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Location: Subtropical Horticulture Research

2011 Annual Report

1a. Objectives (from AD-416)
The development and implementation of an international Marker Assisted Selection (MAS) program for cacao is the major objective of this project. This objective involves a combination of hypothesis-driven and non-hypothesis driven research and includes the training of scientists from cacao producing countries in plant breeding, genetics, and the use of molecular markers in a MAS program.

1b. Approach (from AD-416)
Single Nucleotide Polymorphism (SNP)s, both as single base pair substitutions and single base pair insertions/deletions (indels) are the most common sequence differences found between alleles. Methods have been developed for high-throughput detection of SNPs, but these methods require a priori knowledge of the SNP being assayed or sequence information surrounding the SNP. As more cacao EST sequence data become available, we can use it to screen for SNPs. In addition, SNP markers are completely portable and can be added into the growing international database (CocoaGenDB). Microsatellite allele calls are platform-dependent and there has been no way to efficiently share data among the research groups currently genotyping cacao. Once SNPs have been identified, they can be employed in a genetic assay that does not require electrophoresis or a dedicated molecular genetics facility staffed with highly trained technicians. Because breeding trials are established in cacao producing countries where such molecular genetics facilities do not exist, it is imperative to develop high throughput assays that can be performed and analyzed in the field to be able to use the molecular data for Marker Assisted Selection (MAS). Continue with existing field trials in Costa Rica, Ecuador, Brazil, and Ghana assisted by MAS to validate putative resistance to FP, BP, WB, Ceratocystis, CSSV and VSD. Establish new field trials in Cameroon, Ghana, Ivory Coast and Nigeria. Preventative breeding for Frosty Pod (FP) and Witches Broom (WB) in West Africa and South Asia. Using the markers flanking the Quantitative Trait Loci (QTL) for WB resistance on LG 1 and LG 9, selection of seedlings can be made from within families with ‘SCA6’ or ‘SCA12’ as a parent, that contain the genes conferring resistance to WB.

3. Progress Report
The complete assembled and annotated genome of the cacao cultivar 'Matina 1-6' Ver 0.9 was released on September 15, 2010 and the final Ver 1.0 in August 2011. Marker development expanded greatly with the identification of 300,000 potential SNP markers and the production and use of a 6000 SNP chip. Three mapping populations consisting of over 1000 individuals were analyzed using these markers and new saturated recombination maps produced. These saturated recombination maps from ‘UF273’ x ‘P7’, ‘TSH1188’ x ‘CCN51’ and ‘KA2-101’ x ‘K82’ were used to complete the genome assembly. Quantitative trait loci (QTLs) have been re-identified and refined using these saturated maps. In addition marker trait associations were made for self-compatibility, a very important trait affecting pod production and yield. Progress continued in the breeding effort with phenotypic evaluation at all field locations (Ecuador, Costa Rica, Brazil, Ghana, Cameroon, Nigeria, Cote d'Ivoire, and Papua New Guinea). Foreign collaborating scientists from Indonesia, PNG and Nigeria were trained in molecular marker technology in the Miami lab this year.

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.