Genetic diversity and population structure of fine aroma cacao (Theobroma cacao L.) from north Peru revealed by single nucleotide polymorphism (SNP) markers

Abstract

Cacao (Theobroma cacao L.) is the basis of the lucrative confectionery industry with “fine or flavour” cocoa attracting higher prices due to desired sensory and quality profiles. The Amazonas Region (north Peru) has a designation of origin, Fine Aroma Cacao, based on sensory quality, productivity and morphological descriptors but its genetic structure and ancestry is underexplored. We genotyped 143 Fine Aroma Cacao trees from northern Peru (Bagua, Condorcanqui, Jaén, Mariscal Cáceres, and Utcubamba; mainly Amazonas Region), using 192 single nucleotide polymorphic markers. Identity, group, principal coordinate, phylogenetic and ancestry analyses were conducted. There were nine pairs of matched trees giving 134 unique samples. The only match within 1,838 reference cacao profiles was to a putative CCN 51 by a Condorcanqui sample. The “Peru Uniques” group was closest to Nacional and Amelonado-Nacional genetic clusters based on FST analysis. The provinces of Bagua and Utcubamba were genetically identical (Dest = 0.001; P = 0.285) but differed from Condorcanqui (Dest = 0.016–0.026; P = 0.001–0.006). Sixty-five (49%) and 39 (29%) of the Peru Uniques were mixed from three and four genetic clusters, respectively. There was a common and strong Nacional background with 104 individuals having at least 30% Nacional ancestry. The fine aroma of cacao from Northern Peru is likely due to the prevalent Nacional background with some contribution from Criollo. A core set of 53 trees was identified. These findings are used to support the continuance of the fine or flavour industry in Peru.

Socio‐ecological benefits of fine‐flavor cacao in its center of origin

“…However, this classification still does not adequately describe the existing diversity in cacao. For example in Peru, multiple native fine‐flavor cacao varieties have been recognized at the national level, of which the best known are Chuncho cacao (pertaining to the Contamana genetic group; mostly in the southern Andean foothills of Cusco, e.g., http://www.perupuro.de, https://originalbeans.de), Piura white cacao (Nacional genetic group; in the north‐western coastal plains, e.g., https://cocoarunners.com/grower/norandino/), and Amazonas cacao (of mixed genetic origin, but strong Nacional Piura‐White background; Bustamante et al., 2022). Different cacao varieties exhibit different flavor profiles (Saltini et al., 2013) (http://www.finechocolateindustry.org/about_fine_chocolate.php; http://www.icco.org/fine-or-flavor-cocoa/).…”

“…During the 15th century, the Incas subordinated the “Chachapoyas” to get access to major tropical food resources, including cacao (Díaz‐Valderrama et al., 2020 ). This was likely the native “Cacao Amazonas Peru” variety, which has obtained the status of protected denomination of origin in Peru (Bustamante et al., 2022 ; Ministerium de Desarrollo Agrarian y Rigor, 2021 ). Hence, preference for this variety as well as for Peruvian Chuncho and Nacional Piura‐white cacao is also influenced by farmers’ interest in keeping the endangered cultural heritage of a unique cacao diversity of regional and national importance.…”

Short communication: Opportunities and challenges for Peruvian fine flavored cocoa

“…Entre estas destacan el cacao Chuncho de Cusco, el cacao blanco de Piura y el cacao de Amazonas. Estas variedades no sólo son valoradas por su calidad sensorial, sino también por su importancia cultural y medicinal (Bustamante et al, 2022;Tscharntke et al, 2023). Hoy en día, las variedades nativas de cacao representan una oportunidad única en el mercado, tanto por su calidad como por su historia.…”

“…En el Perú se han reconocido múltiples variedades nativas de cacao con distintos perfiles sensoriales, como el cacao Chuncho en las estribaciones andinas del sur de Cusco, el cacao blanco de Piura (también llamado Porcelana) en las llanuras costeras del noroeste, y el cacao de Amazonas, que muestra una mezcla genética con un fuerte antecedente del cacao blanco de Piura. Estas variedades no sólo destacan por sus sabores únicos, sino que también reflejan la rica diversidad genética del cacao peruano (Bustamante et al, 2022;Oliva-Cruz et al, 2021, 2022) (Figura 2).…”

Atributos morfológicos y sensorialesde cacao nativo, Bagua, Perú

“…fino de aroma, en base a sus peculiares características en cuanto a su sensibilidad de calidad de aroma y sabor (Bustamante et al, 2022).…”