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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT OF AN INTERNATIONAL MARKER ASSISTED SELECTION PROGRAM FOR CACAO

Location: Subtropical Horticulture Research

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

Genetic diversity, population structure, conservation and utilization of Theobroma cacao L., genetic resources in the Dominican Republic     Reprint Icon - (Peer Reviewed Journal)
Boza, E.J., Irish, B.M., Meerow, A.W., Rodriguez, O.A., Ventura-Lopez, M., Gomez, J.A., Moore, J.M., Zhang, D., Motamayor, J.C., Schnell Ii, R.J. 2012. Genetic diversity, population structure, conservation and utilization of Theobroma cacao L., genetic resources in the Dominican Republic. Tree Genetics and Genomes. Available:http://www.bionity.com/en/publications/424313/genetic-diversity-conservation-and-utilization-of-theobroma-cacao-l-genetic-resources-in-the-dominican-republic.html.
The South Florida Avocado Breeding Program at USDA-Agricultural Research Service Subtropical Horticulture Research Station (USDA-ARS SHRS) - (Peer Reviewed Journal)
Kuhn, D.N., Tondo, C.L., Freeman, B.L., Winterstein, M.C., Livingstone, D., Ayala Silva, T., Gutierrez, O.A., Schnell, R.J. 2012. The South Florida Avocado Breeding Program at USDA-Agricultural Research Service Subtropical Horticulture Research Station (USDA-ARS SHRS). Trade Journal Publication. 2(1):22-29.
Applying SNP marker technology in the cacao breeding program at the Cocoa Research Institute of Ghana - (Peer Reviewed Journal)
Takrama, J., Dadzie, A., Opoku, S.Y., Padi, F., Adomako, B., Adu-Ampomah, Y., Livingstone, D., Motamayor, J.C., Schnell II, R.J., Kuhn, D.N. 2012. Applying SNP marker technology in the cacao breeding program at the Cocoa Research Institute of Ghana. African Crop Science Journal. 20(1):67-75.
Association mapping in cacao - (Abstract Only)
Gutierrez, O.A., Nagai, C., Heinig, R., Boza, E.J., Tondo, C.L., Motamayor, J.C., Schnell, R.J. 2012. Association mapping in cacao. Annual International Plant & Animal Genome Conference. XX Annual International Plant & Animal Genome Conference,January 14-18, 2012, San Diego, CA.
A genetically anchored physical framework for Theobroma cacao cv. Matina 1-6 - (Peer Reviewed Journal)
Saski, C.A., Feltus, F.A., Staton, M.E., Blackmon, B.P., Ficklin, S.P., Kuhn, D.N., Schnell Ii, R.J., Shapiro, H., Motamayor, J.C. 2011. A genetically anchored physical framework for Theobroma cacao cv. Matina 1-6. Biomed Central (BMC) Genomics. 12:413. DOI: 10.1186/1471-2164-12-413.
Identification and mapping of conserved ortholog set(COS) II sequences of cacao and their conversion to SNP markers for marker-assisted selection in Theobroma cocoa and comparative genomics studies     Reprint Icon - (Peer Reviewed Journal)
Kuhn, D.N., Livingstone, D., Main, D., Zheng, P., Saski, C., Feltus, F.A., Mockaitis, K., Farmer, A., May, G., Schnell Ii, R.J., Motamayor, J.C. 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 cocoa and comparative genomics studies. Tree Genetics and Genomes. 8:97–11.
Evaluation of Methods for de novo Genome assembly from High-throughput Sequencing Reads Reveals Dependencies that Affect the Quality of the Results     Reprint Icon - (Peer Reviewed Journal)
Haiminen, N., Kuhn, D.N., Parida, L., Rigoutsos, I. 2011. Evaluation of Methods for de novo Genome assembly from High-throughput Sequencing Reads Reveals Dependencies that Affect the Quality of the Results. PLoS One. 6(9): e24182.
Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes - (Peer Reviewed Journal)
Feltus, F.A., Saski, C.A., Mockaitis, K., Haiminen, N., Parida, L., Smith, Z.M., Ford, J., Staton, M., Ficklin, S.P., Blackmon, B.P., Schnell II, R.J., Kuhn, D.N., Motamayor, J.C. 2011. Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes. Biomed Central (BMC) Genomics. 12:379. DOI: 10.1186/1471-2164-12-379.
