SINGLE NUCLEOTIDE POLYMORPHISM (SNP) RESOURCES FOR CACAO GERMPLASM CHARACTERIZATION
Sustainable Perennial Crops
2009 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 large set of SNP markers defined in expressed genes were identified from EST libraries built by CIRAD from different tissues collected from a diverse group of genotypes, including Trinitario, Criollo, and Upper Amazon Forastero. The first panel of 1536 SNPs, detected in genes with a known or putative function, were used to genotype 500 cocoa accessions representing the global diversity. The result is being evaluated in CIRAD in terms of the classical parameters of genetic diversity and population genetics. Out of the identified SNPs, one hundred of them have been transferred to the Sustainable Perennial Crops Laboratory of USDA/ARS. These 100 SNPs are being evaluated in terms of their suitability for cacao cultivar identification using Sequenorm genotyping platform. The progress of this agreement, which is described in this report, was monitored by site visits, e-mails, and phone or personal communications between the principal investigator and the principal collaborators listed for this project.