Page Banner

United States Department of Agriculture

Agricultural Research Service

Related Topics

David Kuhn
Subtropical Horticulture Research
General Biological Science

Phone: (786) 573-7087
Fax: (786) 573-7100

13601 OLD CUTLER ROAD
MIAMI , FL 33158

Projects
Conservation, Genetic Analyses, and Utilization of Subtropical/Tropical Fruit Crops, Sugarcane, and Miscanthus Genetic Resources
Appropriated (D)
  Accession Number: 424610
Genetics and Genomics of Tropical Fruit, Sugarcane and Grasses
Specific Cooperative Agreement (S)
  Accession Number: 425090
GENOMICS AND SINGLE NUCLEOTIDE POLYMORPHISM (SNP) MARKER DISCOVERY IN TROPICAL AND SUBTROPICAL FRUIT TREES
Specific Cooperative Agreement (S)
  Accession Number: 421988
Genetic Mapping, Germplasm Evaluation and Development of Genomic Tools for Mango to Accelerate Breeding of Improved Cultivars
Trust (T)
  Accession Number: 428550

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Development of single nucleotide polymorphism (SNP) markers from the mango (Mangiferaindica) transcriptome for mapping and estimation of genetic diversity -
California avocados in Florida? Finding the perfect avocado for production in East-Central Florida -
Pisani, C., Ritenour, M.A., Stover, E., Plotto, A., Gutierrez, O.A., Kuhn, D. 2015. California avocados in Florida? Finding the perfect avocado for production in east-central Florida. In: Proceedings of Florida State Horticultural Society. 127:131-134.
Mango (Mangifera indica L.) cv. Kent fruit mesocarp de novo transcriptome assembly identifies gene families important for ripening -
Kuhn, D.N., Mitzuko, D., Adrian, O., Carme, C.R., Magda, P., Sergio, C., Alejandro, S., Maria, I. 2015. Mango (Mangifera indica L.) cv. Kent fruit mesocarp de novo transcriptome assembly identifies gene families important for ripening. Frontiers in Plant Science. 6:62 doi: 10.3389/flps.2015.00062.
Topological Signatures for Population Admixture -
Kuhn, D.N., Deniz, Y., Filipo, U., Laxmi, P., Saugata, B. 2015. Topological Signatures for Population Admixture. Research Computational Molecular Biology (RECOMB). LNBI 9029, pp 261-275.
Promoting utilization of Saccharum spp. genetic resources though genetic diversity analysis and core collection construction -
Nayak, S.N., Song, J., Villa, A., Pathak, B., Ayala Silva, T., Yang, X., Todd, J.R., Glynn, N.C., Kuhn, D.N., Glaz, B.S., Gilbert, R., Comstock, J.C., Wang, J. 2014. Promoting utilization of Saccharum spp. genetic resources though genetic diversity analysis and core collection construction. PLoS One. 9(10):e110856. doi: 10.1371/journal.pone.0110856.
Making a chocolate chip: development and evaluation of a 6K SNP array for Theobroma cacao. -
Livingstone Iii, D., Royaert, S., Stack, C., Mockatis, K., Schenll, R., Kuhn, D.N., Motomayer, J. 2015. Making a chocolate chip: development and evaluation of a 6K SNP array for Theobroma cacao.. Meeting Abstract. 2015, 1-13.
Morphological and physio-chemical characterization of five Canistel accessions at the subtropical horticulture research station in Miami Florida -
Characterization and evaluation of five jaboticaba accessions at the subtropical horticulture research station in Miami, Florida -
Morphological and chemical characterization of the kei apple (Dovyalis spp) -
Phenotypic Characterization of the Miami World Collection of Sugarcane and Related Grasses for Selecting a Representative Core -
Todd, J.R., Wang, J., Glaz, B.S., Sood, S.G., Ayala Silva, T., Nayak, S.N., Glynn, N.C., Gutierrez, O.A., Kuhn, D.N., Tahir, M., Comstock, J.C. 2014. Phenotypic Characterization of the Miami World Collection of Sugarcane and Related Grasses for Selecting a Representative Core. Crop Science. 61:1-16.
