Plant & Animal Genomes XVIII Conference

January 9-13, 2010
Town & Country Convention Center
San Diego, CA

A Genetically Anchored Physical Map Of The Cacao Genome

Christopher A Saski¹ , Barbara P Blackmon¹ , Margaret E Staton¹ , Stephen Ficklin¹ , Frank A Feltus¹ , Raymond Schnell³ , Juan Carlos Motamayor² , David Kuhn³

¹  Clemson University Genomics Institute, 51 New Cherry Street, SC, 29634

²   Mars Incorporated, McLean, VA 22101, USA

³   USDA-ARS Subtropical Horticulture Research Station (SHRS), Miami, FL 33158, USA

Mars Incorporated and the United States Department of Agriculture have undertaken the sequencing of the genome of Theobroma cacao, which produces cocoa beans, the key ingredient in chocolate. Genetic information, such as whole genome sequence is necessary to better understand and improve cacao. In most genomic projects, a physical map is considered the centerpiece of genome research. A comprehensive integrated genomic framework is invaluable for aligning the resulting sequence contigs, which are positioned onto the map by comparison to BAC-end sequence, electronic fingerprints and other lab-based methods.
The Clemson University Genomics Institute (CUGI) has developed a genetically anchored physical map of cacao genome. Three BAC libraries were fingerprinted by high information content fingerprinting (HICF) covering the cacao genome approximately 30 times. 250 genetic markers from the genetic recombination map have been integrated with the physical map by pooled overgo hybridization. Based on a 440Mbp genome, our fingerprinting assembly resulted in 295 contigs ranging from 50kb to greater than 10 Mbp in size at 1e-80 cut-off. According to the consensus band (CB) algorithm, we estimate to have anchored 72% of the cacao genome and captured up to 96% with physical contigs. The development and progress of a genetically anchored physical map for cacao will be discussed.