As the source of chocolate, cacao has become one of the most important crops in the world.
The identification of molecular markers to understand the demographic history, genetic diversity
and population structure plays a pivotal role in cacao breeding programs. Here, we report the
use of a modified genotyping-by-sequencing (GBS) approach for large-scale single nucleotide
polymorphism (SNP) discovery and allele ancestry mapping. We identified 12,357 bi-allelic
SNPs after filtering, of which, 7,009 variants were ancestry informative. The GBS approach
proved to be rapid, cost-effective, and highly informative for ancestry assignment in this species
