VEVEY, Switzerland — Nestlé and a group of research partners said Nov. 24 they have built a cocoa diversity map that condenses hundreds of cacao samples into a 96-variety “core collection” capturing 99.6% of the genetic breadth within a major research dataset. Using genome sequencing and data analysis, the team said the approach should speed the hunt for trees with traits such as heat tolerance, disease tolerance, yield and sensory quality as climate change and pests threaten production, Nov. 24, 2025.
In Nestlé’s announcement, the company said the map reflects more than 95% of global cocoa genetic diversity and is meant to make breeding research more efficient by focusing work on a smaller set of representative trees.
What the cocoa diversity map shows
The peer-reviewed science behind the cocoa diversity map was published Oct. 8 in BMC Genomics. Researchers analyzed 310 cacao accessions from international collections using 26,601 single-nucleotide polymorphisms, identified 10 distinct genetic groups and selected a 96-accession core set that retained 99.6% of the genetic diversity within the dataset while representing all 10 groups.
Nestlé said partners included The Pennsylvania State University, the Tropical Agricultural Research and Higher Education Center, known as CATIE, Fox Consultancy and Nestlé Research. CATIE, which maintains one of the world’s largest living cacao collections, said in its project summary that the smaller reference collection is intended to help researchers and breeders identify climate-resilient and disease-tolerant material more quickly.
Nestlé framed the effort as both conservation and supply-chain risk management. Jeroen Dijkman, head of the Nestlé Institute of Agricultural Sciences, compared the project to a “Noah’s Ark” approach to preserving cocoa diversity. Patrick Descombes, a senior expert in genomics at the Nestlé Institute of Food Safety and Analytical Sciences, said “only a small percentage of global cocoa diversity is currently used in commercial production,” a concentration that can leave supply chains exposed when weather extremes or disease outbreaks hit a popular cultivar.
How the cocoa diversity map builds on earlier cocoa genomics
The “10 genetic groups” referenced in the new core collection echo a shift that began nearly two decades ago. A 2008 PLoS ONE paper proposed a classification of cacao germplasm into 10 major genetic clusters, moving beyond the older Criollo/Forastero/Trinitario shorthand and giving breeders a clearer way to track diversity.
A few years later, a 2011 Nature Genetics study published a draft cacao genome, giving researchers a roadmap for linking genetic markers to traits that matter to farmers and chocolate makers. The cocoa diversity map builds on that foundation, but packages it into a working reference set meant to be easier to maintain, share and use in targeted breeding programs.
Even so, a map is not a new tree in the ground. Field trials and regulatory steps can take years, and adoption depends on farmer training, nursery capacity and the economics of replanting. Industry coverage has described the cocoa diversity map as a long-term tool that will likely need to be paired with strong on-farm support to translate genetic gains into steadier harvests, as reported by Baking Business.</p
