Illinois Data Bank - Dataset

Improving precision and accuracy of genetic mapping with genotyping-by-sequencing data in outcrossing species
Cite this dataset:
LaBonte, Nicholas R.; Zerpa-Catanho, Dessiree P.; Liu, Siyao; Xiao, Liang; Dong, Hongxu; Clark, Lindsay V.; Sacks, Erik J. (2024): Improving precision and accuracy of genetic mapping with genotyping-by-sequencing data in outcrossing species. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1435220_V1
Dataset Description

This dataset contains all data and supplementary materials from "Improving precision and accuracy of genetic mapping with genotyping-by-sequencing data in outcrossing species". An Excel file a list of all QTLs and linkage group length (in cM) obtained with two different SNP-calling methods (Tassel-Uneak and Tassel-GBS), genetic map-construction method (linkage-only and reference order-corrected) and depth filters (12x, 20x, 30x and 40x) for genetic mapping of 18 biomass yield traits in a biparental Miscanthus sinensis population using RAD-Seq SNPs is provided as "Supplementary file 1". A Perl script with the code for filtering VCF and HapMap-formatted data files is provided as “Supplementary file 2”. Phenotype data used for QTL mapping is provided as “Supplementary File 3”. A Perl script with the code for the simulation study is provided as “Supplementary file 4”.
Subject Life Sciences
Keywords HapMapParser; GenotypingSimulator
License CC0
Funder U.S. Department of Energy (DOE)-Grant:DE-SC0018420
Funder U.S. Department of Agriculture (USDA)-Grant:2019-67012-29628
Corresponding Creator Erik J. Sacks
Downloaded 38 times
Version DOI Comment Publication Date
1 10.13012/B2IDB-1435220_V1 2024-07-31

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Dataset update: {"publication_state"=>["file embargo", "released"]} 2024-07-31T13:00:07Z
Dataset update: {"publication_state"=>["released", "file embargo"]} 2024-06-13T19:02:17Z
Dataset update: {"publication_state"=>["file embargo", "released"]} 2024-06-13T19:02:17Z
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RelatedMaterial update: {"uri"=>["", "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA273067"], "uri_type"=>["", "URL"], "citation"=>["Liu, S., Clark, L.V., Swaminathan, K., Gifford, J.M., Juvik, J.A. and Sacks, E.J. (2016), High-density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe. GCB Bioenergy, 8: 616-630. https://doi.org/10.1111/gcbb.12275", "Sequencing data from this study"], "datacite_list"=>["", "IsSupplementedBy"]} 2024-06-13T19:02:16Z
Dataset update: {"publication_state"=>["released", "file embargo"]} 2024-05-09T21:10:40Z
Dataset update: {"publication_state"=>["file embargo", "released"]} 2024-05-09T21:10:39Z
RelatedMaterial update: {"uri"=>[nil, ""], "uri_type"=>[nil, ""], "datacite_list"=>[nil, ""], "note"=>[nil, ""]} 2024-05-09T21:10:38Z
Dataset update: {"version_comment"=>[nil, ""], "subject"=>[nil, "Life Sciences"]} 2024-05-09T21:10:38Z