Phenotypic and genetic variation in pataxte (Theobroma bicolor Humb. & Bonpl.) from cacao growing regions from southeastern Mexico

Background: Theobroma bicolor is a relative of cacao that distributes in Mexico. It is considered a semidomesticated species that has been seldom studied. Questions: What levels of genetic and morphological variation can be found in pataxte from cacao growing regions in Mexico? Study species: Theobroma bicolor (Humb. & Bonpl.). Study site and date: Cacao growing regions from the states of Oaxaca, Guerrero, Chiapas and Tabasco, Mexico, 2021-2024. Methods: We collected fruits and leaves for morphological and genetic analyses. For molecular analyses we obtained sequences for four chloroplast and five nuclear regions to estimate genetic diversity and genetic structure. For morphological analyses, we calculated the mean and standard deviation of fruit and leaf morphological traits and obtained violin plots to observe the distribution and density of the data. We also conducted principal component analyses for fruit and leaf morphological traits. Results: No genetic variation was found among the analyzed DNA regions. Nonetheless, regarding morphological traits, our data suggest morphological variation in leaves and fruit across cacao growing regions in Mexico. Conclusions: The lack of genetic variation Theobroma bicolor may be explained by its population history. Morphological variation may be present between cacao growing regions, but additional samples are required to test this hypothesis. Implementing genotyping by sequencing or a whole genome sequencing approach will allow analyzing genome wide genetic diversity. Genotype, phenotype and environmental interactions should also be considered in future studies to inform management in terms of seed exchange and plant selection.