Data from: Legacy genetics of Arachis cardenasii in the peanut crop - v2

[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.

• Resource Title: Data dictionary.

  File Name: data_dictionary.txt




• Resource Title: Dataset S1: Axiom Arachis genotyping of 707 polymorphisms in 256 wild Arachis accessions.

  File Name: DataSetS1-CardAlleles-iii.xlsx

  Resource Description: Dataset S1: Axiom Arachis genotyping of 707 polymorphisms in 256 wild Arachis accessions representing almost all botanical collections of the 31 described diploid species in the botanical section Arachis (including all 19 accessions of A. cardenasii), and 383 A. hypogaea of pure pedigree from the US mini Core collection.




• Resource Title: Dataset S2: Introgressions in breeding lines and cultivars.

  File Name: DataSetS2-WGSIntrogression.tar.gz

  Resource Description: Genotype data (VCF format tsv files, compressed), for six breeding lines and cultivars: Bailey2, GPBD4, IAC322, ICGV86855, Sutherland, VG9514; and 12 control peanuts of pure pedigree. Alleles were determined using Whole Genome Sequencing. The file Acard-diag_bases.txt (tsv, compressed) lists the full set of 2,337,866 A. cardenasii GKP 10017 diagnostic bases (SNPs) relative to pure pedigree A. hypogaea. Positions are relative to the genome of A. cardenasii GKP 10017.




• Resource Title: Dataset S3: Worldwide genotypes with A. cardenasii GKP 10017 introgressions.

  File Name: DataSetS3-WorldwideGenotypes-ii.xlsx

  Resource Description: Single nucleotide polymorphism genotyping of 118 DNA samples from peanut lines and cultivars from twelve countries from around the world. Most have introgressed chromosome segments from the wild species accession Arachis cardenasii GKP 10017, a few are pure pedigree cultivated peanuts for controls.




• Resource Title: Dataset S4: Lineages and field data for lines containing Arachis cardenasii GKP 10017 genetic material..

  File Name: DataSetS4-LineagesFieldData-iv.xlsx

  Resource Description: Catalog of accessions and lines containing A. cardenasii genetic material, including pedigrees, agronomic traits, selection timelines, selected field data, and references.




• Resource Title: Dataset S5: Genetic fingerprint data.

  File Name: DataSetS5-Fingerprints.tar.gz

  Resource Description: Genetic fingerprint (marker) data for 45 accessions. Archive contains 10 spreadsheets with whole genome sequence counts for A and B genome alleles.




• Resource Title: Dataset S6: Analysis of introgression regions in progeny of cultivars Middleton and Sutherland.

  File Name: DataSetS6-Austp183.xlsx

  Resource Description: Excel file contains data of 270 Recombinant Inbred Lines developed from a cross of Arachis hypogaea cv. Middleton by cv. Sutherland - Sutherland having A. cardenasii introgressions that provide foliar disease resistance. Middleton having the preferred agronomic profile.