QTL mapping for resistance to frosty pod and black pod diseases in an f1 population of Theobroma cacao L -
Identification of candidate genes involved in witches’ broom disease resistance in a segregating mapping population of Theobroma cacao L. in Brazil -
Forging New Cocoa Keys: The Impact of Unlocking the Cocoa Bean’s Genome on Pre-harvest Food Safety -
Kuhn, D.N. 2013. Forging New Cocoa Keys: The Impact of Unlocking the Cocoa Bean’s Genome on Pre-harvest Food Safety. Meeting Abstract. International Association of Food Protection, Charlotte NC July 29-31, 2013.
iXora1: exact haplotype inferencing and trait association -
Utro, F., Haiminen, N., Livingstone Iii, D., Cornejo, O.E., Royaert, S., Schnell, R.J., Motamayor, J.C., Kuhn, D.N., Parida, L. 2013. iXora1: exact haplotype inferencing and trait association. BioMed Central (BMC) Genetics. 14:48.
Core Selection from the Miami World Collection of Sugarcane and Related Grasses using Phenotypic Markers -
Todd, J.R., Ayala Silva, T., Glaz, B.S., Wang, J., Sood, S.G., Nayak, S.N., Glynn, N.C., Gutierrez, O.A., Kuhn, D.N., Comstock, J.C. 2013. Core Selection from the Miami World Collection of Sugarcane and Related Grasses using Phenotypic Markers. Sugar Journal. p. 3.
The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color -
Motamayor, J.C., Mockaitis, K., Schmutz, J., Haiminen, N., Livinstone Iii, D., Cornejo, O., Findley, S., Zheng, P., Utro, F., Royaert, S., Saski, C., Jenkins, J., Podicheti, R., Zhao, M., Scheffler, B.E., Stack, J.C., Feltus, A., Mustiga, G., Amores, F., Phillips, W., Marelli, J., May, G.D., Shapiro, H., Ma, J., Bustamante, C.D., Schnell, R.J., Main, D., Gilbert, D., Parida, L., Kuhn, D.N. 2013. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biology. Genome Biology 2013, 14:R53 doi:10.1186/gb-2013-14-6-r53.
Genome Size Evolution in Theobroma cacao: Recent Sequencing of Two Cacao Genomes of Different Size -
Kuhn, D.N., Ma, J., Zheng, P., Main, D., Haiminen, N., Parida, L., Cornejo, O., Findley, S., Livingstone Iii, D.S., Mustiga, G., Schnell, R.J., Mockaitis, K., Motamayor, J. 2013. Genome Size Evolution in Theobroma cacao: Recent Sequencing of Two Cacao Genomes of Different Size. Meeting Abstract. Plant and Animal Genome Meeting XXI, January 12-16, 2013 San Diego, CA.
Generation of a Saturated Genetic Recombination Map for Avocado (Persea americana) -
Borrone JW, Brown JS, Tondo CL, Mauro-Herrera M, Kuhn DN, Violi HA, Sautter RT, Schnell RJ (2009) An EST-SSR-based linkage map for Persea americana Mill. (avocado). Tree Genet Genomes 5 (4):553-560. doi:10.1007/s11295-009-0208-y
Building genomic resources for Theobroma cacao -
Cornejo, O., Kuhn, D.N., Livingstone Iii, D.S., Mockaitis, K., Mustiga, G., Yee, M., Findley, S.D., Schnell, R.J., Motamayor, J., Bustamante, C. 2013. Building genomic resources for Theobroma cacao. Meeting Abstract. Plant and Animal Genome Meeting XXI, January 12-16, 2013 San Diego, CA.
