Cacao and arbuscular mycorrhizal fungi : Breeding prospects

Cacao (Theobroma cacao) has been cultivated in Panama since at least 1500 BC, predominantly within traditionally managed agroforestry systems overseen by Indigenous communities. Despite this long history and the country’s strategic biogeographical position for cacao semi-domestication, the genetic identity of cacao cultivated in Panama and the management practices shaping it remain poorly documented. This research provides the first comprehensive characterization of cacao germplasm used across Panamanian farms while integrating environmental, agronomic, and microbial dimensions to understand how plant genetics and soil biota jointly influence cacao production. Across 16 farms in the provinces of Bocas del Toro and Herrera, we collected leaf and root samples from five trees per farm and genotyped them using a 96-SNP array. We also recorded detailed management practices and environmental variables, including soil nutrients and physiographic conditions. Cacao genetic diversity in Bocas del Toro displayed extensive admixture, representing all major cacao genetic groups, whereas farms in Herrera were dominated by Amelonado and Criollo germplasm, including individuals with pure Criollo ancestry. Limited germplasm exchange between provinces contributed to these distinct genetic compositions. While seed propagation was common nationwide, grafting frequency varied substantially, being more prevalent in Bocas del Toro (55%) than in Herrera (16%). These findings reveal Panama’s unrecognized cacao genetic diversity and underline its potential for strengthening national cacao improvement programs. Because cacao is a mycotrophic species reliant on belowground symbioses, we also assessed how genotypic and environmental variables shape arbuscular mycorrhizal fungal (AMF) communities associated with the sampled trees. Using molecular AMF community profiling, paired with analyses of scion and rootstock genotypes, root traits, and soil chemistry, we found that Glomus was the dominant AMF genus across all sites. AMF community structure was significantly influenced by scion genotype, root nutrient concentrations (N and P), elevation, and available soil P, whereas rootstock genotype and root morphological traits were not major determinants. High between-farm variation highlighted the sensitivity of AMF communities to local environmental contexts. These results underscore the importance of considering both host genetics and soil chemistry when designing strategies to optimize plant–fungal mutualisms in cacao agroforestry. To further explore opportunities for breeding cacao cultivars with improved symbiotic performance, we evaluated selfed progenies of three cacao clones previously selected for high yield and bean quality. Progenies were grown under four distinct AMF inocula representative of Panama’s environmental gradients, plus a non-inoculated control. Significant main effects of both AMF treatments and progeny identity were detected for aboveground biomass, with interactive effects between AMF communities and progenies. Root nitrogen content and diameter varied significantly among progenies and mycorrhizal treatments, while root tissue density and specific root length differed primarily among mycorrhizal treatments. These findings emphasize the relevance of root functional traits in mediating cacao–AMF interactions and highlight the potential to breed cacao varieties optimized for beneficial symbioses. Collectively, this research provides an integrated perspective on cacao genetic diversity, traditional management, AMF communities, and root functional traits in Panama, offering actionable insights for sustainable cacao agroforestry and future cacao improvement initiatives.