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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.
- Data dictionarytxt Dataset data dictionary
Description of all files in this Dataset. Changes were made to this file on...
MD5:Explore Data4.44 KB - Main descriptive information about genotyped accessionsxlsx
The main descriptive information about the genotyped accessions, including:...
MD5:Explore Data586.73 KB - SNPs as called by the Axiom suite Data
The original genotype calls for the Axiom array (for poly-high resolution...
MD5:Explore Data4.13 MB - Genotyping calls in VCF formatData
The Axiom array genotype calls, in VCF format. Changes were made to this...
MD5:Explore Data3.38 MB - DNA variants for all accessions, including from genome assemblies, in TSV formatData
The predominant DNA variants at each SNP location, for all accessions,...
MD5:Explore Data5.47 MB - DNA variants for all accessions, including from genome assemblies, in fasta formatData
The predominant DNA variants at each SNP location, for all accessions,...
MD5:Explore Data2.92 MB - Base-calls for selected accessions, relative to A- and B-genome progenitorsxlsx
DNA base-calls for 16 selected, diverse accessions, with comparisons to the...
MD5:Explore Data25.78 MB - Reduced fasta alignments, at 98% identityData
Reduced fasta alignments (relative to the complete alignment file, S5). File...
MD5:Explore Data1.37 MB - Reduced fasta alignments, at 99% identityData
Reduced fasta alignments (relative to the complete alignment file, S5). File...
MD5:Explore Data1.72 MB - Phylogenetic tree of genotype dataData
Phylogenetic tree (Newick format) calculated from the alignent in S5, and...
MD5:Explore Data18.63 KB - Structure membership breakdownpdf
The proportion of accessions assigned to clusters 1-5 in a Structure...
MD5:Explore Data6.76 KB - Structure membership assignments for accessionsxlsx
The proportional assignments of each cluster to all accessions (relative to...
MD5:Explore Data27.56 KB - Principal components analysispdf
Principal Component Analysis of 1120 samples based on 2063 unlinked SNP...
MD5:Explore Data343.81 KB - Subgenome origins of SNPs relative to the A-genome and B-genome progenitorsxlsx
Inferred subgenome origins of SNPs relative to the A-genome and B-genome...
MD5:Explore Data2.81 MB - Pod images for PI 497426Data
Pods from accession PI 497426 (clade 4), illustrating the distinctive...
MD5:Explore Data69.4 KB - Peruvian Moche-era peanut necklaceData
Picture of necklace of peanuts, sculpted in gold and silver, from the Moche-...
MD5:Explore Data72.63 KB
| Field | Value |
|---|---|
| Tags | |
| 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 | |
| Data Dictionary | |
| Contact Name | Cannon, Ethy |
| Contact Email | |
| Public Access Level | Public |
| Program Code | 005:040 - Department of Agriculture - National Research |
| Bureau Code | 005:18 - Agricultural Research Service |