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File S1.xlsx (421.24 kB)
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nsgc.gdv.gln.cohort.clean.maf01maxmiss75diploid.beagle_sorted_filt.gt.vcf (1.1 GB)
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File S2.xlsx (990.29 kB)
.GEOJSON
Rahman_et_al_2024_Metadata.geojson (179.91 kB)
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SBATCH_RUN_nsgc_deepvariant_glsnexus.sh (1.36 kB)
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Data from: A global assembly of landrace oat (Avena sativa L.) accessions is a discovery resource for adaptive variation, association mapping, and trait deployment

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posted on 2024-10-28, 21:12 authored by Craig CarlsonCraig Carlson

Oat Landrace Diversity (OLD) Panel phenotypes, genotypes, and metadata from: Rahman et al. (2024) "A global assembly of landrace oat (Avena sativa L.) accessions is a discovery resource for adaptive variation, association mapping, and trait deployment".

"File S1" and "File S2" include population metadata and phenotypic (environmental) data used in association mapping, of which mapping results are listed in "File S3".

"Rahman_et_al_2024_Metadata.geojson" is geographical information of OLD Panel accessions surveyed in this study.

"SBATCH_RUN_nsgc_deepvariant_glsnexus.sh" and "RUN_nsgc_deepvariant_glsnexus.sh" are scripts for variant calling and filtering in SciNet clusters from GBS alignments. IMPORTANT: Do not pull containers in $HOME directory - put them in the main path (for use in SciNet clusters). Google DeepVariant - generates "deepvariant_1.6.0.sif" (RUN: singularity pull docker://google/deepvariant:1.6.0); GLNexus - generates "glnexus_v1.4.1.sif" (RUN: singularity pull docker://google/glnexus:1.4.1). "DeepVariantWGS.yml" is the config file for running GLNexus.

"nsgc.gdv.gln.cohort.clean.maf01maxmiss75diploid.beagle_sorted_filt.gt.vcf" is the final genotype file described in the study.

Funding

USDA-ARS: 3060-21000-046-000-D

USDA-ARS: 2050-21000-034-000-D

History

Data contact name

Carlson, Craig, H.

Data contact email

craig.h.carlson@usda.gov

Publisher

Ag Data Commons

Intended use

This dataset is open to the public.

Temporal Extent Start Date

2024-09-24

Theme

  • Geospatial

Geographic Coverage

{ "type": "FeatureCollection", "features": [ { "type": "Feature", "geometry": { "type": "Polygon", "coordinates": [ [ [-153.00, -42.65], [174.88571, -42.65], [174.88571, 65.00], [-153.00, 65.00], [-153.00, -42.65] ] ] }, "properties": {} } ] }

Geographic location - description

Worldwide. See file: Rahman_et_al_2024_Metadata.geojson for Point locations.

ISO Topic Category

  • climatologyMeteorologyAtmosphere
  • elevation
  • environment
  • geoscientificInformation
  • imageryBaseMapsEarthCover
  • location

Ag Data Commons Group

  • AgBioData

National Agricultural Library Thesaurus terms

landraces; oats; Avena sativa; chromosome mapping; phenotype; genotype; metadata; spatial data; containers; climate change; climate; annuals; grasses; species diversity; ploidy; spring; gluten-free foods; cosmetics; economic valuation; grain crops; genomics; genetic variation; phenotypic variation; genotyping by sequencing; soil properties; quantitative trait loci; cultivars; plant breeding; breeding programs; founder effect

OMB Bureau Code

  • 005:18 - Agricultural Research Service

OMB Program Code

  • 005:040 - National Research

ARS National Program Number

  • 301

ARIS Log Number

419190

Pending citation

  • Yes

Public Access Level

  • Public

Preferred dataset citation

Carlson, Craig. (2024). Data from: A global assembly of landrace oat (Avena sativa L.) accessions is a discovery resource for adaptive variation, association mapping, and trait deployment. DOI: 10.15482/USDA.ADC/27095383

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    Categories

    Keywords

    AdaptationOatsFounder populationGWASQTLFunctional traitsClimate changeLandrace

    Licence

    CC BY 4.0

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