Impact Of Selfing On The Inference Of Demographic History From Whole Genomes In Theobroma cacao L. -
Cornejo, O., Kuhn, D.N., Livingstone Iii, D.S., Mockaitis, K., Royaert, S., Findley, S.D., Mustiga, G., Schnell, R.J., Bustamante, C., Motamayor Arias, J. 2013. Impact Of Selfing On The Inference Of Demographic History From Whole Genomes In Theobroma cacao L.. Meeting Abstract. Plant and Animal Genome Meeting XXI, January 12-16, 2013 San Diego, CA.
Toward The Identification Of Candidate Genes Involved In Black Pod Disease Resistance In Theobroma cacao L. -
Livingstone Iii, D.S., Gutierrez, O.A., Royaert, S., Epaina, P., Kuhn, D.N., Schnell, R.J., Motamayor, J. 2013. Toward The Identification Of Candidate Genes Involved In Black Pod Disease Resistance In Theobroma cacao L.. Meeting Abstract. Plant and Animal Genome Meeting XXI, January 12-16, 2013 San Diego, CA.
iXora: Haplotype Inferencing and Trait Association -
Utro, F., Haiminen, N., Livingstone Iii, D.S., Cornejo, O., Royaert, S., Schnell, R.J., Motamayor, J., Kuhn, D.N., Parida, L. 2013. iXora: Haplotype Inferencing and Trait Association . Meeting Abstract. Plant and Animal Genome Meeting XXI, January 12-16, 2013 San Diego, CA.
Towards The Identification Of Candidate Genes Involved In Witches' Broom Disease Resistance In Theobroma cacao L. -
Royaert, S., Moore, M.J., Santos Araujo, I., Viana Da Silva, D., Martins De Jesus, S., Livingstone Iii, D.S., Marelli, J., Kuhn, D.N., Gutierrez, O.A., Correa, R.X., Schnell, R.J., Motamayor Arias, J. 2013. Towards The Identification Of Candidate Genes Involved In Witches' Broom Disease Resistance In Theobroma cacao L.. Meeting Abstract. Plant and Animal Genome Meeting XXI, January 12-16, 2013 San Diego, CA.
The Role Of Haplotyping In Mapping The Pod Color Trait -
Haiminen, N., Livingstone Iii, D.S., Cornejo, O., Utro, F., Royaert, S., Mockaitis, K., Motamayor Arias, J., Parida, L., Kuhn, D.N. 2013. The Role Of Haplotyping In Mapping The Pod Color Trait. Meeting Abstract. Plant and Animal Genome Meeting XXI, January 12-16, 2013 San Diego, CA.
The Genome of the Most Widely Cultivated Cacao Type and Its Use to Identify Candidate Genes Regulating Traits: Pod Color as an Example -
Motamayor, J., Mockaitis, K., Schmutz, J., Haiminen, N., Livingstone Iii, D.S., Cornejo, O., Findley, S.D., Zheng, P., Utro, F., Royaert, S., Saski, C., Jenkins, J., Podicheti, R., Zhao, M., Scheffler, B.E., Feltus, A.F., Amores, F.M., Phillips, W., Marelli, J., May, G.D., Shapiro, H., Ma, J., Bustamante, C., Schnell, R.J., Main, D., Gilbert, D., Parida, L., Kuhn, D.N. 2013. The Genome of the Most Widely Cultivated Cacao Type and Its Use to Identify Candidate Genes Regulating Traits: Pod Color as an Example . Meeting Abstract. Plant and Animal Genome Meeting XXI, January 12-16, 2013 San Diego, CA.
The Genome of the Most Widely Cultivated Cacao Type and Its Use to Identify Candidate Genes Regulating Traits: Pod Color as an Example -
Motamayor Arias, J., Mockaitis, K., Schmutz, J., Haiminen, N., Livingstone Iii, D.S., Cornejo, O., Findley, S.D., Zheng, P., Utro, F., Royaert, S., Saski, C., Jenkins, J., Podicheti, R., Zhao, M., Scheffler, B.E., Feltus, A.F., Amores, F.M., Phillips, W., Marelli, J., May, G., Shapiro, H., Ma, J., Bustamante, C., Schnell, R.J., Main, D., Gilbert, D., Parida, L., Kuhn, D.N. 2013. The Genome of the Most Widely Cultivated Cacao Type and Its Use to Identify Candidate Genes Regulating Traits: Pod Color as an Example. Meeting Abstract. Plant and Animal Genome Meeting XXI, January 12-16, 2013 San Diego, CA.
