Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids
Cite this dataset:
Njuguna, Joyce; Clark, Lindsay; Lipka, Alexander; Anzoua, Kossonou; Bagmet, Larisa; Chebukin, Pavel; Dwiyanti, Maria; Dzyubenko, Elena; Dzyubenko, Nicolay; Ghimire, Bimal; Jin, Xiaoli; Johnson, Douglas; Kjeldsen, Jens; Nagano, Hironori; Oliveira, Ivone; Peng, Junhua; Petersen, Karen; Sabitov, Andrey; Seong, Eun; Yamada, Toshihiko; Yoo, Ji; Yu, Chang; Zhao, Hu; Munoz, Patricio; Long, Stephen; Sacks, Erik (2023): Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4829913_V2
Use this persistent URL to link to this dataset:
Dataset Description

This dataset contains all data used in the paper "Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids". The dataset includes genotypes and phenotypic data from two autotetraploid species Miscanthus sacchariflorus and Vaccinium corymbosum that was used used for genome wide association studies and genomic prediction and the scripts used in the analysis.

In this V2, 2 files have the raw data are added:

"Miscanthus_sacchariflorus_RADSeq.vcf" is the VCF file with the raw SNP calls of the Miscanthus sacchariflorus data used for genotype calling using the 6 genotype calling methods.

"Blueberry_data_read_depths.RData" is the a RData file with the read depth data that was used for genotype calling in the Blueberry dataset.
Subject Life Sciences
Keywords Polyploid; allelic dosage; Bayesian genotype-calling; Genome-wide association; Genomic prediction
License CC BY
Funder U.S. Department of Energy (DOE)-Grant:DE-SC0012379
Funder U.S. Department of Energy (DOE)-Grant:DE-SC0018420
Funder U.S. National Science Foundation (NSF)-Grant:1661490
Corresponding Creator Erik Sacks
Downloaded 101 times
Version DOI Comment Publication Date
2 10.13012/B2IDB-4829913_V2 Added 2 new files: Blueberry_data_read_depths.RData and Miscanthus_sacchariflorous_RADSeq.vcf 2023-07-05
1 10.13012/B2IDB-4829913_V1 2023-03-30
Open in Globus File Manager what's this?
4.86 KB File
138 KB File
1.42 GB File
71.6 KB File
1.51 GB File
530 MB File
491 MB File
1.51 GB File
530 MB File
491 MB File
1.42 KB File
3.26 KB File
15.8 KB File
5.86 GB File
1.51 GB File
1.51 GB File
18.3 KB File
1.51 GB File
1.51 GB File
530 MB File
491 MB File
530 MB File
491 MB File
530 MB File
491 MB File
530 MB File
491 MB File

Contact the Research Data Service for help interpreting this log.

RelatedMaterial create: {"material_type"=>"Article", "availability"=>nil, "link"=>"https://doi.org/10.1002/tpg2.20401", "uri"=>"10.1002/tpg2.20401", "uri_type"=>"DOI", "citation"=>"Njuguna, J. N., Clark, L. V., Lipka, A. E., Anzoua, K. G., Bagmet, L., Chebukin, P., Dwiyanti, M. S., Dzyubenko, E., Dzyubenko, N., Ghimire, B. K., Jin, X., Johnson, D. A., Kjeldsen, J. B., Nagano, H., de Bem Oliveira, I., Peng, J., Petersen, K. K., Sabitov, A., Seong, E. S., … Sacks, E. J. (2023). Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids. The Plant Genome, 00, e20401. https://doi.org/10.1002/tpg2.20401", "dataset_id"=>2535, "selected_type"=>"Article", "datacite_list"=>"IsSupplementTo", "note"=>nil, "feature"=>nil} 2023-11-03T14:50:57Z
RelatedMaterial update: {"note"=>[nil, ""], "feature"=>[nil, false]} 2023-11-03T14:50:57Z
RelatedMaterial update: {"note"=>[nil, ""], "feature"=>[nil, false]} 2023-11-03T14:50:57Z
RelatedMaterial update: {"uri"=>["", "10.1534/genetics.118.301468"], "uri_type"=>["", "DOI"], "datacite_list"=>["", "IsSupplementedBy"], "note"=>[nil, ""], "feature"=>[nil, false]} 2023-11-03T14:50:57Z
RelatedMaterial update: {"uri"=>["", "10.1093/bioinformatics/btx587"], "uri_type"=>["", "DOI"], "datacite_list"=>["", "IsSupplementedBy"], "note"=>[nil, ""], "feature"=>[nil, false]} 2023-11-03T14:50:57Z
RelatedMaterial update: {"uri"=>["", "10.1534/g3.118.200913"], "uri_type"=>["", "DOI"], "datacite_list"=>["", "IsSupplementedBy"], "note"=>[nil, ""], "feature"=>[nil, false]} 2023-11-03T14:50:57Z
RelatedMaterial update: {"uri"=>["", "10.13012/B2IDB-8170405_V1"], "uri_type"=>["", "DOI"], "datacite_list"=>["", "IsSupplementedBy"], "note"=>[nil, ""], "feature"=>[nil, false]} 2023-11-03T14:50:57Z
RelatedMaterial update: {"uri"=>["", "10.13012/B2IDB-0170190_V3"], "uri_type"=>["", "DOI"], "datacite_list"=>["", "IsSupplementedBy"], "note"=>[nil, ""], "feature"=>[nil, false]} 2023-11-03T14:50:57Z
RelatedMaterial update: {"uri"=>["", "10.5061/dryad.8pk0p2nk9"], "uri_type"=>["", "DOI"], "datacite_list"=>["", "IsSupplementTo"], "note"=>[nil, ""], "feature"=>[nil, false]} 2023-11-03T14:50:57Z
Creator update: {"family_name"=>["Lipka ", "Lipka"], "identifier"=>["", "0000-0003-1571-8528"]} 2023-07-05T21:09:59Z