Supplementary Data S1 for "Sequence-based harmonization of cacao marker resources clarifies coverage of aroma-associated loci"

<p>Supplementary Data S1 accompanying the manuscript “Sequence-based harmonization of cacao marker resources clarifies coverage of aroma-associated loci.”</p> <p>This Excel workbook contains source-derived records and analytical results for evaluating the physical representation of published aroma-associated loci across cacao (<em>Theobroma cacao</em> L.) marker resources. It includes 106 analytical worksheets, together with README, Contents, and Columns sheets describing their organization, provenance, and field definitions.</p> <p>The workbook provides association-record reconciliation, marker identifiers and sequences, reference-guided mapping decisions, original and harmonized SNP coordinates, candidate-gene annotations, fixed-marker coverage comparisons, chromosome-matched marker-count resampling, annotated-gene background comparisons, genotype quality control, and conditional unphased dosage-correlation analyses.

Analytical units include 1,415 distinct master association-peak positions, 804 fruity-subset peak positions, 457 unique candidate genes, and a separately analyzed subset of 453 protein-coding candidates.</p> <p>Primary resources were obtained from the COCOA module of TropGeneDB and the supplementary workbooks of the Nacional fruity-aroma study by Colonges et al. (2022). Reference sequence and annotation were obtained from Ensembl Plants release 62 for the Criollo v2 assembly, GCA_000208745.2.