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ARS Home » Southeast Area » Miami, Florida » Subtropical Horticulture Research » Research » Publications at this Location » Publication #274249
Title: Theobroma cacao: A genetically integrated physical map and genome-scale comparative synteny analysis

Author
item SASKI, CHRISTOPHER - Clemson University
item BLACKMON, BARBARA - Clemson University
item STATON, MARGARET - Clemson University
item FELTUS, FRANK - Clemson University
item FICKLIN, STEPHEN - Clemson University
item Kuhn, David
item Schnell Ii, Raymond
item Livingstone, Donald
item MOTAMAYOR, JUAN - Mars, Inc

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 1/16/2011
Publication Date: 1/16/2011
Citation: 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.

Interpretive Summary: Theobroma cacao, the source of cocoa beans for chocolate, is an important tropical agriculture commodity that is affected by a number of fungal pathogens and insect pests, as well as concerns about yield and quality. We are trying to find molecular genetic markers that are linked to disease resistance and other important economic traits to aid in a marker assisted selection (MAS) breeding program for cacao to ensure a reliable supply of cocoa for the US confectionary industry. A comprehensive integrated genomic framework is considered a centerpiece of genomic research. In collaboration with the USDA-ARS (SHRS) and Mars Inc., the Clemson University Genomics Institute (CUGI) has developed a genetically anchored physical map of the T. cacao genome. The structural organization of the cacao genome and a comprehensive genome-scale syntenic comparative analysis to Arabidopsis thaliana, Oryza sativa, Vitis vinifera, and Populus trichoptera will be discussed. The physical map was used to improve the assembly of the cacao genome, which will result in the identification of genetic markers and candidate genes related to disease resistance and other important horticultural traits. Our results are important to scientists trying to understand the mechanism of disease resistance and, eventually, to cacao farmers who will benefit from superior disease resistant and more productive cultivars produced through our MAS breeding program.

Technical Abstract: A comprehensive integrated genomic framework is considered a centerpiece of genomic research. In collaboration with the USDA-ARS (SHRS) and Mars Inc., the Clemson University Genomics Institute (CUGI) has developed a genetically anchored physical map of the T. cacao genome. Three BAC libraries containing 110,592 BACs were fingerprinted by high information content fingerprinting (HICF) covering the cacao genome approximately 30 times. 250 genetic markers from the high-resolution genetic recombination map and 96 Arabidopsis derived conserved ortholog set (COS) II markers were anchored by pooled overgo hybridization. A dense minimal tile path (MTP) consisting of 31,478 BACs was selected and end sequenced. The physical map consists of 155 contigs, and 4,268 singletons. Forty-nine contigs are genetically anchored and ordered to chromosomes for a total span of 307.2 Mbp. The unanchored contigs (106) span 67.4 Mbp giving an estimated genome size of 374.7 Mbp. Using the integrated physical map pseudomolecules, a comparative genomic analysis was performed to the genomes of Arabidopsis thaliana, Oryza sativa, Vitis vinifera, and Populus trichoptera to identify syntenic genomic regions. Alignment to Arabidopsis resulted in 26 syntenic blocks totaling 40 Mbp, alignment to Oryza resulted in 9 syntenic blocks totaling 56 Mbp, alignment to Vitis resulted in 56 syntenic blocks totaling 345 Mbp, and alignment to Populus resulted in 62 syntenic blocks totaling 390 Mbp. The structural organization of the cacao genome and a comprehensive genome-scale syntenic comparative analysis to Arabidopsis thaliana, Oryza sativa, Vitis vinifera, and Populus trichoptera will be discussed.