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United States Department of Agriculture

Agricultural Research Service

2013 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 long-term objective of this project is to genetically improve Theobroma cacao L. using a Marker Assisted Selection (MAS) approach. Project objectives that were achieved included the saturation of current linkage maps with Single Nucleotide Polymorphism (SNP) markers, also the development and testing of SNP assays that were used in field breeding programs to determine off-types within clonal cacao populations. Several foreign collaborating scientists from Africa, Asia, South and Central America were trained in molecular marker technology at the USDA-ARS facilities in Miami, FL. In addition, new mapping populations of cacao were developed in Costa Rica, Ecuador, Brazil, Papa New Guinea, and Ghana to identify additional QTL for resistance to BP, WB, FP, incompatibility, productivity and quality traits. Also using marker technology, QTLs for WB and FP resistance from Central and South American germplasm were moved into West African and South Asian breeding populations. Furthermore, association mapping techniques were also used to identify new QTL from non-structured populations from cacao populations in Hawaii. Moreover, the complete assembled and annotated genome of the cacao cultivar 'Matina 1-6' Ver 0.9 was released on September 15, 2010 and the updated version Ver 1.1 has been completed. A cacao genome database ( has been developed and all the sequence information is currently available to the cacao scientific community. Finally, breeding populations were established and evaluated, and MAS projects and field trials were conducted in Costa Rica, Ecuador, Brazil, Ghana, Cameroon, Nigeria, Cote d'Ivoire, and PNG and several superior varieties with disease resistance and quality attributes required by the confectionary industry were released and are currently being planted in cacao producing countries in Africa, Asia, South and Central America.

1. The MAS breeding program continues to move forward. Collection of phenotypic and molecular data continued for all the breeding projects. Twenty six new selections developed in Ecuador with resistance to WB and FP 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. The complete genome of the clone 'Matina 1-6' was assembled, annotated and released in a user friendly database. A 6,000 SNP Illumina chip was designed and used on over 1000 genotypes. Three fully saturated linkage maps were produced using the SNP and SSR markers and these were used to complement the genome assembly and to refine the QTL areas for FP, WB and VSD resistance.

Last Modified: 9/3/2015
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