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United States Department of Agriculture

Agricultural Research Service


Location: Subtropical Horticulture Research

2011 Annual Report

4. Accomplishments
1. The Marker Assisted Selection breeding program continues to move forward. Phenotypic and molecular data continued to be collected for all the breeding projects. Fifteen new selections developed in Ecuador with resistance to Witches Broom and Frosty Pod were moved to the quarantine facility in Miami. After release from quarantine these selections will be distributed to breeding programs in West Africa, East Asia and Central and South America for use as parents and testing as clones for resistance to disease. The impact will be superior plants for cocoa breeders.

2. The complete genome of the clone 'Matina 1-6' was assembled, annotated and released in a user friendly database. A 6,000 Single Nucleotide Polymorphism (SNP) chip was designed by Illumina and used on over 1,000 genotypes. Three fully saturated linkage maps were produced using the SNP and Simple Sequence Repeat (SSR) markers, and these were used to complement the genome assembly and to refine the Quantitative Trait Loci areas for Frosty Pod, Witches Broom and Vascular Steak Dieback resistance. These linkage maps will assist cocoa breeders to select clones for major agronomic traits. By implementing the selection for a particular desired trait, it will improve material in the farmers' fields.

Review Publications
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.

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.

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.

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.

Last Modified: 08/16/2017
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