SINGLE NUCLEOTIDE POLYMORPHISM (SNP) RESOURCES FOR CACAO GERMPLASM CHARACTERIZATION
Sustainable Perennial Crops
2013 Annual Report
1a.Objectives (from AD-416):
1. To develop single nucleotide polymorphism (SNP) resources for the molecular characterization Theobroma cacao germplasm. This approach will utilize cacao accessions that have been shown to have different physiological, morphological and molecular characteristics. Random SNP analysis of the entire genome is hypothesized to greatly facilitate the identification of molecular markers for particular traits of interest. These markers will improve the efficiency and reliability for cacao genotyping and utilization of cacao germplasm in breeding programs. Furthermore, this technology could greatly improve our understanding of the genetic diversity that exists in the cacao population and thus promote rational conservation of cacao genetic resources.
2. To develop genomic and expression bases analyses of Theobroma cacao germplasm.
1b.Approach (from AD-416):
CIRAD actively promotes sustainable cacao production through cacao research. This specific cooperative agreement (SCA) will emphasize the coordination of research approaches of the USDA/ARS and CIRAD and promote the use of new technological breakthroughs such as SNP analysis to improve the utilization and conservation of unique cacao germplasm. The agreement promotes international partnerships and cooperation with the USDA-ARS.
A total of 1560 candidate SNP markers were developed based on the sequences from different cacao organs and were evaluated using a diverse array of cacao germplasm types. Selection was made based on the level of diversity and their distribution across the ten chromosomes in cacao. A subset of 800 was selected and used for cacao genotype identification and diversity analysis. Among these selected SNP markers 144 were adapted for high throughput SNP genotyping. This system is ideal for the identification of mislabeling in cacao breeding programs and germplasm collections. This information will be used by researchers and cacao breeders to improve the accuracy and efficiency in cacao germplasm conservation and utilization. This is the final report for this agreement.