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.
- PDFStructure membership breakdown
- XLSXStructure membership assignments for accessions
- PDFPrincipal components analysis
- JPEGPod images for PI 497426
- TXTData dictionary
- XLSXMain descriptive information about genotyped accessions
- BINSNPs as called by the Axiom suite
- BINGenotyping calls in VCF format
- BINDNA variants for all accessions, including from genome assemblies, in TSV format
- BINDNA variants for all accessions, including from genome assemblies, in fasta format
- XLSXBase-calls for selected accessions, relative to A- and B-genome progenitors
- BINReduced fasta alignments, at 98% identity
- BINReduced fasta alignments, at 99% identity
- BINPhylogenetic tree of genotype data
- XLSXSubgenome origins of SNPs relative to the A-genome and B-genome progenitors
- JPEGPeruvian Moche-era peanut necklace