Toward the identification of candidate genes involved In black pod disease resistance in Theobroma cacao L. -
Livingstone Iii, D., Gutierrez, O.A., Royaert, S., Epaina, P., Kuhn, D.N., Schnell, R.J., Motamayor, J. 2013. Toward the identification of candidate genes involved In black pod disease resistance in Theobroma cacao L.. Meeting Abstract. Int'l Plant & Animal Genome XXI Conference, San Diego, CA, January 12-16, 2013.
Toward The identification Of candidate genes involved in black pod disease resistance in Theobroma cacao L. -
Royaert, S., Moore, J.M., Santos Araujo, I., Viana Da Silva, D., Martins De Jesus, S., Livingstone Iii, D., Marelli, J., Kuhn, D.N., Gutierrez, O.A., Correa, R., Schnell, R.J., Motamayor, J. 2013. Toward The identification Of candidate genes involved in black pod disease resistance in Theobroma cacao L.. Meeting Abstract. Plant & Animal Genome XXI Conference, San Diego, CA January 12-16, 2013.
An example of association mapping in Cacao. -
Gutierrez, O.A., Schnell, R.J., Motamayor, J., Kuhn, D.N., Tondo, C.L., Boza, E.J., Livingstone, D., Royaert, S., Nagai, C., Phillips, W., Amores, F., Lopes, U., Takrama, J., Padi, F., Aikpokpodion, P., Pokou, D., Efombagn, I., Sounigo, O., Epaina, P. 2012. An example of association mapping in Cacao.. Meeting Abstract. Seven INGENIC Workshop, Yaounde, Cameroon, October 21-22, 2013.
Exploring Broad Genetic Resources Available to Sugarcane -
Wang, J.P., Ayala-Silva, T., Nayak, S.N., Todd, J.R., Villa, A., Glynn, N.C., Yang, X., Glaz, B.S., Comstock, J.C., Kuhn, D.N., Gutierrez, O.A., Gilbert, R. 2012. Exploring Broad Genetic Resources Available to Sugarcane. Symposium on New Paradigms in Sugarcane Research, October 15-17, 2012, Coimbatore, India. p.172. Ed. by R. Viswanathan et al.
Phenotypic evaluation of the World Collection of Sugarcane and Related Grasses -
Todd, J.R., Glynn, N.C., Ayala Silva, T., Glaz, B.S., Wang, J., Sood, S.G., Nayak, S.N., Gutierrez, O.A., Kuhn, D.N., Comstock, J.C. 2013. Phenotypic evaluation of the World Collection of Sugarcane and Related Grasses. Plant and Animal Genome Conference. P. 7.
Interrelationships of petiole air canal architecture, water depth and convective air flow in Nymphaea odorata (Nymphaeaceae) -
Exploring the T. cacao genome sequence for marker/trait associations useful in cacao breeding -
Schnell, R.J., Kuhn, D.N., Gutierrez, O.A., Motamayor, J. 2012. Exploring the T. cacao genome sequence for marker/trait associations useful in cacao breeding. Meeting Abstract. 17th Int'l Cocoa Research Conference, Yaounde, Cameroon, October 15-20, 2012.
World Saccharum Collection at the USDA Subtropical Research Station, National Germplasm Repository Miami, Florida -
Race, Interracial Admixture and Genetic Differentiation of Avocado (Persea americana Mill) -
Boza, E.J., Tondo, C.L., Kuhn, D.N., Meerow, A.W., Moore, M.J., Campbell, R., Ledesma, N., Gutierrez, O.A., Schnell, R.J. 2012. Race, Interracial Admixture and Genetic Differentiation of Avocado (Persea americana Mill). Meeting Abstract. Supplement of HortScience Volume 47(9) September 2012.
