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Part 1: Document Description
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Citation |
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Title: |
Genotype data for "Oryza glumaepatula: A wild relative to improve drought tolerance in cultivated rice" |
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Identification Number: |
doi:10.7910/DVN/U40WOU |
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Distributor: |
Harvard Dataverse |
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Date of Distribution: |
2023-09-11 |
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Version: |
1 |
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Bibliographic Citation: |
Thathapalli Prakash, Parthiban; Chebotarov, Dmytro; Zhang, Jianwei; Kudrna, David A; Torres, Ronaldo; Natividad, Mignon A; Quintana, Marinell R; Song, Jiaming; Maldonado Londoño, Carlos Ernesto; Hechanova, Sherry Lou; Jena, Kshirod; Wing, Rod; Henry, Amelia, 2023, "Genotype data for "Oryza glumaepatula: A wild relative to improve drought tolerance in cultivated rice"", https://doi.org/10.7910/DVN/U40WOU, Harvard Dataverse, V1 |
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Citation |
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Title: |
Genotype data for "Oryza glumaepatula: A wild relative to improve drought tolerance in cultivated rice" |
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Identification Number: |
doi:10.7910/DVN/U40WOU |
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Authoring Entity: |
Thathapalli Prakash, Parthiban (International Rice Research Institute; University of Illinois at Urbana-Champaign) |
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Chebotarov, Dmytro (International Rice Research Institute) |
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Zhang, Jianwei (Arizona Genomics Institute; National Key Laboratory of Crop Genetic Improvement) |
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Kudrna, David A (Arizona Genomics Institute) |
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Torres, Ronaldo (International Rice Research Institute) |
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Natividad, Mignon A (International Rice Research Institute) |
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Quintana, Marinell R (International Rice Research Institute) |
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Song, Jiaming (Arizona Genomics Institute) |
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Maldonado Londoño, Carlos Ernesto (Arizona Genomics Institute) |
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Hechanova, Sherry Lou (International Rice Research Institute) |
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Jena, Kshirod (International Rice Research Institute) |
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Wing, Rod (Arizona Genomics Institute, Center for Desert Agriculture)) |
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Henry, Amelia (International Rice Research Institute) |
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Software used in Production: |
PLINK (https://www.cog-genomics.org/plink/) |
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Software used in Production: |
GATK |
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Distributor: |
Harvard Dataverse |
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Access Authority: |
Chebotarov, Dmytro |
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Depositor: |
Chebotarov, Dmytro |
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Date of Deposit: |
2023-09-11 |
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Holdings Information: |
https://doi.org/10.7910/DVN/U40WOU |
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Study Scope |
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Keywords: |
Agricultural Sciences, SNP, wild rice, drought |
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Abstract: |
This archive holds single nucleotide polymorphism (SNP) data derived from second-generation sequencing (NGS) of the Oryza glumaepatula panel described in the manuscript below. The SNPs were called against a new Oryza glumaepatula reference genome described in the manuscript (NCBI accession # ALNU03000000 ). The format is binary PLINK format (dataset consists of 3 files: bed,bim,fam files where bin is a SNP map, .fam is a sample information table, and .bed is a binary encoded genotype call matrix) Please refer to PLINK 1.9 documentation for conversion to other formats: https://www.cog-genomics.org/plink/ Two archives are uploaded here: the full 14M SNP dataset, and the subset used for GWAS analysis (785k SNPs) |
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Methodology and Processing |
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Sources Statement |
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Data Access |
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Other Study Description Materials |
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Related Publications |
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Citation |
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Title: |
Parthiban Thathapalli Prakash, Dmytro Chebotarov, Jianwei Zhang, David A Kudrna, Rolando O Torres, Mignon A Natividad, Marinell R Quintana, Jiaming Song, Carlos E Maldonado L, Sherry Lou Hechanova, Kshirod Jena, Rod A Wing, Amelia Henry, Oryza glumaepatula: A wild relative to improve drought tolerance in cultivated rice, Plant Physiology, 2023;, kiad485, https://doi.org/10.1093/plphys/kiad485 doi: 10.1093/plphys/kiad485 |
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Identification Number: |
10.1093/plphys/kiad485 |
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Bibliographic Citation: |
Parthiban Thathapalli Prakash, Dmytro Chebotarov, Jianwei Zhang, David A Kudrna, Rolando O Torres, Mignon A Natividad, Marinell R Quintana, Jiaming Song, Carlos E Maldonado L, Sherry Lou Hechanova, Kshirod Jena, Rod A Wing, Amelia Henry, Oryza glumaepatula: A wild relative to improve drought tolerance in cultivated rice, Plant Physiology, 2023;, kiad485, https://doi.org/10.1093/plphys/kiad485 doi: 10.1093/plphys/kiad485 |
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Label: |
pruned98.bed |
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Text: |
PLINK1.90 binary encoded genotype matrix of the GWAS-ready cleaned genotype dataset |
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Notes: |
application/vnd.realvnc.bed |
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Label: |
pruned98.bim |
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Notes: |
application/octet-stream |
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Label: |
pruned98.fam |
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Notes: |
application/octet-stream |
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Label: |
prefilt2bed.bed |
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Notes: |
application/vnd.realvnc.bed |
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Label: |
prefilt2bed.bim |
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Notes: |
application/octet-stream |
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Label: |
prefilt2bed.fam |
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Notes: |
application/octet-stream |