Genomic Exploration of Local Varieties of Theobroma Cacao: A CaseStudy in Tabasco México

Cultivated diversity in Theobroma cacao L. reflects natural differentiation, domestication, human-mediated dispersal, selection, and admixture. This critical narrative review examines advances in population genetics and genomics and evaluates their relevance for local cacao germplasm in Tabasco, Mexico. A structured literature search combined backward citation tracking with metadata verification through publisher records, DOI registries, Crossref, and PubMed. International evidence demonstrates that the conventional Criollo, Forastero, and Trinitario categories inadequately represent population structure. Reference genomes, dense SNP (Single Nucleotide Polymorphism) datasets, structural-variant analyses, genome-wide association studies, genomic prediction, and functional genomics now permit finer examination of ancestry, identity, adaptation, and agronomic traits. Direct evidence from Tabasco remains limited, however, and currently relies on regional sampling with low-density markers. Consequently, local names cannot yet be equated with exclusive genomic lineages. They remain valuable biocultural hypotheses and practical units for participatory inventory. We propose a phased regional strategy that combines farm-based sampling, georeferenced passport data, SNP-based identity control, dense genotyping or whole-genome sequencing of representative subsets, multiyear phenotyping, and integrated on-farm and ex situ conservation. The main constraint is no longer technological availability. It is the absence of a comparable regional baseline linking genome, phenotype, environment, propagation history, and farmer knowledge. Building that baseline would support defensible conservation, reduce redundancy, and create a sound foundation for sustainable cacao improvement in Tabasco.