E. Arevalo Gardini, L.A. Motilal, V. Baligar, B. Bailey, L. Zuñiga-Cernades, C.E. Arevelo-Arevalo, L. Meinhardt. [PDF: 711KB] posted April 4, 2011.
• Genetic diversity and spatial structure in a new distinct Theobroma cacao L. population in Bolivia. Genetic Resources and Crop Evolution, pp. 1-14. DOI 10.1007/s10722-011-9680-y, 2011 by D. Zhang, W.J. Martínez, E.S. Johnson, E. Somarriba, W. Phillips-Mora, C. Astorga, S. Mischke, L.W. Meinhardt. [PDF: 404KB] posted May 3, 2011

• Avaliação e seleção de híbridos de cacaueiro em Rondônia.  Pesquisa Agropecuária Brasileira, vol. 36, p. 1043-1051, 2001 by C.G.P. Carvalho, C.M. Almeida, C. Vasconcellos, C.D. Cruz, P.F.R. Machado. [PDF: 258KB] posted June 8, 2011

• Molecular Ecology of genetic diversity of cacao cultivated in the south-east region of Nicaragua. International Research Journal of Agricultural Science, vol. 1(1), pp. 6-13, 2011 by J. C. Ruiz, O. Roa Gamboa, I. Marin Arguello. [PDF: 394KB] posted June 8, 2011

• Seleção de clones experimentais de cupuaçu para características agroindustriais via modelos mistos.  Selection of experimental clones of cupuaçu for the agro industry using mixed models. Revista Agro, vol. t, p. 35-43, 2011 by M.C.C. Maia, M.D. Vilela de Resende, L.C. de Oliveira, V. de Souza Álvares, V.T. Maciel, A. Costa de Lima.  [PDF: 407KB] posted June 8, 2011

• Microsatellite fingerprinting in the International Cocoa Genebank, Trinidad: accession and plot homogeneity information for germplasm management. Plant Genetic Resources: Characterization and Utilization (2011); 1-9. doi: 10..1017/S147926211100058X. Motilal, L.A., Zhang, D., Umaharan, P., Mischke, S., Pinney, S., Meinhardt, L.W. [120K] posted November 2, 2011
• A genetically anchored physical framework for Theobroma cacao cv. Matina 1-6. BMC Genomics. 2011 Aug 16;12(1):413. [Epub ahead of print]. Saski, C.A., Feltus, F.A., Staton, M.E., Blackmon, B.P., Ficklin, S.P., Kuhn, D.N., Schnell, R.J., Shapiro, H., Motamayor, J.C. [PDF: 7.3MB] posted November 18, 2011
• Sequencing of a QTL-rich Region of the Theobroma cacao Genome using Pooled BACs and the Identification of Trait Specific Candidate Genes.  BMC Genomics, 2011, vol.12 (1):379. [Epub ahead of print]. Feltus, F.A., Saski, C.A., Mockaitis, K., Haiminen, N., Parida, L., Smith, Z., Ford, J., Staton, M.E., Ficklin, S.P., Blackmon, B.P., Cheng, C.H., Schnell, R.J., Kuhn, D.N., Motamayor, J.C. [PDF: 522KB] posted November 18, 2011
• Optimization of a SNP assay for genotyping Theobroma cacao under field conditions. Molecular Breeding, 2011, pp. 1-20. Article in Press. Livingstone III, D.S., Freeman, B., Motamayor, J.C., Schnell, R.J., Royaert, S., Takrama, J., Meerow, A.W., Kuhn, D.N. [PDF: 560KB] posted November 18, 2011
• Identification of marker-trait associations for self-compatibility in a segregating mapping population of Theobroma cacao L. Tree Genetics and Genomes, 2011, pp. 1-10. Article in Press. Royaert, S., Phillips-Mora, W., Arciniegas Leal, A.M., Cariaga, K., Brown, J.S., Kuhn, D.N., Schnell, R.J., Motamayor, J.C.  [PDF: 373KB] posted November 18, 2011
• Identification and mapping of conserved ortholog set (COS) II sequences of cacao and their conversion to SNP markers for marker-assisted selection in Theobroma cacao and comparative genomics studies. Tree Genetics and Genomes, pp. 1-15, 2011. Article in Press. Kuhn, D.N., Livingstone III, D., Main, D., Zheng, P., Saski, C. Feltus, F.A., Mockaitis, K., Farmer, A.D., May, G.D., Schnell, R.J., Motamayor, J.C.  [PDF: 290KB] posted November 29, 2011
• Population structure and molecular characterization of Nigerian field genebank collections of cacao, Theobroma cacao L. Silvae Genetica 59, 6, 2010. Aikpokpodion, P.O., Kolesnikova-Allen, M., Adetrimirin, V.O., Guiltinan, M.J., Eskes, A.B.,  Motamayor, J.-C., Schnell, R.J.  [PDF: 2.8KB] posted on December 14, 2011