In a comprehensive study of 390 traditional cacao trees representing Amazonian varieties, researchers discovered four previously unidentified genetic lineages. Notably, two of these lineages exhibited ancestry linked to exceptional flavor potential, opening up new avenues for growers and artisanal chocolate makers.
Motilal et al. Cacao samples were collected from eight departments in Peru. Image credit: Fernando Granier.
Cacao (Theobroma cacao) is a valuable outcrossed understory tree species native to the Amazon basin, primarily known for its economically significant beans.
These beans are essential in the multibillion-dollar chocolate industry and are utilized in various food and cosmetic applications, making cocoa an important agricultural commodity.
Cacao farming is a vital livelihood for millions of smallholder farmers in tropical regions and plays a critical role in global trade and the economies of producing nations.
In Peru, the world’s 8th largest cocoa producer, over 80,000 farmers rely on cocoa production as of 2024.
Many farms in Peru cultivate wild and semi-wild cacao varieties that have remained largely unchanged by breeding or genetic engineering.
Prior research indicated that native cacao trees in Peru and other countries can be classified into 10 genetic groups based on their similarities. Each tree may belong to a pure group or a combination of several groups.
However, recent studies have challenged this 10-group framework, with few focused specifically on Peru.
In a groundbreaking study, Dr. Lambert Motilal of the Cocoa Research Center at the University of St. Augustine of the West Indies, alongside colleagues, examined the genetic diversity of 390 wild and semi-wild cacao trees from indigenous farms across various Peruvian regions.
The researchers concentrated on single nucleotide polymorphisms (SNPs)—single-letter variations in the DNA of individual trees—to assess genetic diversity and relationships, thus categorizing them into genetically similar groups.
This analysis unveiled four previously unrecognized genetic groups in addition to the existing ten. While some trees were classified into pure groups, others were mixed.
Findings revealed that different areas of Peru exhibit unique genetic traits, showcasing fine-scale geographical variations in the genetic structure of cultivated cacao trees.
Remarkably, two of the four newly identified groups possess ancestry suggesting they may yield particularly high-quality, flavorful beans, according to the researchers.
This research also shed light on the ancestry of a notable cacao variety known as CCN51, which is cultivated for its high yields and disease resistance, gaining increasing economic significance.
The results indicate that Peru possesses unique genetic resources ripe for exploration regarding desirable traits in the cocoa and chocolate industries.
“Our study highlights that while Peru’s cacao trees share a common genetic foundation, each region maintains a distinct genetic identity, allowing for the identification of four entirely new cacao lineages,” the authors stated.
“This research not only transforms our understanding of Peru’s genetic landscape but also equips us with invaluable resources for conservation and the premium chocolate market.”
“One particularly rewarding aspect was engaging directly with trees on indigenous farms spanning eight diverse sectors, from the lush lowlands of Amazonas to the Andean foothills.”
“It was enlightening to realize these invaluable genetic treasures are not confined to laboratory settings but are genuinely thriving in farmers’ backyards, awaiting proper characterization and value for the premium market.”
Findings are part of a study featured in this week’s issue of PLoS ONE.
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LA Motilal et al. 2026. The genetic structure of traditional cacao reveals four new genetic lineages in indigenous regions of the Peruvian Amazon. PLoS One 21 (7): e0351690; doi: 10.1371/journal.pone.0351690
Source: www.sci.news
