Cacao Genome Sequencing Project

Organizer:
David Kuhn(USDA, ARS SHRS)
Date: Sunday, January 15, 2012
Time: 1:30 PM-6:00 PM
Room: Royal Palm Salons 3-4
Chair:
David Kuhn
1:30 PM
Introductory Remarks


1:35 PM
Adding value to T. cacao germplasm collections combining GWAS and genome sequence analysis
Claire Lanaud, CIRAD-UMR AGAP; Alejandra Santos, INIAP; Juan Carlos Jimenez, INIAP; Arnaud Lemainque, CEA-Centre National de Genotypage; Sylvana Pavek, CEA-Centre National de genotypage; Xavier Argout, CIRAD-BIOS - UMR/AGAP; Olivier Fouet, CIRAD-UMR AGAP; Edward Seguine, Mars Global Chocolate; Sophie Assemat, CIRAD-UMR Qualisud; Fabrice Davrieux, CIRAD-UMR Qualisud; Renaud Boulanger, CIRAD-UMR Qualisud; Emile Cros, CIRAD-UMR Qualisud; Rey G. Loor, INIAP (Instituto Nacional Investigaciones Agropecuarias)

1:50 PM
Germplasm Resources and their use in the Genomics Era
Pathmanathan Umaharan, The University of the West Indies

2:05 PM
Assessing the evolutionary history of Theobroma cacao from resequenced genomes
Omar Cornejo, Stanford University; Keithanne Mockaitis, Indiana University Center for Genomics and Bioinformatics; Muh-Ching Yee, Stanford University; Stefan Royaert, USDA ARS SHRS; Donald Livingstone III, MARS Inc.; Ram Podicheti, Indiana University; David Kuhn, USDA, ARS SHRS; Carlos Bustamante, Stanford University; Juan Carlos Motamayor, MARS Inc.

2:20 PM
Origin and domestication of the Nacional cacao variety from Ecuador and collecting expedition of new related genetic resources
Rey G. Loor, INIAP (Instituto Nacional Investigaciones Agropecuarias); Olivier Fouet, CIRAD-UMR AGAP; Arnaud Lemainque, CEA-Centre National de Genotypage; Sylvana Pavek, CEA-Centre National de genotypage; Ange-Marie Risterucci, CIRAD; Brigitte Courtois, CIRAD; Michel Boccara, CIRAD- Cocoa Research Unit - University of West Indies; Xavier Argout, CIRAD-BIOS - UMR/AGAP; Philippe Lachenaud, CIRAD; Eric Rosenquist, USDA - ARS (retired); Emile Cros, CIRAD-UMR Qualisud; Renaud Boulanger, CIRAD-UMR Qualisud; Fredy Amores, INIAP, Ecuador; Alfonso Vasco, INIAP - Universidad Tecnica Estatal de Quevedo; Claire Lanaud, CIRAD-UMR AGAP

2:35 PM
Gene synteny among cacao and other plants
Niina Haiminen, IBM T J Watson Research - Computational Biology Center; Laxmi Parida, IBM T J Watson Research - Computational Biology Center

2:50 PM
Break


3:10 PM
Identification, analysis and mapping of SNP markers in Theobroma cacao
Donald Livingstone III, MARS Inc.; Stefan Royaert, USDA ARS SHRS; Keithanne Mockaitis, Indiana University Center for Genomics and Bioinformatics; Gregory D. May, National Center for Genome Resources (NCGR); Andrew Farmer, National Center for Genome Resources; Christopher Saski, Clemson University Genomics Institute; Raymond J. Schnell, MARS Inc.; Juan Carlos Motamayor, MARS Inc.; David Kuhn, USDA, ARS SHRS

3:25 PM
A Core Set of SNPs for Cacao Genotyping
David Kuhn, USDA-ARS SHRS; Donald Livingstone III, USDA-ARS SHRS; Keithanne Mockaitis, Indiana University Center for Genomics and Bioinformatics; Andrew Farmer, National Center for Genome Resources; Gregory D. May, National Center for Genome Resources; Raymond J. Schnell, MARS Inc.; Juan Carlos Motamayor, MARS Inc.

3:40 PM
Marker-assisted farmer participatory selection of cacao (Theobroma cacao L.) – progress and challenges
Dapeng Zhang, Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS; Enrique Arevalo Gardini, Intituto de Cultivos Tropicales (ICT); Kun Ji, College of Horticulture and Landscape Architecture, Southwest University; Lyndel Meinhardt, Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS

3:55 PM
Construction of Genomic Library of Theobroma cacao using Genotyping by Sequencing (GBS)
Jemmy Takrama, Cocoa Research Institute of Ghana; David Kuhn, USDA, ARS SHRS; Osman Ariel Gutierrez, USDA-ARS; Raymond Schnell, USDA-ARS SHRS; Theresa Fulton, Cornell University; Robert J. Elshire, Cornell University; Edward Buckler, USDA-ARS-Cornell University; Sharon E. Mitchell, Cornell University

4:10 PM
Break


4:30 PM
Use of the Matina 1-6 Cacao Genome Sequence to Identify Marker-Trait Associations for Witches' Broom Resistance in Theobroma cacao L
Stefan Royaert, USDA-ARS SHRS; Ioná Santos Araújo, Universidade Federal Rural do Semi-Árido - Departamento de Ciências Vegetais; Donald Livingstone III, USDA-ARS SHRS; Jean-Philippe Marelli, Mars Inc.; Daniela Viana da Silva, Universidade Estadual de Santa Cruz - Laboratory of Genomics; Samuel Martins de Jesus Branco, Universidade Estadual de Santa Cruz - Laboratory of Genomics; Ronan Xavier Corrêa, Universidade Estadual de Santa Cruz - Laboratory of Genomics; David Kuhn, USDA-ARS SHRS; Raymond J. Schnell, MARS Inc.; Juan Carlos Motamayor, MARS Inc.

4:45 PM
Functional analysis of cacao disease resistance genes
Mark Guiltinan, The Pennsylvania State University; Zi Shi, The Pennsylvania State University; Yufan Zhang, The Pennsylvania State University; Brett Tyler, Virgina Polytechnic Institute and State University; Shunyuan Xiao, University of Maryland; Luis C. Mejia, Smithsonian Tropical Research Institute; Siela Maximova, The Pennsylvania State University

5:00 PM
Developing a reliable assay for Cacao Swollen Shoot Virus using quantitative PCR
Pilar Maul, Saint Thomas University; Donald Livingstone III, USDA-ARS SHRS; Juan Carlos Motamayor, MARS Inc.; Raymond J. Schnell, MARS Inc.; David Kuhn, USDA-ARS SHRS

5:15 PM
Whole genome microarray and proteomics analysis of cacao embryogenesis
Siela Maximova, The Pennsylvania State University; Niemenak Niemenak, University of Yaounde I; Xiangling Shen, The Pennsylvania State University; Monica Santos-Mendoza, The Pennsylvania State University; Zi Shi, The Pennsylvania State University; Yufan Zhang, The Pennsylvania State University; Sergio L Florez, The Pennsylvania State University; Wayne Curtis, The Pennsylvania State University; Mark Guiltinan, The Pennsylvania State University

5:30 PM
Association mapping in cacao
Osman Ariel Gutierrez, USDA-ARS; Chifumi Nagai, Hawaii Agriculture Research Center; Rebecca Heinig, Hawaii Agriculture Center; Edward Boza, USDA-ARS; Cecile Tondo, USDA-ARS; Juan Carlos Motamayor, MARS Inc.; Raymond J. Schnell, MARS Inc.

5:45 PM
Concluding Remarks


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