QTL mapping for Cold Tolerance and Flower Type in a Reciprocal F1 Florida Avocado Mapping population -
Gutierrez, O.A., Schnell, R.J., Kuhn, D.N., Tondo, C.L., Borrone, J.W. 2012. QTL mapping for Cold Tolerance and Flower Type in a Reciprocal F1 Florida Avocado Mapping population. Meeting Abstract. Supplement to HortScience Volume 47(9) September 2012.
The South Florida Avocado Breeding Program at USDA-Agricultural Research Service Subtropical Horticulture Research Station (USDA-ARS SHRS) -
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 -
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.
Molecular Characterization and Genetic Structure in Avocado (Persea americana Mill.) Using Simple Sequence Repeat (SSR) Markers -
Boza, E.J., Tondo, C.L., Kuhn, D.N., Meerow, A.W., Moore, J.M., Campbell, R.J., Ledesma, N., Gutierrez, O.A., Schnell, R.J. 2012. Molecular Characterization and Genetic Structure in Avocado (Persea americana Mill.) Using Simple Sequence Repeat (SSR) Markers. Annual International Plant & Animal Genome Conference. Annual International Plant & Animal Genome Conference, January 14-18, 2012, San Diego, CA.
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 -
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.
A genetically anchored physical framework for Theobroma cacao cv. Matina 1-6 -
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.
Evaluation of Methods for de novo Genome assembly from High-throughput Sequencing Reads Reveals Dependencies that Affect the Quality of the Results Reprint Icon -
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 -
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.
Spacial analysis of avocado sunblotch disease in an avocado germplasm collection -
Schnell Ii, R.J., Tondo, C.L., Kuhn, D.N., Winterstein, M.C., Ayala Silva, T. 2011. Spacial analysis of avocado sunblotch disease in an avocado germplasm collection. Journal of Phytopathology. DOI: 10.1111/j.1439-0434.2011.01838.x.
Identification of marker-trait associations for self-compatibility in a segregating mapping population of Theobroma cacao L -
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 -
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.
The genetic mosiac of iris series Hexagonae in Florida: inferences on the Holocene history of the Louisiana irises and anthropogenic effects on their distribution. -
Meerow, A.W., Gideon, M., Kuhn, D.N., Mopper, S., Nakamura, K. 2011. The genetic mosiac of iris series Hexagonae in Florida: inferences on the Holocene history of the Louisiana irises and anthropogenic effects on their distribution. International Journal of Plant Science. 172(8):1026-1052.
SNP discovery in avocado from second generation sequencing of the leaf and flower transcriptome -
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.
Comparison of single nucleotide polymorphisms and simple sequence repeats in genotype identification and diversity assessment of cacao germplasm -
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.
Theobroma cacao: A genetically integrated physical map and genome-scale comparative synteny analysis -
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.
Building a next generation platform for association studies in cacao -
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.
Putting the cacao genome to work: Development and utilization of Theobroma cacao SNP markers -
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.
Pooled-BAC sequencing of a black pod resistance region (cBPQTL12) in T. cacao -
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.
Identification of differentially expressed genes involved in self-incompatibility in Theobroma cacao L. -
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.
Transcriptome characterization for genome annotation and functional genomics in Theobroma cacao -
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.
Cocoa/Cotton Comparative Genomics -
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.
Genomics of Tropical Fruit Tree Crops Reprint Icon -
Arias De Ares, R.S., Borrone, J.W., Tondo, C.L., Kuhn, D.N., Schnell Ii, R.J. 2012. Genomics of Tropical Fruit Tree Crops. Book Chapter. In: Schnell, R.J., Priyadarshan, P.M., editors. Genomics of Tree Crops. Heidelberg, Germany: Springer. p. 209-239.
Better chocolate through genomics -
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 -
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.
