Genotype variant files for: Harnessing citizen science to contextualize adaptation mechanism discovery
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.
Complete Metadata
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|---|---|
| accessLevel | public |
| bureauCode |
[
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|
| 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 | 2026-01-20 |
| 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 |
