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. Resources in this dataset:Resource Title: Data dictionary. File Name: data_dictionary.txtResource Title: Dataset S1: Axiom Arachis genotyping of 707 polymorphisms in 256 wild Arachis accessions. File Name: DataSetS1-CardAlleles-iii.xlsxResource 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.gzResource 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.xlsxResource 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.xlsxResource 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.gzResource 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.xlsxResource 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.

本数据集收录了论文《花生作物中Arachis cardenasii的遗传遗产：国际种子交换的深远益处》的补充数据，该论文通过分析花生野生近缘种Arachis cardenasii的等位基因在多个国家栽培品种和育种系中的影响，揭示了这些等位基因的遗传效应。自20世纪60年代末首次进行的四倍体栽培花生（Arachis hypogaea）与二倍体物种A. cardenasii之间的挑战性杂交以来，后续研究成功培育出含有A. cardenasii渗入区域的四倍体系。这些染色体区域，其中一些含有重要的抗性基因，被广泛应用于众多育种系中。本数据集中收录的文件记录了来自A. cardenasii的遗传遗产。信息包括花生栽培品种和育种系的基因分型数据，这些数据通过基因分型芯片（SNP芯片）和全基因组测序方法生成。本数据集还包括与A. cardenasii对现代花生品种抗病性和抗虫性影响相关的数据。数据集包含以下资源：

资源标题：数据字典。文件名：data_dictionary.txt

资源标题：数据集S1：Axiom Arachis对256个野生Arachis种质资源中的707个多态性的基因分型。文件名：DataSetS1-CardAlleles-iii.xlsx

资源描述：数据集S1：对代表Arachis属中31个描述的二倍体物种的几乎所有植物收集的256个野生Arachis种质资源中的707个多态性进行Axiom Arachis基因分型，包括A. cardenasii的所有19个种质资源，以及来自美国迷你核心收集的383个纯系A. hypogaea。

资源标题：数据集S2：育种系和品种中的渗入。文件名：DataSetS2-WGSIntrogression.tar.gz

资源描述：六个育种系和品种的基因分型数据（VCF格式tsv文件，压缩），包括Bailey2、GPBD4、IAC322、ICGV86855、Sutherland、VG9514；以及12个纯系对照花生。等位基因是通过全基因组测序确定的。文件Acard-diag_bases.txt（tsv，压缩）列出了2,337,866个A. cardenasii GKP 10017诊断基础（SNPs）的全集，相对于纯系A. hypogaea。位置相对于A. cardenasii GKP 10017的基因组。

资源标题：数据集S3：包含A. cardenasii GKP 10017渗入的全球基因型。文件名：DataSetS3-WorldwideGenotypes-ii.xlsx

资源描述：来自世界12个国家花生品种和品种的118个DNA样本的单核苷酸多态性基因分型。大多数样本含有来自野生物种存系的Arachis cardenasii GKP 10017的渗入染色体片段，少数为纯系对照栽培花生。

资源标题：数据集S4：包含Arachis cardenasii GKP 10017遗传物质的品种和田间数据。文件名：DataSetS4-LineagesFieldData-iv.xlsx

资源描述：包含A. cardenasii遗传物质的种质资源和品种目录，包括家系、农艺性状、选择时间表、选择田间数据和参考文献。

资源标题：数据集S5：遗传指纹数据。文件名：DataSetS5-Fingerprints.tar.gz

资源描述：45个种质资源的遗传指纹（标记）数据。存档包含10个工作表，包含A和B基因组等位基因的全基因组序列计数。

资源标题：数据集S6：Middleton和Sutherland品种后代的渗入区域分析。文件名：DataSetS6-Austp183.xlsx

资源描述：Excel文件包含由Arachis hypogaea cv. Middleton与cv. Sutherland杂交产生的270个重组自交系的遗传数据，Sutherland具有来自A. cardenasii的提供叶部病害抵抗力的渗入。

Middleton具有首选的农艺特征。