Results of the 2009 ASBVd survey of avocado accessions in the national germplasm collection in Florida -
Tondo, C.L., Schnell Ii, R.J., Kuhn, D.N. 2011. Results of the 2009 ASBVd survey of avocado accessions in the national germplasm collection in Florida. Journal of Florida State Horticulture Society. 1.
Evaluating Theobroma grandiflorum for comparative genomic studies with Theobroma cacao Reprint Icon -
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 -
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. -
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.
A genetically anchored physical map of the cacao genome -
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.
Design and implementation of the cacao genome database -
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.
The need for an assembly pilot project -
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.
Outcrossing in Florida and California commercial avocado (Persea americana Mill) orchards estimated using microsatellite markers and the development of a genetic linkage map -
The international marker assisted selection program for cacao -
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 -
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.
T. cacao Transcriptome Sequencing -
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 -
Status of cacao breeding in Ghana -
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.
Cacao single-nucleotide polymorphism (SNP) markers: A discovery strategy to identify SNPs for genotyping, genetic mapping and genome wide association studies (GWAS) -
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.
El nombre 'Forastero' no más: A new protocol for meaningful cacao germplasm classification. -
Motamayor, J.C., Lechenaud, P., Da Silva E Mota, J.W., Loor, R., Kuhn, D.N., Schnell Ii, R.J. 2011. El nombre 'Forastero' no más: A new protocol for meaningful cacao germplasm classification.. Proceedings of the International Cocoa Producer's Conference. 1.
Genetics of reproductive self-compatibility in Theobroma cacao L. -
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 -
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.
Development of Single Nucleotide Polymorphism markers in Theobroma cacao and comparison to Simple Sequence Repeat markers for genotyping of Cameroon clones. -
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
Phylogenetic analysis of seven WRKY genes across the palm subtribe Attaleinae (Areceaceae) identifies Syagrus as sister to the coconut -
Meerow, A.W., Borrone, J.W., Couvreur, T.L., Mauro-Herrera, M., Hahn, W.J., Kuhn, D.N., Nakamura, K., Schnell Ii, R.J. 2009. Phylogenetic analysis of seven WRKY genes across the palm subtribe Attaleinae (Areceaceae) identifies Syagrus as sister to the coconut. PLoS One. DOI http://dx.plos.org/10.1371/journal.pone.0007353
Out-crossing between 'Bacon' pollinizers and adjacent 'Hass' avocado and the identification of two new avocado lethal mutants -
Schnell Ii, R.J., Tondo, C.L., Brown, J.S., Ayala Silva, T., Borrone, J.W., Davenport, T.L., Kuhn, D.N. 2009. Out-crossing between 'Bacon' pollinizers and adjacent 'Hass' avocado trees and the description of two new lethal mutants. HortScience. 44(6):1522-1526.
Improvement of High-throughput Genotype Analysis After Implementation of a Dual-curve Sybr Green I-based Quantification and Normalization Procedure -
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.
Sequencing the Cacao Genome: Overall Strategy and SNP Discovery for Cacao Improvement. -
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. -
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 -
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) -
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. -
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.
Geographic and genetic population differentiation of the Amazonian chocolate tree -
Motamayor, J.C., Lachenaud, P., Wallace, J., Loor, G., Kuhn, D.N., Brown, J.S., Schnell Ii, R.J. 2008. Geographic and genetic population differentiation of the Amazonian chocolate tree. PLoS One. Available: DOI: 10.1007/s12042-008-9011-4
SSCP markers provide a useful alternative to microsatellites in genotyping and estimating genetic diversity in populations and germplasm collections of plant specialty crops. -
Kuhn, D. N., J. C. Motamayor, A. W. Meerow, J. W. Borrone and R. J. Schnell. SSCP markers provide a useful alternative to microsatellites in genotyping and estimating genetic diversity in populations and germplasm collections of plant specialty crops. Electrophoresis29: 4096–4108 . 2008.
