2026-10-13T16:06:52Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33951178 2026-09-21T15:28:04Z category_30563 portal_1059 item_type_3 month_year_09_2026

Supplementary Data S1 for "Sequence-based harmonization of cacao marker resources clarifies coverage of aroma-associated loci" Ezekiel Ahn (6697256) Insuck Baek (13502608) Moon S. Kim (2338096) Sunchung Park (85517) Lyndel W. Meinhardt (11617192) Agricultural, veterinary and food sciences Theobroma cacao coordinate harmonization marker coverage linkage disequilibrium aroma genetics genomic data integration reproducibility <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. Original identifiers and source worksheet names are retained for traceability. No new sequencing reads or phenotype measurements were generated.</p> <p>Nacional G7 and MAF5 are overlapping genotype exports of the same collection, not independent populations. Physical coverage and dosage correlations should not be interpreted as independent validation of aroma effects or the tagging of unobserved causal variants. Resampling ranges describe the sampled comparison distributions rather than biological confidence intervals.</p> <p>This record contains the supplementary dataset only. Analysis and figure-generation code are distributed separately.</p> 2026-09-14T00:00:00Z Dataset Dataset 10.5281/zenodo.22755806 https://figshare.com/articles/dataset/Supplementary_Data_S1_for_Sequence-based_harmonization_of_cacao_marker_resources_clarifies_coverage_of_aroma-associated_loci_/33951178 CC BY 4.0