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Nestlé and Research Partners Map Cocoa Diversity to Safeguard Chocolate’s Future

In a major step toward protecting the future of chocolate, Nestlé and its research collaborators have created a ‘core collection’ of 96 cocoa varieties that represent more than 95% of the global genetic diversity of the crop

,   and  Anthony Myers
3 min read
Image shows a pile of colourful cocoa pods at the bottom of a tree
The team analysed more than 300 cocoa varieties using deep genome sequencing. Image: cocoaradar.com

A Strategic Move in the Face of Increasing Pressures

With climate change, pests and diseases threatening cocoa yields and the livelihoods of millions of smallholder farmers, the new genetic road map provides what scientists describe as a ‘Noah’s Ark’ of cocoa diversity — making it easier to identify plants with traits such as climate resilience, disease tolerance, higher yield and fine flavour.

“We assembled the world’s genetic diversity of cocoa into a well-curated collection,” said Jeroen Dijkman, Head of the Nestlé Institute of Agricultural Sciences. “It makes sense from a conservation point of view — and it allows us to uncover key traits that can be used in traditional breeding programmes to safeguard the future of cocoa.”

The Science Behind the Collection

The project involved researchers from The Pennsylvania State University (Penn State), the Tropical Agricultural Research and Higher Education Center (CATIE) in Costa Rica, Fox Consultancy and Nestlé Research.

The team analysed more than 300 cocoa varieties using deep genome sequencing, bioinformatics and high-resolution data analysis to map genetic similarities and differences. The result was the identification of 96 varieties that capture nearly the entire genetic landscape of the cocoa species.

The genomic data have been made publicly available through the National Center for Biotechnology Information (NCBI), with additional genetic trees hosted by Penn State, CATIE and other institutions — giving scientists, breeders, and policymakers open access to the findings.

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Why Broader Cocoa Stakeholders Say it Matters

Currently, only a narrow fraction of cocoa’s total genetic diversity is used in commercial production. This limited diversity leaves supply chains extremely vulnerable to fungal pathogens like Fusarium, rising temperatures and increasingly erratic rainfall patterns.

Independent experts told CocoaRadar that a project of this scale has been long overdue.

“Cocoa breeding has historically lagged behind major crops like maize or rice,” said Dr Emmanuelle Boivin, an agricultural geneticist unaffiliated with the project. “Creating a standardised, representative core collection knocks down one of the biggest barriers — fragmented, inaccessible genetic data.”

Climate-risk specialists in West Africa, where about 70 % of the world’s cocoa is grown, echo that view.

“If we want farmers to stay in cocoa, they need access to varieties that can withstand tomorrow’s climate, not yesterday’s,” notes Kwame Owusu, a Ghana-based agronomist. “This type of global genetic work is essential—but it must translate into real planting materials reaching farms.”

Market and Industry Implications

Chocolate-sector analysts say the initiative could help stabilise supply chains that have faced extreme volatility, including historically high cocoa prices driven by crop losses and ageing tree stock.

“Genetic resilience directly affects price stability,” says Maria Lentz, commodity analyst at AgroCon Markets. “If breeding programmes can accelerate the development of hardier cocoa strains, industry players from farmers to major chocolate companies benefit.”

Still, analysts caution that genetic breakthroughs must be paired with investment in distribution, farmer training and long-term sustainability programs.

Nestlé’s Broader Sustainability Agenda

The project aligns with the Nestlé Cocoa Plan, which aims to promote responsible sourcing and support farmer livelihoods. Nestlé is also exploring post-harvest innovations — such as a patented technique that uses under-utilised components of the cocoa pod to create cocoa flakes — unlocking added value and reducing waste.

What Comes Next?

With the core collection established, breeding programmes worldwide can more efficiently identify climate-resilient, disease-tolerant and high-quality cocoa varieties. Whether these advances reach farmers at scale — and how quickly they help stabilise global cocoa supply — will be pivotal to watch.

For the chocolate industry, this marks a significant scientific milestone. For cocoa-producing communities, the real test will be turning genetic potential into tangible resilience on the ground.

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