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Data from: Genetic variation among 481 diverse soybean accessions

This data is from the manuscript titled: "Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing". SNP calls were obtained from resequencing 481 diverse soybean lines comprising 52 wild (Glycine soja) and 429 cultivated (Glycine max). This dataset contains 6 gzipped VCF (Variant Call Format) files with variant calls for all 481 USB accessions, all G. max accessions, G. soja accessions, accessions sequenced at 15x coverage, accessions sequenced at 40x coverage, and 106 accessions re-sequenced from a previous study (Valliyodan et al. 2016). SNPs were called using the Haplotype caller algorithm from the Genome Analysis Toolkit (GATK) version gatk-2.5-2-gf57256b. A total of 7.8 million SNPs were identified between the 481 re-sequenced accessions. SNPs were assigned IDs using the script "assign_name.awk" available at https://github.com/soybase/SoySNP-Names. SNP effects were predicted using SnpEff 3.0.

Dataset also available at https://soybase.org/data/v2/Glycine/max/diversity/Wm82.gnm2.div.Valliyod...

Funding support provided by the United Soybean Board for the large-scale sequencing of soybean genomes (project #1320-532-5615), Bayer (previously Monsanto and Bayer), and Corteva (previously Dow AgroSciences), with in-kind support for analysis from USDA Agricultural Research Service project 5030-21000-069-00-D.

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FieldValue
Tags
soybean
genetic variation
SNPs
resequencing
SoyBase
np301
Modified
2022-06-01
Release Date
2020-02-27
Identifier
c816b299-60fd-47a4-8a6a-4ad1e7285daf
Publisher
Ag Data Commons
License
U.S. Public Domain
Data Dictionary

https://data.nal.usda.gov/dataset/data-genetic-variation-among-481-diver...
Contact Name
Brown, Anne V.
Contact Email
anne.brown@usda.gov
Public Access Level
Public
Program Code
005:040 - Department of Agriculture - National Research
Bureau Code
005:18 - Agricultural Research Service
Extended Metadata: 
FieldValue
Authors
Valliyodan, Babu (ORCID)
Brown, Anne V. (ORCID)
Cannon, Steven B. (ORCID)
Nguyen, Henry (ORCID)
Peer Reviewed
No
Intended Use
To study genetic variation in diverse soybean accessions and can be used in future genome wide association studies.
Funding Sources
United Soybean Board
1320-532-5615
Bayer CropScience
Agricultural Research Service
5030-21000-069-00-D
Primary Article

Valliyodan, B., Brown, A. V., Wang, J., Patil, G., Liu, Y., Otyama, P. I., Nelson, R. T., Vuong, T., Song, Q., Musket, T. A., Wagner, R., Marri, P., Reddy, S., Sessions, A., Wu, X., Grant, D., Bayer, P. E., Roorkiwal, M., Varshney, R. K., … Nguyen, H. T. (2021). Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing. Scientific Data, 8(1). https://doi.org/10.1038/s41597-021-00834-w
Method Citation

Valliyodan, B., Brown, A. V., Wang, J., Patil, G., Liu, Y., Otyama, P. I., Nelson, R. T., Vuong, T., Song, Q., Musket, T. A., Wagner, R., Marri, P., Reddy, S., Sessions, A., Wu, X., Grant, D., Bayer, P. E., Roorkiwal, M., Varshney, R. K., … Nguyen, H. T. (2021). Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing. Scientific Data, 8(1). https://doi.org/10.1038/s41597-021-00834-w
Dataset DOI (digital object identifier)
10.15482/USDA.ADC/1518301
Product Type
Dataset
Cites Other Datasets
SoyBase and the Soybean Breeder's Toolbox
Related Content
soybase.org - Glycine max diverse accessions
FieldValue
ARIS Log Number
371638
OSTI Identifier
ISO Topic(s)
biota
farming
National Agricultural Library Thesaurus Term
genetic variation
soybeans
genomics
single nucleotide polymorphism
data collection
haplotypes
algorithms
sequence analysis
Glycine max
Glycine soja
Ag Data Commons Keywords
  • Plants & Crops
  • Plants & Crops
  • Traits
  • Genomics & Genetics
  • Genomics & Genetics
  • Sequence Assembly

Suggested Citations:

(original article) Valliyodan, B., Brown, A. V., Wang, J., Patil, G., Liu, Y., Otyama, P. I., Nelson, R. T., Vuong, T., Song, Q., Musket, T. A., Wagner, R., Marri, P., Reddy, S., Sessions, A., Wu, X., Grant, D., Bayer, P. E., Roorkiwal, M., Varshney, R. K., … Nguyen, H. T. (2021). Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing. Scientific Data, 8(1). https://doi.org/10.1038/s41597-021-00834-w

(dataset) Valliyodan, Babu; Brown, Anne V.; Cannon, Steven B.; Nguyen, Henry (2020). Data from: Genetic variation among 481 diverse soybean accessions. Ag Data Commons. https://doi.org/10.15482/USDA.ADC/1518301. Accessed 2023-12-07.