Three de novo assembled wild cacao genomes from the Upper Amazon

Theobroma cacao, the chocolate tree, is indigenous to the Amazon basin, the greatest biodiversity hotspot on earth. Recent advancement in plant genomics highlights the importance of de novo sequencing of multiple reference genomes to capture the genome diversity present in different cacao populations. In this study, three high-quality chromosome-level genomes of wild cacao were constructed, de novo assembled with HiFi long reads sequencing, and scaffolded using a reference-free strategy. These genomes represent the three most important genetic clusters of cacao trees from the Upper Amazon region. The three wild cacao genomes were compared with two reference genomes of domesticated cacao. The five cacao genetic clusters were inferred to have diverged in the early and middle Pleistocene period, approximately 1.83-0.69 million years ago. The results shown here serve as an example of understanding how the Amazonian biodiversity was developed. The three wild cacao genomes provide valuable resources for studying genetic diversity and advancing genetic improvement of this species.

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

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.