SSCP markers provide a useful alternative to microsatellites in genotyping and estimating genetic diversity in populations and germplasm collections of specialty crops -
Kuhn, D.N., Meerow, A.W., Borrone, J.W., Motamayor, J.C., Schnell Ii, R.J. 2008. Sscp markers provide a useful alternative to microsatellites in genotyping and estimating genetic diversity in populations and germplasm collections of specialty crops. Plant and Animal Genome Conference.
A composite linkage map from the combination of three crosses made from commercial clones of cacao, T. cacao L. -
Brown, J.S., Sautter, R.T., Tondo, C.T., Borrone, J.W., Kuhn, D.N., Motamayor, J.C., Schnell II, R.J. 2008. A composite linkage map from the combination of three crosses made from commercial clones of cacao, T. cacao L.. Tropical Plant Biology. DOI 10.1007/s12042-008-9011-4
Out-crossing in Florida avocados as measured using microsatellite markers -
Borrone, J.W., Tondo, C.T., Kuhn, D.N., Brown, J.S., Schnell Ii, R.J., Violi, H.A. 2008. Out-crossing in Florida avocados as measured using microsatellite markers. J. Amer. Soc. Hort Sci. 133(2):255-261.
Development of marker assisted selection program for cacao -
Schnell Ii, R.J., Kuhn, D.N., Brown, J.S., Tondo, C.T., Motamayor, J.C. 2007. Development of marker assisted selection program for cacao. Journal of Phytopathology. 97(12):1664-1669.
An estimation of outcrossing in Florida avocado (Persea americana Mill.) using microsatellite markers -
Borrone, J.W., Olano, C.T., Kuhn, D.N., Brown, J.S., Violi, H., Ploetz, R., Schnell Ii, R.J. 2007. An estimation of outcrossing in Florida avocado (Persea americana Mill.) using microsatellite markers. Botanical Society of America Proceedings.
The potential of the WRKY gene family for phylogenetic reconstruction: an example from the Malvaceae. -
Borrone, J.W., Meerow, A.W., Kuhn, D.N., Whitlock, B.A., Schnell Ii, R.J. 2007. The potential of the WRKY gene family for phylogenetic reconstruction: an example from the Malvaceae.. Annals Of Botany.
Usefulness of WRKY gene-derived markers for assessing genetic diversity of Florida coconut cultivars -
Mauro Herrera, M., Meerow, A.W., Borrone, J.W., Kuhn, D.N., Schnell Ii, R.J. 2007. Usefulness of WRKY gene-derived markers for assessing genetic diversity of Florida coconut cultivars. Scientia Horticultureae. 115:19-26.
Genetic structure and gene flow among South Florida populations of Iris hexagona Walt. (Iridaceae) assessed with 19 microsatellite DNA loci -
Meerow, A.W., Gideon, M., Kuhn, D.N., Motamayor, J., Nakamura, K. 2007. Genetic structure and gene flow among South Florida populations of Iris hexagona Walt. (Iridaceae) assessed with 19 microsatellite DNA loci. International Journal of Plant Science. 168:1291-1309.
Development of Mapping Populations for Avocado. -
Tondo, C.T., Borrone, J.W., Kuhn, D.N., Brown, J.S., Violi, H.A., Ploetz, R., Schnell Ii, R.J. 2007. Development of Mapping Populations for Avocado. Proceedings of Florida State Horticultural Society. 120:26-29
The potential of the WRKY gene family for phylogenetic reconstruction: an example from the Malvaceae -
Borrone, J.W., Meerow, A.W., Kuhn, D.N., Whitlock, B.A., Schnell Ii, R.J. 2007. The potential of the WRKY gene family for phylogenetic reconstruction: an example from the Malvaceae. Molecular Phylogenetics and Evolution. 44:1141-1154.
Integrating genomics into an applied cacao breeding program. -
Schnell Ii, R.J., Motomayor, J.C., Brown, J.S., Kuhn, D.N., Olano, C.T., Borrone, J.W., Ploetz, R., Rosenquist, E. 2007. Integrating genomics into an applied cacao breeding program.. Meeting Abstract.
