Genomic Sampling and Population Structure of Farmer-Maintained Varieties Reveal Previously Uncharacterized Diversity of Theobroma cacao L. in Costa Rica.

Understanding crop genetic diversity is essential for conservation and breeding, yet farmer-maintained germplasm remains largely underrepresented in genomic studies. Theobroma cacao L. has a complex domestication history, extensive global diversity, and is currently cultivated in Central America. Costa Rican cacao has been understudied compared to South American and Mexican cultivars despite cultural and historical importance. In this study, we investigate the genetic diversity of cacao from farmer-managed systems across Costa Rica to search for Criollo germplasm while identifying and characterizing unique local genetic groups. Ninety-four trees were sampled for whole genome resequencing from 17 farms across four regions of the country. Farmer materials were analyzed alongside 166 previously characterized reference accessions representing major cacao genetic groups. Population structure analyses, phylogenetic reconstruction, and network approaches revealed that Costa Rican cacao encompasses multiple known genetic groups, including Criollo-derived lineages while also harbouring locally distinct diversity not represented in current global reference collections. Analyses revealed close kinship between many accessions with no clear geographic patterns corresponding to the observed population differentiation, reflecting the influence of farmers in generating the dominant patterns of gene flow through seed-saving, clonal propagation, and sharing of genotypes among farms. Heterozygosity levels varied substantially among individuals, consistent with a mixture of highly inbred Criollo trees and more heterozygous, admixed genotypes. We find that farmer-managed cacao systems are reservoirs of genetic diversity that can include rare or historically important lineages, underscoring the value of these farming systems for effective conservation and management of genomic resources for cacao resilience and improvement.