High-throughput genotyping has revolutionized horticultural breeding, yet the efficient utilization of genomic data remains a bottleneck for germplasm curation and downstream selection. Translating complex genomic information into cost-effective and readily applicable tools for clonally propagated crops requires a shift from maximizing marker density to optimizing information content. Here, we reinterpret cacao (Theobroma cacao L.) genotyping as an information-allocation problem and introduce an information-theoretic framework for designing minimalist, trait-enriched single nucleotide polymorphism (SNP) barcodes. Using a diverse international collection from Trinidad (ICGT) and an independent field trial in Puerto Rico (USDA-ARS Tropical Agriculture Research Station), we compress a 500+ SNP panel into a 32-marker ‘CacaoCipher’ barcode that preserves pairwise genetic distance structure at coarse resolution while retaining trait-aligned signal for pod index and related yield components. Barcode–space axes correlate with agronomic traits measured across environments in a limited overlap subset, supporting the portability of key signals beyond the training setting. We further quantify a heuristic ‘genomic bit budget’, showing how information is allocated across unique identification, ancestry structure, and trait variation. Together, this framework converts cacao germplasm from an analog collection of names into a compact digital code and provides a general template for designing low-cost, high-information marker panels for germplasm quality control and stratified screening in clonally propagated crops.

One-sentence summary

We introduce a ‘genomic bit budget’ framework to design a minimalist 32-SNP barcode that supports germplasm quality control, coarse ancestry screening, and trait-aligned stratification with limited cross-environment portability.

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