Identification of marker-trait associations for self-compatibility in a segregating mapping population of Theobroma cacao L - (Peer Reviewed Journal)
Royaert, S.E., Phillips-Mora, W., Arciniegas Leal, A.M., Cariaga, K.A., Brown, J.S., Kuhn, D.N., Schnell Ii, R.J., Motamayor, J. 2011. Identification of marker-trait associations for self-compatibility in a segregating mapping population of Theobroma cacao L. Tree Genetics and Genomes. DOI 10.1007/s11295-011-0403-5.
Optimization of a SNP assay for Genotyping Theobroma cacao under field conditions - (Peer Reviewed Journal)
Livingstone, D., Freeman, B.L., Motamayor, J.C., Schnell Ii, R.J., Royaert, S.E., Takrama, J., Meerow, A.W., Kuhn, D.N. 2011. Optimization of a SNP assay for Genotyping Theobroma cacao under field conditions. Molecular Breeding. DOI 10.1007/s11032-011-9596-4.
Theobroma cacao: A genetically integrated physical map and genome-scale comparative synteny analysis - (Abstract Only)
Saski, C.A., Blackmon, B.P., Staton, M.E., Feltus, F.A., Ficklin, S.P., Kuhn, D.N., Schnell II, R.J., Livingstone, D., Motamayor, J.C. 2011. Theobroma cacao: A genetically integrated physical map and genome-scale comparative synteny analysis. Annual International Plant & Animal Genome Conference. 1.
Putting the cacao genome to work: Development and utilization of Theobroma cacao SNP markers - (Abstract Only)
Livingstone, D., Mockaitis, K., Farmer, A., May, G., Saski, C., Schnell Ii, R.J., Motamayor, J.C., Kuhn, D.N. 2011. Putting the cacao genome to work: Development and utilization of Theobroma cacao SNP markers. Annual International Plant & Animal Genome Conference. 1.
Building a next generation platform for association studies in cacao - (Abstract Only)
Cornejo, O.E., Myles, S.M., Mockaitis, K., Royaert, S.E., Livingstone, D., Kuhn, D.N., Schnell Ii, R.J., Bustamante, C.D., Motamayor, J.C. 2011. Building a next generation platform for association studies in cacao. Annual International Plant & Animal Genome Conference. 1.
Cocoa/Cotton Comparative Genomics - (Abstract Only)
ay, G.D., Mudge, J., Crow, J.A., Bharti, A.K., Woodward, J.E., Ramaraj, T., Farmer, A.D., Rice, B.J., Kramer, R.S., Wilkins, T.A., Schmutz, J., Kim, R.W., Mockaitis, K., Saski, C., Scheffler, B.E., Main, D., Jenkins, J., Livingstone, D., Zheng, P., Gilbert, D., Feltus, A., Haiminen, N., Parida, L., Tondo, C.L., Royaert, S.E., Phillips, W., Shapiro, H., Schnell, R.J., Kuhn, D.N., Motamayor, J. 2011. Cocoa/Cotton Comparative Genomics. Annual International Plant & Animal Genome Conference. 2011.
SNP discovery in avocado from second generation sequencing of the leaf and flower transcriptome - (Abstract Only)
Kuhn, D.N., Livingstone, D., Mockaitis, K., Tondo, C.L., Schnell II, R.J. 2011. SNP discovery in avocado from second generation sequencing of the leaf and flower transcriptome. Annual International Plant & Animal Genome Conference. 2011.
Pooled-BAC sequencing of a black pod resistance region (cBPQTL12) in T. cacao - (Abstract Only)
Feltus, F.A., Saski, C.A., Mockaitis, K., Choi, J., Blackmon, B., Ficklin, S.P., Haiminen, N., Kuhn, D.N., Motamayor, J.C., Schnell II, R.J. 2011. Pooled-BAC sequencing of a black pod resistance region (cBPQTL12) in T. cacao. Annual International Plant & Animal Genome Conference. 2011.
Transcriptome characterization for genome annotation and functional genomics in Theobroma cacao - (Abstract Only)
Mockaitis, K., Gilbert, D., May, G., Podicheti, R., Smith, Z.M., Ford, J.B., Royaert, S.E., Marelli, J.P., Cahoon, E.B., Kuhn, D.N., Schnell II, R.J., Motamayor, J.C. 2011. Transcriptome characterization for genome annotation and functional genomics in Theobroma cacao. Annual International Plant & Animal Genome Conference. 2011.
