In an analysis of 390 traditionally cultivated cacao trees representing traditional Amazonian varieties, researchers identified four previously unknown genetic lineages, with two showing ancestry linked to exceptional flavor potential and offering new opportunities for growers and chocolate makers.
Motilal et al. collected cacao samples from eight departments of Peru. Image credit: Fernando Graniel.
Cacao (Theobroma cacao), an outcrossing understorey tree species native to the Amazon basin, holds significant economic value due to its beans.
These beans serve as the primary raw material for the multibillion dollar chocolate industry and are also used in various food and cosmetic products, making cocoa beans a vital agricultural commodity.
Cacao cultivation remains a crucial income source for millions of small-scale farmers in tropical areas, playing a pivotal role in global trade and the economies of producer nations.
In Peru, the eighth-largest cocoa producer, more than 80,000 farming families relied on cocoa cultivation as of 2024.
Many Peruvian farms grow wild and semi-wild cacao varieties that have not been significantly altered by such means as selective breeding or genetic engineering.
Prior research suggests that indigenous cacao trees farmed in Peru and other countries can be categorized into 10 groups, based on their genetic similarity to each other. Individual trees may represent a pure group or a combination of various groups.
However, more recent research has challenged the 10-group framework, and few studies have focused specifically on Peru.
In a new study, Dr. Lambert Motilal from the Cocoa Research Centre at the University of the West Indies, St. Augustine in Trinidad and Tobago and colleagues analyzed the genetic diversity of 390 wild and semi-wild cacao trees grown on indigenous farms in various regions across Peru.
Specifically, they focused single-nucleotide polymorphisms (SNPs), single-letter differences between individual trees’ DNA code that help to illuminate their genetic diversity and relationship to each other, enabling categorization into genetically similar groups.
The analysis revealed four previously unidentified genetic groups, in addition to the 10 already known. Some of the analyzed trees fell into one pure group, while others were mixes.
The scientists found that different regions of Peru had their own, distinct genetic signatures, highlighting fine-scale geographic differences in the genetic composition of farmed cacao trees.
Two of the four groups have ancestry that suggests they might produce especially high-quality, well-flavored beans, according to the researchers.
The analysis also helped to clarify the ancestry of a particular cacao variety known as CCN 51, which was deliberately cultivated for high yield and disease resistance and is increasingly economically important.
The findings suggest that Peru harbors unique genetic resources that could be explored for valuable traits for the cacao and chocolate market.
“Our research reveals that while Peru’s cacao trees share a common genetic thread across the country, each region harbors a unique genetic signature and we’ve successfully pinpointed four entirely new cacao lineages,” the authors said.
“This blueprint not only reshapes our understanding of Peru’s genetic landscape but provides a tangible new resource for conservation and the fine flavor chocolate industry.”
“One of the most rewarding aspects was working directly with Indigenous on-farm trees across eight vastly different departments, from the Amazonas lowlands to the Andean foothills.”
“It was eye-opening to realize that these invaluable genetic treasures weren’t locked away in a lab.”
“They were literally growing in farmers’ backyards, waiting to be characterized and valued for the premium market.”
The results appear this week in the journal PLoS ONE.
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L.A. Motilal et al. 2026. Genetic structure of traditional cacao reveals four new genetic lineages in indigenous Amazonian sites in Peru. PLoS One 21 (7): e0351690; doi: 10.1371/journal.pone.0351690
