Data and code from: Association mapping and genome prediction reveals a complex genetic architecture for resistance to black and frosty pod rot in cacao ( Theobroma cacao L.) populations

This dataset contains genomic and phenotypic data generated from cacao (Theobroma cacao L.) breeding populations evaluated for resistance to black pod rot (Phytophthora spp.) and frosty pod rot (Moniliophthora roreri), two of the most economically important diseases affecting cacao production worldwide. The resource includes genotypic information derived from high-density single nucleotide polymorphism (SNP) markers, phenotypic measurements collected from multi-year field evaluations, and associated trait data related to disease resistance and productivity. Variables are provided in standard tabular formats with accompanying metadata describing genotype identifiers, marker positions, phenotypic traits, disease assessments, and population assignments. All data were generated from plant materials and field evaluations and do not contain personally identifiable information or data from human participants. No special ethical restrictions apply beyond compliance with the terms of use associated with the repository. The dataset is intended to support open, reproducible research and facilitate the development of disease-resistant and productive cacao varieties through data-driven breeding approaches.