Comparison of single nucleotide polymorphisms and simple sequence repeats in genotype identification and diversity assessment of cacao germplasm - (Abstract Only)
Zhang, D., Livingstone, D., Irish, B.M., Kuhn, D.N., Schnell II, R.J., Meinhardt, L.W. 2011. Comparison of single nucleotide polymorphisms and simple sequence repeats in genotype identification and diversity assessment of cacao germplasm. Annual International Plant & Animal Genome Conference. 2011.
Identification of differentially expressed genes involved in self-incompatibility in Theobroma cacao L. - (Abstract Only)
Royaert, S.E., Mockaitis, K., May, G., Haiminen, N., Parida, L., Phillips-Mora, W., Marelli, J., Freeman, B.L., Kuhn, D.N., Schnell II, R.J., Motamayor, J.C. 2011. Identification of differentially expressed genes involved in self-incompatibility in Theobroma cacao L. . Annual International Plant & Animal Genome Conference. 2011.
Better chocolate through genomics - (Popular Publication)
Schnell Ii, R.J., Tondo, C.L., Kuhn, D.N., Livingstone, D., Royaert, S.E., Motamayor, J.C. 2011. Better chocolate through genomics. Popular Publication. 1.
The value of wild Theobroma germplasm in genomics - (Abstract Only)
Schnell Ii, R.J., Kuhn, D.N., Tondo, C.L., Motamayor, J.C. 2010. The value of wild Theobroma germplasm in genomics. American Society of Horticulture Science Meeting. 1.
Evaluating Theobroma grandiflorum for comparative genomic studies with Theobroma cacao     Reprint Icon - (Peer Reviewed Journal)
Kuhn, D.N., Figueira, A., Lopes, U., Motamayor, J., Meerow, A.W., Cariaga, K.A., Freeman, B.L., Livingstone, D., Schnell Ii, R.J. 2010. Evaluating Theobroma grandiflorum for comparative genomic studies with Theobroma cacao. Tree Genetics and Genomes. DOI 10.1007/s11295-010-0291-0
A Snp Assay for Genotyping Theobroma Cacao Suitable for Use under Field Conditions - (Abstract Only)
Livingstone, D., Freeman, B.L., Motamayor, J.C., Dadzie, A.M., Takrama, J., Schnell Ii, R.J., Kuhn, D.N. 2010. A SNP assay for genotyping Theobroma cacao suitable for use under field conditions. Plant and Animal Genome Conference. a.
Characterization of reproductive self-compatibility in Theobroma cacao L. - (Abstract Only)
Royaert, S.E., Cariaga, K.A., Freeman, B.L., Phillips, W., Lopes, U.V., Brown, J.S., Kuhn, D.N., Schnell Ii, R.J., Motamayor, J.C. 2010. Characterization of reproductive self-compatibility in Theobroma cacao L.. Plant and Animal Genome Conference. 1.
Design and implementation of the cacao genome database - (Abstract Only)
Zheng, P., Jung, S., Staton, M., Svancera, R., Lee, T., Ficklin, S., Kuhn, D.N., Schnell Ii, R.J., Motamayor, J.C., Main, D. 2010. Design and implementation of the cacao genome database. Plant and Animal Genome Conference. 1.
A genetically anchored physical map of the cacao genome - (Abstract Only)
Blackmon, B., Saski, C., Schnell Ii, R.J., Motamayor, J.C., Kuhn, D.N. 2010. A genetically anchored physical map of the cacao genome. Plant and Animal Genome Conference. 1.
The need for an assembly pilot project - (Abstract Only)
Kuhn, D.N., Saski, C., Feltus, F.A., Haiminen, N., Main, D., May, G.D., Schnell Ii, R.J., Motamayor, J.C., Mockaitis, K., Scheffler, B.E., Shapiro, H. 2010. The need for an assembly pilot project. Plant and Animal Genome Conference. 1.
The international marker assisted selection program for cacao - (Proceedings)
Schnell Ii, R.J., Motamayor, J.C., Brown, J.S., Kuhn, D.N., Tondo, C.L., Livingstone, D., Royaert, S.E., Nagai, C., Phillips, W., Amores, F., Suarez-Capello, C., Lopes, U., Takrama, J., Padi, F., Opoku, S., Efombagan, I.B., Aikpokpodion, P., Pokou, D., Epaina, P., Marfu, J. 2010. The international marker assisted selection program for cacao. Proceedings of the International Cocoa Producer's Conference.
The detection and utilization of disease resistance, quality, and productivity QTLs in cacao breeding - (Abstract Only)
Schnell Ii, R.J., Brown, J.S., Tondo, C.L., Kuhn, D.N., Phillips, W., Amores, F., Takrama, J., Motamayor, J.C. 2010. The detection and utilization of disease resistance, quality, and productivity QTLs in cacao breeding. Plant and Animal Genome Conference. 1.
