Traditional cacao from Peru reveals four new strains

Researchers have identified four new genetic lineages in traditional cacao trees grown in indigenous and Amazonian areas of Peru. The study analyzed 390 Theobroma cacao trees from eight Peruvian departments and used 192 SNP markers to assess genetic identity, differentiation between groups, phylogeny, and ancestry (DOI 10.1371/journal.pone.0351690).

The new populations were associated with four clades. Clade I was named Chuncho 1. Clade II was named Awajun. Clade III was named Porcelana. Clade IV was named Chuncho 2. The data indicate a relationship between these lineages and known genetic groups of cacao. Chuncho 2 showed an association with Contamana. Chuncho 1 showed an association with Púrus. Awajun and Porcelana showed an association with Nacional.

The research evaluated materials from the departments of Amazonas, Ayacucho, Cajamarca, Cusco, Madre de Dios, Piura, San Martín, and Ucayali. The sampled trees were approximately 50 years old, according to traditional knowledge of the farmers. The material represents unimproved traditional lineages and primary wild or semi-wild germplasm.

Genetic mix

Researchers found variable genetic mixing among the materials. The samples contained pure members of the new populations and individuals with ancestry combined with Amelonado, Contamana, Criollo, Curaray, Guiana, Iquitos, Marañon, Nacional, Nanay, and Púrus. The result reinforces the presence of regional diversity in Peruvian cocoa. Each region maintained its own genetic composition, even with genetic relationships between departments.

Four clades comprised 313 of the 390 trees analyzed. This total corresponds to 80,3 percent of the samples. Clade I included 45 samples, mainly from Cusco and Ayacucho. Clade II included 52 samples, predominantly from Amazonas. Clade III included 99 samples, with a strong presence of Amazonas and Piura. Clade IV included 117 samples, predominantly from Cusco and Ayacucho.

The identity analysis found 25 groups of duplicate samples. Most of these groups occurred within the same department. This pattern indicates local propagation of genotypes, possibly due to recurrent use of selected plants by farmers. Piura, Ayacucho, and Cusco concentrated the highest frequency of duplicates.

Database

The study also compared the Peruvian samples with a database from the Cocoa Research Centre at the University of the West Indies. This database contains more than 27 samples from 32 countries. Only one match appeared: sample CCA015, from Condorcanqui, in Amazonas, corresponded to the cultivar CCN 51.

The ancestry of CCN 51 received a new interpretation in the study. The cultivar presented an estimated composition of 15 percent Amelonado, 13 percent Criollo, 25 percent Iquitos, and 45 percent Awajun. According to the researchers, this result changes the interpretation of the genetic origin of the material and relates a significant part of its ancestry to one of the new Peruvian lineages.