Germplasm Resources and their use in the Genomics Era

The cacao ex situ germplasm resources are distributed in two public germplasm repositories in Trinidad and Costa Rica, as well as in a number of national genebanks, mainly in the Americas. The level of curation of the genetic resources varies considerably from collection to collection. CacaoNet – a network of germplasm managers supported by the Bioversity international is developing a comprehensive system to safeguarding the collection as well as ensuring its effective management and utilization.  Recently, two cacao genome projects have been completed.  The DNA sequencing technologies are advancing at a rapid pace and continuing become cheaper and faster. If the ultimate aim of developing strategies for efficient improvement of cacao is to be realized candidate gene markers should be identified for yield components, biotic and abiotic stress tolerance and quality.  Genome-wide association studies (GWAS) would form the first step in identifying association signals.  The advent of high throughput targeted resequencing technologies with careful DNA pooling can allow the detection of allelic variants associated with extreme phenotypes.  Genome-wide expression patterns through micro-array analysis provide additional opportunities to identify candidate genes associated with extreme phenotypes in populations.  Functional analysis can be carried out using both forward and reverse genetics based on mutants identified in germplasm collections or induced mutations.  The genes identified can be validated in segregating populations and developed in PCR based markers for rapid screening in breeding programmes.  The paper will discuss a coordinated strategy to candidate gene identification for agronomically important traits.