Status of cacao breeding in Ghana - (Abstract Only)
Padi, F.K., Opoku, S.Y., Adomako, B., Adu-Ampomah, Y., Motamayor, J.C., Kuhn, D.N., Schnell Ii, R.J., Takrama, J. 2010. Status of cacao breeding in Ghana. Plant and Animal Genome Conference. 1.
T. cacao Transcriptome Sequencing - (Abstract Only)
Mockaitis, K., Kuhn, D.N., Main, D., Haiminen, N., May, G., Saski, C., Scheffler, B.E., Schnell Ii, R.J., Harkins, T., Motamayor, J.C., Shapiro, H. 2010. T. cacao Transcriptome Sequencing. Plant and Animal Genome Conference. 1.
Linkage disequilibrium in Theobroma cacao L. populations - (Abstract Only)
(03-Jan-10)
Genetics of reproductive self-compatibility in Theobroma cacao L. - (Abstract Only)
Royaert, S.E., Cariaga, K.A., Phillips, W., Lopes, U., Kuhn, D.N., Schnell Ii, R.J., Motamayor, J.C. 2011. Genetics of reproductive self-compatibility in Theobroma cacao L.. Proceedings of the International Cocoa Producer's Conference. 1.
Genetic marker comparison for the purpose of determining off-type cacao clones within a West African germplasm collection - (Abstract Only)
Livingstone, D., Motamayor, J.C., Schnell Ii, R.J., Souniga, O., Efombagn, B., Padi, F.K., Dadzie, A.M., Kuhn, D.N. 2010. Genetic marker comparison for the purpose of determining off-type cacao clones within a West African germplasm collection. Proceedings of the International Cocoa Producer's Conference. 1.
Cacao single-nucleotide polymorphism (SNP) markers: A discovery strategy to identify SNPs for genotyping, genetic mapping and genome wide association studies (GWAS) - (Proceedings)
Kuhn, D.N., Schnell Ii, R.J., Motamayor, J.C., Livingstone, D., May, G., Rigoutsos, I., Haiminem, N. 2011. Cacao single-nucleotide polymorphism (SNP) markers: A discovery strategy to identify SNPs for genotyping, genetic mapping and genome wide association studies (GWAS). Proceedings of the International Cocoa Producer's Conference. pp. 135-142.
Development of Single Nucleotide Polymorphism markers in Theobroma cacao and comparison to Simple Sequence Repeat markers for genotyping of Cameroon clones. - (Peer Reviewed Journal)
Livingstone, D., Motamayor, J.C., Schnell Ii, R.J., Cariaga, K.A., Freeman, B.L., Meerow, A.W., Brown, J.S., Kuhn, D.N. 2011. Development of Single Nucleotide Polymorphism markers in Theobroma cacao and comparison to Simple Sequence Repeat markers for genotyping of Cameroon clones. Molecular Breeding. DOI 10.1007/s1 1032-010-9416-2
Improvement of High-throughput Genotype Analysis After Implementation of a Dual-curve Sybr Green I-based Quantification and Normalization Procedure - (Peer Reviewed Journal)
Livingstone, D., Freeman, B.L., Tondo, C.L., Cariaga, K.A., Kuhn, D.N. 2009. Improvement of High-throughput Genotype Analysis After Implementation of a Dual-curve Sybr Green I-based Quantification and Normalization Procedure. HortScience. 44: 1228-1232.
Parentage analysis and outcrossing patterns in cacao (Theobroma cacao L.) farms in Cameroon - (Peer Reviewed Journal)
Efombagn, M., Sounigo, O., Eskes, A.B., Motamayor, J.C., Manzanares-Dauleux, J.J., Schnell Ii, R.J., Nyasse, S. 2009. Parentage analysis and outcrossing patterns in cacao (Theobroma cacao L.) farms in Cameroon. Heredity. p.1-8.
Regional selection of hybrid Nacional cacao genotypes in Coastal Ecuador     Reprint Icon - (Trade Journal)
Ramlachan, N., Agama, J., Amores, F., Quiroz, J., Vaca, D., Zamora, C., Moore, J.M., Brown, J.S., Schnell Ii, R.J., Motamayor, J.C. 2009. Regional selection of hybrid Nacional cacao genotypes in Coastal Ecuador. Ingenic Newsletter.
