{"@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 \u00d7 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>", "distribution": [{"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/60491909", "format": "bcf", "mediaType": "application/x-gzip", "title": "Chr06N_maf0.05_20missing.recode.bcf"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/60491915", "format": "bcf", "mediaType": "application/x-gzip", "title": "Chr04N_maf0.05_20missing.recode.bcf"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/60491921", "format": "bcf", "mediaType": "application/x-gzip", "title": "Chr05K_maf0.05_20missing.recode.bcf"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/60491924", "format": "bcf", "mediaType": "application/x-gzip", "title": "Chr03K_maf0.05_20missing.recode.bcf"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/60491951", "format": "bcf", "mediaType": "application/x-gzip", "title": "Chr01N_maf0.05_20missing.recode.bcf"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/60491987", "format": "bcf", "mediaType": "application/x-gzip", "title": "Chr02N_maf0.05_20missing.recode.bcf"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/60491990", "format": "bcf", "mediaType": "application/x-gzip", "title": "Chr03N_maf0.05_20missing.recode.bcf"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/60491999", "format": "bcf", "mediaType": "application/x-gzip", "title": "Chr09N_maf0.05_20missing.recode.bcf"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/60514001", "format": "bcf", "mediaType": "application/x-gzip", "title": "Chr06K_maf0.05_20missing.recode.bcf"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/60514004", "format": "bcf", "mediaType": "application/x-gzip", "title": "Chr04K_maf0.05_20missing.recode.bcf"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/60514010", "format": "bcf", "mediaType": "application/x-gzip", "title": "Chr07K_maf0.05_20missing.recode.bcf"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/60514013", "format": "bcf", "mediaType": "application/x-gzip", "title": "Chr07N_maf0.05_20missing.recode.bcf"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/60514016", "format": "bcf", "mediaType": "application/x-gzip", "title": "Chr01K_maf0.05_20missing.recode.bcf"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/60514019", "format": "bcf", "mediaType": "application/x-gzip", "title": "Chr08K_maf0.05_20missing.recode.bcf"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/60514022", "format": "bcf", "mediaType": "application/x-gzip", "title": "Chr08N_maf0.05_20missing.recode.bcf"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/60514028", "format": "bcf", "mediaType": "application/x-gzip", "title": "Chr02K_maf0.05_20missing.recode.bcf"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/60514031", "format": "bcf", "mediaType": "application/x-gzip", "title": "Chr09K_maf0.05_20missing.recode.bcf"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/60514034", "format": "bcf", "mediaType": "application/x-gzip", "title": "Chr05N_maf0.05_20missing.recode.bcf"}], "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": {"@type": "org:Organization", "name": "Agricultural Research Service"}, "temporal": "2020-04-01/2025-12-12", "title": "Genotype variant files for: Harnessing citizen science to contextualize adaptation mechanism discovery"}