Developing a core collection for the conservation of Theobroma cacao’s genetic diversity

Background: Crop core collections serve as a means of conserving genetic variation and providing a diverse array of accessions for future research and breeding endeavours. Despite the challenges posed by diseases and climate change to global cacao production, no centralized core collection currently exists. To address this gap, we have assembled a new, general-purpose cacao core collection from accessions present in international collections. Results: A dataset of 310 cacao accessions from international collections were selected based on material availability, geographic origin, and known phenotypic characteristics. Population structure analysis of 26,601 single nucleotide polymorphisms (SNPs) from these accessions revealed ten distinct genetic groups, consistent with previous studies. A core collection of 96 accessions was subsequently selected, encompassing 99.6% of the genetic diversity within the dataset. This collection comprises representatives of all ten genetic groups, as well as accessions exhibiting high productivity and pathogen resistance. Conclusions: This core collection will serve as a crucial genetic resource for the cacao community. Cultivating and maintaining the plants from this core collection will contribute to the preservation of genetic diversity within the population. Furthermore, this collection, when combined with appropriate phenotyping, will establish a foundation for novel breeding programs aimed at enhancing crop improvement in the future.