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Genotype variant files for: Harnessing citizen science to contextualize adaptation mechanism discovery

Published by Agricultural Research Service | Department of Agriculture | Catalog Last Checked: June 12, 2026 at 11:17 PM | Dataset Last Updated: May 27, 2026
Summary: Genome-wide polymorphisms called from publicly-available switchgrass genotype data. These variants are used in a publication under review, Harnessing citizen science to contextualize adaptation mechanism discovery by Tibbs-Cortes et al. The source genotype data was described in Lovell et al. 2021 (https://doi.org/10.1038/s41586-020-03127-1) and is available at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA622568.Genotype data collection: See Lovell et al. 2021 for full description. Briefly, rhizome plug samples from 789 diverse tetraploid switchgrass accessions were sequenced using Illumina HiSeq X10 and Illumina NovaSeq 6000 paired-end sequencing (2 × 150 bp) at HudsonAlpha Institute for Biotechnology and the Joint Genome Institute.Variant calling: The paired-end sequence reads were downloaded from the NCBI SRA. Reads were aligned to the AP13 v5 reference genome with BWA-mem and biallelic polymorphisms were called with bcftools. Polymorphisms with minor allele frequency above 0.05 and missing rate below 20% were retained.Funding acknowledgement: This research used resources provided by the SCINet project and/or the AI Center of Excellence of the USDA Agricultural Research Service, ARS project numbers 0201-88888-003-000D and 0201-88888-002-000D.

Resources

18 resources available

  • Chr06N_maf0.05_20missing.recode.bcf

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  • Chr04N_maf0.05_20missing.recode.bcf

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  • Chr05K_maf0.05_20missing.recode.bcf

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  • Chr03K_maf0.05_20missing.recode.bcf

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  • Chr01N_maf0.05_20missing.recode.bcf

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  • Chr02N_maf0.05_20missing.recode.bcf

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  • Chr03N_maf0.05_20missing.recode.bcf

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  • Chr09N_maf0.05_20missing.recode.bcf

    BCF
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  • Chr06K_maf0.05_20missing.recode.bcf

    BCF
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  • Chr04K_maf0.05_20missing.recode.bcf

    BCF
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  • Chr07K_maf0.05_20missing.recode.bcf

    BCF
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  • Chr07N_maf0.05_20missing.recode.bcf

    BCF
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  • Chr01K_maf0.05_20missing.recode.bcf

    BCF
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  • Chr08K_maf0.05_20missing.recode.bcf

    BCF
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  • Chr08N_maf0.05_20missing.recode.bcf

    BCF
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  • Chr02K_maf0.05_20missing.recode.bcf

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  • Chr09K_maf0.05_20missing.recode.bcf

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  • Chr05N_maf0.05_20missing.recode.bcf

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Complete Metadata
@type dcat:Dataset
accessLevel public
bureauCode 
[
  "005:18",
  "005:20"
]
contactPoint 
{
  "fn": "Li, Xianran",
  "hasEmail": "mailto:xianran.li@usda.gov"
}
description <p dir="ltr">Summary: Genome-wide polymorphisms called from publicly-available switchgrass genotype data. These variants are used in a publication under review, Harnessing citizen science to contextualize adaptation mechanism discovery by Tibbs-Cortes et al. The source genotype data was described in Lovell et al. 2021 (https://doi.org/10.1038/s41586-020-03127-1) and is available at <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA622568" target="_blank">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA622568</a>.</p><p dir="ltr">Genotype data collection: See Lovell et al. 2021 for full description. Briefly, rhizome plug samples from 789 diverse tetraploid switchgrass accessions were sequenced using Illumina HiSeq X10 and Illumina NovaSeq 6000 paired-end sequencing (2 × 150 bp) at HudsonAlpha Institute for Biotechnology and the Joint Genome Institute.</p><p dir="ltr">Variant calling: The paired-end sequence reads were downloaded from the NCBI SRA. Reads were aligned to the AP13 v5 reference genome with BWA-mem and biallelic polymorphisms were called with bcftools. Polymorphisms with minor allele frequency above 0.05 and missing rate below 20% were retained.</p><p dir="ltr">Funding acknowledgement: This research used resources provided by the SCINet project and/or the AI Center of Excellence of the USDA Agricultural Research Service, ARS project numbers 0201-88888-003-000D and 0201-88888-002-000D.</p>
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identifier 10.15482/USDA.ADC/30915350.v1
keyword 
[
  "Panicum virgatum (switchgrass)",
  "adaptation",
  "citizen science",
  "flowering time",
  "phenotypic plasticity"
]
license https://www.usa.gov/publicdomain/label/1.0/
modified 2026-05-27
programCode 
[
  "005:040"
]
publisher 
{
  "name": "Agricultural Research Service",
  "@type": "org:Organization"
}
temporal 2020-04-01/2025-12-12
title Genotype variant files for: Harnessing citizen science to contextualize adaptation mechanism discovery

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