Sequencing the Cacao Genome: Overall Strategy and SNP Discovery for Cacao Improvement. - (Abstract Only)
Kuhn, D.N., Schnell Ii, R.J., Livingstone, D., Scheffler, B., Motamayor, J., Shapiro, H., Bennett, A., Main, D., Blackmon, B., Saski, C., Dean, M., Rigoutsos, I. 2009. Sequencing the Cacao Genome: Overall Strategy and SNP Discovery for Cacao Improvement.. Plant and Animal Genome Conference.
Increasing the efficiency of traditional cacao breeding using whole genome sequencing information. - (Abstract Only)
Schnell Ii, R.J., Brown, J.S., Kuhn, D.N., Tondo, C.L., Motamayor, H.Y., Shapiro, H., Scheffler, B., Main, D., Isidore, R. 2009. Increasing the efficiency of traditional cacao breeding using whole genome sequencing information.. Plant and Animal Genome Conference.
Comparison of SNPs and microsatellites in identifying offtypes of cacao clones from Cameroon - (Abstract Only)
Livingstone, D., Motamayor, J., Schnell Ii, R.J., Kuhn, D.N. 2009. Comparison of SNPs and microsatellites in identifying offtypes of cacao clones from Cameroon. Plant and Animal Genome Conference.
An EST-SSR based linkage map for Persea americana Mill. (avocado) - (Peer Reviewed Journal)
Borrone, J., Brown, J.S., Tondo, C.L., Mauro-Herrera, M., Kuhn, D.N., Violi, H., Sautter, R.T., Schnell Ii, R.J. 2009. An EST-SSR based linkage map for Persea americana Mill. (avocado). Tree Genetics and Genomes. 10.1007/s11295-009-0208-y
Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions. - (Peer Reviewed Journal)
Argout, X., Fouet, O., Wincker, P., Gramacho, K., Legavre, T., Sabau, X., Risterucci, A.M., Da Silva, C., Cascardo, J., Allegre, M., Kuhn, D.N., Verica, J., Courtois, B., Loor, G., Babin, R., Sounigo, O., Ducamp, M., Guiltinan, M.J., Ruiz, M., Alemanno, L., Machado, R., Phillips, W., Schnell Ii, R.J., Gilmour, M., Rosenquist, E., Butler, D., Maximova, S., Lanaud, C. 2008. Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions.. Biomed Central (BMC) Genomics. 2008.9:512.
Population structure and molecular characterization of Nigerian field genebank collections of cacao, Theobroma cacao L - (Peer Reviewed Journal)
Aikpokpodion, P.O., Kolesnikova-Allen, M., Adetimirin, V.0., Guiltinan, M.J., Eskes, A.B., Motamayor, J.C., Schnell Ii, R.J. 2010. Population structure and molecular characterization of Nigerian field genebank collections of cacao, Theobroma cacao L. SILVAE GENETICA. 59(6):273-285.
Microsatellite markers reveal low breeding system efficacy and pollen contamination can limit production of full-sib avocado progeny - (Peer Reviewed Journal)
Violi, H.A., Brown, J.S., Tondo, C.L., Borrone, J.W., Ploetz, R., Schnell Ii, R.J. 2009. Microsatellite markers reveal low breeding system efficacy and pollen contamination can limit production of full-sib avocado progeny. Scientia Horticultureae. doi:10.1016/j.scienta.2008.11.011
Recurrent selection of cocoa populations in Cote d'Ivoire: comparative genetic diversity between the first and second cycles - (Peer Reviewed Journal)
Pokou, N.D., N'Goran, J.A., Lachenaud, P., Eskes, A.B., Motamayor, J.C., Schnell Ii, R.J., Kolesnikova-Allen, M., Clement, D., Sangare, A. 2009. Recurrent selection of cocoa populations in Cote d'Ivoire: comparative genetic diversity between the first and second cycles. Plant Breeding. 128: 514-520.
Mapping of quantitative trait loci for butter content and hardness in cocoa beans (Theobroma cacao L.) - (Peer Reviewed Journal)
Araujo, I.S., De Souza Filho, G.A., Faleiro, F.G., Queiroz, V.T., Moreira, M.A., De Barros, E.G., Guimaraes, C.T., Machado, R.C., Pires, J.L., Lopes, U.V., Schnell Ii, R.J. 2008. Mapping of quantitative trait loci for butter content and hardness in cocoa beans (Theobroma cacao L.). Plant Molecular Biology Reporter. DOI 10.1007/s11105-008-0069-9
Last Modified: 7/28/2014
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