This collection contains supplementary information for the manuscript “Genetic mapping and QTL analysis for peanut smut resistance”, which reports the genetic map and quantitative trait loci associated with resistance to peanut smut, a disease caused by the fungus Thecaphora frezii. The information includes genotyping data of a 103 recombinant inbred line (RIL) population {susceptible Arachis hypogaea subsp.hypogaea × resistant synthetic amphidiploid [(A. correntina × A. cardenasii) × A. batizocoi]⁴ˣ} and parental lines, generated with the Axiom_Arachis2 SNP array. For more information about this dataset contact: Renee Arias: Renee.Arias@usda.gov or Alicia Massa: Alicia.Massa@usda.gov

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.

[Note: this dataset has been superseded by version 2: https://doi.org/10.15482/USDA.ADC/1522673 ] This collection contains supplementary data for the manuscript "Legacy genetics of Arachis cardenasii in the peanut crop shows profound benefits of international seed exchange," which describes the impact of alleles from a wild relative of peanut, Arachis cardenasii, through analysis of those alleles across cultivars and breeding lines across many countries. The initial challenging cross, between tetraploid cultivated peanut (Arachis hypogaea) and the diploid species A. cardenasii, was carried out in the late 1960s. Subsequent work produce a tetraploid line that contained introgressed regions from A. cardenasii. Those chromosomal regions, several containing important resistance genes, were used in numerous breeding lines. The genetic legacy from A. cardenasii is documented in the files in this collection. The information includes genotyping data across peanut cultivars and breeding lines, generated through both genotyping arrays ("SNP chips") and whole-genome sequencing. Information in this collection also includes data related to impact of A. cardenasii on disease- and pest resistance in modern peanut varieties.

[Note: This version supersedes version 1: https://doi.org/10.15482/USDA.ADC/1520889 Changes in version 2: A new Dataset was added - DataSet1-CardAlleles-iii.xlsx Datasets were renamed and renumbered in accordance to article revisions, and some changes made (see below for details): SupplementaryData1-Worldwide-genotypes-ii.xlsx => DataSet3-Worldwide-genotypes-ii.xlsx (Data with very minor changes, including the removal of three of 710 markers) SupplementaryData2-Lineages-FieldData-ii.xlsx => DataSet4-Lineages-FieldData-iv.xlsx (this file underwent minor revisions, with some extra comments added) SupplementaryData3-Fingerprints.tar => DataSet5-Fingerprints.tar (Data unchanged) SupplementaryData4-Austp183.xlsx => DataSet6-Austp183.xlsx (Data unchanged) SupplementaryData5-introgression.tar => DataSet2-WGSIntrogression.tar (A Dataset more stringently filtered with more control genotypes was used, cutting the number of markers from 2,566,180 to 2,337,866. More genotype output files were added, including controls. A genome-ordered list of A. cardenasii GKP 10017 diagnostic bases was added (Acard-diag_bases.txt.gzip).] Description This collection contains supplementary data for the manuscript "Legacy genetics of Arachis cardenasii in the peanut crop shows profound benefits of international seed exchange," which describes the impact of alleles from a wild relative of peanut, Arachis cardenasii, through analysis of those alleles across cultivars and breeding lines across many countries. The initial challenging cross, between tetraploid cultivated peanut (Arachis hypogaea) and the diploid species A. cardenasii, was carried out in the late 1960s. Subsequent work produce a tetraploid line that contained introgressed regions from A. cardenasii. Those chromosomal regions, several containing important resistance genes, were used in numerous breeding lines. The genetic legacy from A. cardenasii is documented in the files in this collection. The information includes genotyping data across peanut cultivars and breeding lines, generated through both genotyping arrays ("SNP chips") and whole-genome sequencing. Information in this collection also includes data related to impact of A. cardenasii on disease- and pest resistance in modern peanut varieties.

The Legume Information System (legumeinfo.org) is the USDA-ARS genetics and genomics database for legume crops and relatives. Researchers can also submit their data directly. LIS houses data for more than a dozen species such as common bean and chickpea, peanut, and soybean, with genome sequences, genes and predicted functions, families of related genes, views of evolutionary relationships between genomic regions, genetic maps, markers, and links to germplasm resources.

PeanutBase (peanutbase.org) is the primary genetics and genomics database for cultivated peanut and its wild relatives. It houses information about genome sequences, genes and predicted functions, genetic maps, markers, links to germplasm resources, and maps of peanut germplasm origins. This resource is being developed for U.S. and International peanut researchers and breeders, with support from The Peanut Foundation and the many contributors that have made the Peanut Genomics Initiative possible. Funded by The Peanut Foundation as part of the Peanut Genomics Initiative. Additional support from USDA-ARS. Database developed and hosted by the USDA-ARS SoyBase and Legume Clade Database group at Ames, IA, with NCGR and other participants.

Raw genome sequencing data of 17 isolates of Aspergillus flavus and Aspergillus parasiticus collected from peanuts from Ethiopia. These isolates were selected as representative of the genetic diversity of Aspergillus section Flavi found colonizing peanut seeds in four peanut-farming districts of Ethiopia, these are Darolabu, Gursum, Fedis, and Babile.