Nestlé reveals “Noah’s Ark” cocoa mapping venture with key research players

Specialist plant scientists at Nestlé have collaborated with key research institutions in a breakthrough initiative mapping the diversity of cocoa, establishing a “Noah’s Ark” collection of of 96 core varieties, writes Neill Barston.

According to the major food group, the joint project with the Tropical Agricultural Research and Higher Education Centre (CATIE), Fox Consultancy, has accounted for 95% of crop genetic diversity.

Crucially, this will be used towards developing new strains of cocoa that are more hardy in regard to handling climate change, pests and disease, that have had a combined negative major impact on core producing nations including Ghana and Ivory Coast in recent years.

As Confectionery Production has reported over the past two years, the cocoa sector has faced sustained pressure and seen crisis conditions in regard to maintaining stability of supplies.

Indeed, according to the International Cocoa Organisation, last year saw 81% of cocoa supplies in Ghana being affected by swollen shoot virus, which markedly affected the volumes of marketable cocoa. This in turn sparked a price spiral for the commodity, which saw rates of up to $12,000 a tonne being commanded on futures commodities platforms in New York and London.

This has now settled somewhat, to levels of around half that figure, which is still more than double the cost of what was being found on average two years ago in terms of average global prices.

Notably, the 2025 edition of Chocoa in Amsterdam, saw technical presentations that highlighted the potential for crops from South America in particular (some of which are known to be resistant to the invasive swollen shoot virus that has hit West Africa crops), so the latest study on mapping cocoa genetics could potentially help accelerate such work. 

Nestlé’s latest study was published in BMC Genomics, and includes several high-quality genome sequences generated by Penn State through its longstanding Molecular Biology of Cacao research venture. Meanwhile, Catie, based in Costa Rica, also provided access to one of the world’s largest living cacao collections.

Study results
As Nestle noted, 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.

Jeroen Dijkman, Head of the Nestlé Institute of Agricultural Sciences, asserted that the project could have significant impact within the sector.

He said: “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,”   “It will also allow us to uncover key traits that can be used in traditional breeding programs to safeguard the future of cocoa.”

In addition, the company explained that the 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 to make maximum use of cacao pods, for cocoa flake production.

Furthermore, as the business noted, its Cocoa Plan initiative has also helped drive its sustainability credentials in the sector, partnering with key farming organisations to help enhance agricultural worker pay and improve living standards for the sector.