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Data from: Genotypic characterization of the U.S. peanut core collection

PI497426 pods - U.S. Peanut Core Collection

This collection contains supplementary data for the manuscript "Genotypic characterization of the U.S. Peanut Core Collection", which describes genotyping results for the USDA peanut core collection. Each accession was genotyped with the Arachis_Axiom2 SNP array, yielding 14,430 high-quality, informative SNPs across the collection. Additionally, a subset of the core collection was replicated genotyped in replicate, using between two and five seeds per accession to assess heterogeneity within an accession. Supplementary files include: descriptive information about the genotyped accessions, SNP genotype calls in several formats, a phylogenetic tree calculated from the genotype data, Structure analysis, PCA analysis, and comparisons with the diploid progenitors.

This research was co-funded by the National Institute of Food and Agriculture and the National Peanut Board.

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FieldValue
Tags
Arachis hypogaea
peanut
SNPs
PeanutBase
core collection
genotype
U.S. Peanut Core Collection
Arachis_Axiom2 SNP array
np301
Modified
2021-02-25
Release Date
2020-04-07
Identifier
c74db002-cb47-47fd-b8b8-ced13ee0e5bf
Publisher
Ag Data Commons
Spatial / Geographical Coverage Location
Dataset derives from peanut germplasm collected worldwide, with many accessions from South America, Africa, and Asia.
License
U.S. Public Domain
Data Dictionary

https://data.nal.usda.gov/dataset/data-genotypic-characterization-us-pea...
Contact Name
Cannon, Ethy
Contact Email
ethy.cannon@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
Otyama, Paul I. (ORCID)
Kulkarni, Roshan (ORCID)
Chamberlin, Kelly (ORCID)
Ozias-Akins, Peggy (ORCID)
Chu, Ye (Scopus Author ID)
Lincoln, Lori (Scopus Author ID)
MacDonald, Gregory E. (Scopus Author ID)
Anglin, Noelle L. (Scopus Author ID)
Dash, Sudhansu (Scopus Author ID)
Bertioli, David (ORCID)
Fernández-Baca, David (ORCID)
Graham, Michelle (ORCID)
Cannon, Steven B. (ORCID)
Cannon, Ethalinda K.S. (ORCID)
Peer Reviewed
No
Intended Use
This genotype data will be useful for identifying and distinguishing peanut accessions, and for conducting genome-wide association analyses with the U.S. peanut core collection.
Funding Sources
National Institute of Food and Agriculture
2018-67013-28138
Primary Article

Otyama, P. I., Kulkarni, R., Chamberlin, K., Ozias-Akins, P., Chu, Y., Lincoln, L. M., MacDonald, G. E., Anglin, N. L., Dash, S., Bertioli, D. J., Fernández-Baca, D., Graham, M. A., Cannon, S. B., & Cannon, E. K. S. (2020). Genotypic Characterization of the U.S. Peanut Core Collection. G3&Amp;#58; Genes|Genomes|Genetics, 10(11), 4013-4026. https://doi.org/10.1534/g3.120.401306
Dataset DOI (digital object identifier)
10.15482/USDA.ADC/1518508
Product Type
Dataset
FieldValue
OSTI Identifier
ISO Topic(s)
biota
farming
location
National Agricultural Library Thesaurus Term
United States
genotyping
USDA
peanuts
single nucleotide polymorphism arrays
single nucleotide polymorphism
seeds
genotype
phylogeny
diploidy
Arachis hypogaea
Ag Data Commons Keywords
  • Plants & Crops
  • Plants & Crops
  • Traits
  • Genomics & Genetics
  • Genome
  • Genomics & Genetics
  • Genome
  • Genome assembly
Program
AgBioData

Suggested Citations:

(original article) Otyama, P. I., Kulkarni, R., Chamberlin, K., Ozias-Akins, P., Chu, Y., Lincoln, L. M., MacDonald, G. E., Anglin, N. L., Dash, S., Bertioli, D. J., Fernández-Baca, D., Graham, M. A., Cannon, S. B., & Cannon, E. K. S. (2020). Genotypic Characterization of the U.S. Peanut Core Collection. G3&Amp;#58; Genes|Genomes|Genetics, 10(11), 4013-4026. https://doi.org/10.1534/g3.120.401306

(dataset) Otyama, Paul I.; Kulkarni, Roshan; Chamberlin, Kelly; Ozias-Akins, Peggy; Chu, Ye; Lincoln, Lori; MacDonald, Gregory E.; Anglin, Noelle L.; Dash, Sudhansu; Bertioli, David; Fernández-Baca, David; Graham, Michelle; Cannon, Steven B.; Cannon, Ethalinda K.S. (2020). Data from: Genotypic characterization of the U.S. peanut core collection. Ag Data Commons. https://doi.org/10.15482/USDA.ADC/1518508. Accessed 2023-12-09.