Nestlé plant scientists, working with leading research institutions, mapped the diversity of cocoa varieties with the goal of supporting the long-term future of chocolate. The project led to a cocoa core collection, a reference set that includes 96 cocoa varieties.

Because it represents over 95% of global cocoa genetic diversity, the collection enables researchers and breeders to identify promising plants more efficiently. It speeds up the search for key traits such as climate resilience, disease tolerance, higher yield and sensory quality.

As climate change, pests, and diseases impact cocoa yields and farmer livelihoods, this work lays a crucial foundation for building a more resilient supply chain.

This research, published in BMC Genomics, was a collaboration between The Pennsylvania State University (Penn State), the Tropical Agricultural Research and Higher Education Center (CATIE), Fox Consultancy, and Nestlé Research. The newly developed core collection includes several high-quality genome sequences generated by Penn State through its longstanding Molecular Biology of Cacao research program. CATIE, based in Costa Rica, also provided access to one of the world’s largest living cacao collections, which includes several genotypes represented in this core collection.

The sequencing data is publicly available via the National Center for Biotechnology Information (NCBI) database, and the corresponding trees are accessible at CATIE, Penn State, and other locations.

The safeguard of the future of cocoa

Cocoa genetic diversity — **Nestlé and research partners map cocoa diversity to safeguard chocolate’s future.**

“Assembling the world’s genetic diversity of cocoa into a well-curated collection, or a ‘Noah’s Ark’ of cocoa diversity, not only makes sense from a conservation point of view,” said Jeroen Dijkman, Head of the Nestlé Institute of Agricultural Sciences. “It will also allow us to uncover key traits that can be used in traditional breeding programs to safeguard the future of cocoa.”

A core collection is a carefully selected group of plant varieties that represents the full range of genetic diversity found in a species. It enables experts to study a smaller, representative sample of varieties without the need to maintain thousands of physical trees, as is typically required.

Patrick Descombes, Senior Expert in Genomics at the Nestlé Institute of Food Safety and Analytical Sciences, explains: “Cocoa is a key ingredient in many of our products, especially chocolate. Yet, the fact that only a small percentage of global cocoa diversity is currently used in commercial production makes its supply chain more vulnerable to a fast-changing world. We leveraged cutting-edge genomic techniques, including deep sequencing of cocoa tree genomes, advanced data analysis, and bioinformatics, to explore genetic similarities and differences across over 300 cocoa varieties and establish this core collection.”

In addition to this research, Nestlé is exploring innovative post-harvest solutions, such as a patented technique that uses underutilized parts of the cocoa pods, like pulp and placenta, to produce cocoa flakes, unlocking more value from the fruit. The company’s sourcing program, known as the Nestlé Cocoa Plan, also plays a key role in sustainable cocoa farming by partnering with farmers and organizations to improve agricultural practices, enhance farmer livelihoods, and ensure responsible sourcing.

All these efforts are part of Nestlé’s broader commitment to strengthening the cocoa supply chain and ensuring that consumers can continue enjoying chocolate for generations to come.