Genetic structure and gene flow among South Florida populations of Iris hexagona Walt.(Iridaceae)assessed with 19 microssatellite DNA loc. -
Meerow, A.W., Gideon, M., Kuhn, D.N., Motomayor, J.C., Nakamura, K. 2007. Genetic structure and gene flow among South Florida populations of Iris hexagona Walt.(Iridaceae)assessed with 19 microssatellite DNA loc.. American Society of Plant Biologists Annual Meeting.
Integrating genomics into an applied cacao breeding program. -
Schnell II, R.J., Motomayor, J.C., Brown, J.S., Kuhn, D.N., Olano, C.T., Borrone, J.W., Ploetz, R., Rosenquist, E. 2007. Integrating genomics into an applied cacao breeding program.. Meeting Abstract.
Cacao genomics and the development of a marker-assisted-selection program for cacao -
Schnell Ii, R.J., Kuhn, D.N., Brown, J.S., Tondo, C.T., Motamayor, J. 2007. Cacao genomics and the development of a marker-assisted-selection program for cacao. Plant and Animal Genome Conference Proceedings.
Development of molecular genetic markers from a cDNA subtraction library of Frosty Pod inoculated cacao -
Kuhn, D.N., Macarthur, H.C., Borrone, J.W., Schnell Ii, R.J., Brown, J.S., Johnson, E., Phillips-Mora, W. 2006. Development of molecular genetic markers from a cDNA subtraction library of Frosty Pod inoculated cacao. Proceedings of the XVth International Cacao Conference.
Development of a high throughput SNP assay for marker-assisted breeding of Theobroma cacao in cacao producing countries -
Kuhn, D.N., Motamayor, J.C., Schnell Ii, R.J. Development of a high throughput SNP assay for marker-assisted breeding of Theobroma cacao in cacao producing countries. Plant and Animal Genome VX Conference Abstracts.
Microsatellite-containing expressed sequence tags for genetic mapping and genotyping Theobroma cacao -
Borrone, J.W., Schnell Ii, R.J., Brown, J.S., Kuhn, D.N. 2007. Microsatellite-containing expressed sequence tags for genetic mapping and genotyping Theobroma cacao. Proceedings of the XVth International Cacao Conference.
Integrating genomics into applied tropical fruit breeding programs -
Schnell II, R.J., Motamayor, J., Brown, J.S., Kuhn, D.N., Cervantesmartinez, C., Olano, C.T., Ploetz, R.C., Ayala Silva, T. 2006. Integrating genomics into applied tropical fruit breeding programs. Meeting Abstract.
ANALYSIS OF OF CLONAL GERMPLASM FROM FIVE SACCHARUM SPECIES: S. BARBERI, S. ROBUSTUM, S. OFFICINARUM, SL. SINENSE AND S. SPONTANEUM. A STUDY OF INTER- AND INTRASPECIES RELATIONSHIPS USING MICROSATELLITE MARKERS -
Brown, J.S., Schnell II, R.J., Power, E.J., Douglas, S.L., David N. Kuhn. 2007. Analysis of clonal germplasm from five saccharum species: s. barberi, s. robustum, s. officinarum, sl. sinense and s. spontaneum. A study of inter- and intraspecies relationships using microsatellite markers. Genetic Resources and Crop Evolution.54:627-648.
Potential phylogenetic utility of WRKY gene family members -
Borrone, J.W., Meerow, A.W., Kuhn, D.N., Schnell Ii, R.J. 2006. Potential phylogenetic utility of WRKY gene family members. Plant and Animal Genome VX Conference Abstracts.
Single strand conformation polymorphism analysis of candidate genes for reliable identification of alleles by capillary array electrophoresis. -
Kuhn, D.N., Borrone, J.W., Meerow, A.W., Motamayor, J., Brown, J.S., Schnell Ii, R.J. 2005. Single strand conformation polymorthism analysis of candidate genes for reliable identification of alleles by capillary array electrophoresis. Electrophoresis. 26:112-125.
ARS News Articles
Last Modified: 5/2/2016
Footer Content Back to Top of Page