Putting the Cocoa Genome to Work

We announced our intention to map the cocoa genome in 2008 and were very excited to finish the project almost 3 years ahead of schedule.  We received many positive reactions, and hundreds of researchers have now downloaded our open-sourced genome dataset from www.cacaogenomedb.org.  The genome is now public property, and we have registered it so that no part of the sequence can be patented.

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This is particularly important because the primary goal of our genome project has always been to improve the quality of those plants that breeders supply to farmers in diverse geographical regions like Ghana, Côte d’Ivoire and Indonesia.  While our foundational genomics work provided much insight into the genomics of the cacao plant, we still need to refine our understanding of cacao genetics in order to identify and characterize traits that are desirable to both breeders and farmers, who ultimately directly benefit from rapid and accurate molecular genetic trait analysis.

In addition to the laboratory work involved in sequencing a genome, our strategy for cacao improvement also requires the establishment of a series of “clonal plots” – large fields of cloned cocoa trees – that permit the rigorous analysis of the performance and traits of genetically identical trees grown under a controlled environment.  Once the genomes of such clonal varieties are mapped and compared, we will know with higher precision, which particular genes in which specific cacao varieties are associated with desirable traits, such as high productivity and enhanced resistance to critical cacao diseases.

As our project moves into its next phase, we’ve partnered with the Department of Genetics from the Stanford School of Medicine to map the genome of an additional 150 diverse cacao varieties originating from clonal plots all over the world.  This larger sample size will allow us to validate which genes, or combination of genes, affect how a specific trait is expressed.  For example, to identify genes responsible for conferring disease resistance, we will need to study several different clones to confirm that the same gene(s) are consistently associated with enhanced disease resistance.

Once we’ve validated these genes, cocoa breeders, who supply farmers with new tree stock, won’t have to wait several years for trees to mature to know if the positive traits are present.  Instead, breeders will be able to directly, genetically test promising trees as seedlings, to verify that the desirable genes are actually present.   This type of analysis is not only powerful, but it’s also very technically straight-forward (and therefore geographically accessible) because it can be carried out with only an inexpensive PCR machine. Once this next phase of work is completed in the next year or so, cocoa breeders will have a much more extensive and accessible genetic database to use as a reference.

Our research has demonstrated that good planting material alone can roughly triplicate yields, and by extension income, the work we’re doing on the genome will directly contribute to a more sustainable cocoa sector in which farmers are able to enjoy economically viable livelihoods.

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