Identification of genetic variation associated with high-temperature tolerance in cowpea
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1970-12-31
Date completed
2023-12-31
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Pacheco, Jacob
Pache105@umn.edu
Pache105@umn.edu
Abstract
This dataset includes filtered and unfiltered variant call files (VCFs), structural variant data (BEDPE), callable and uncallable region masks (BED), and phenotype data collected from mutagenized barley lines and control hybrids. It incorporates sequencing results from 10x Genomics, Oxford Nanopore, PacBio, and Illumina platforms.
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1. File List
A. Filename: Cowpea_enviormental_ancest_822
Short description: Dataset related to environmental ancestry analysis in cowpea lines.
B. Filename: Partner_Favorites.vcf.gz
Short description: VCF file of variants from selected partner-preferred cowpea lines.
C. Filename: README.md
Short description: Markdown-formatted readme containing project metadata and notes.
D. Filename: README_WIP_Roland_Cowpea.txt
Short description: In-progress readme draft with additional annotation and format testing notes.
E. Filename: Readme_published_V5.txt
Short description: Final published version of the project readme with all required metadata.
F. Filename: VIGNA_rate6_ANCEST.bed
Short description: Ancestral state inference output using rate6 model in BED format.
G. Filename: VIGNA_rate6_ANCEST_ESTSFS.bed
Short description: BED file with ancestral states inferred using EST-SFS for comparison.
H. Filename: all_hits_MAF 3.bed.numbers
Short description: BED file annotated with allele frequency hit counts.
I. Filename: cowpea_490_stats_AA_rename.vcf.gz
Short description: VCF file with ancestral allele statistics for 490 cowpea samples.
J. Filename: cowpea_490_stats_AA_rename.vcf.gz.csi
Short description: Index file for the cowpea_490_stats_AA_rename VCF.
K. Filename: iSelect_ancestral.bed
Short description: Ancestral state calls for iSelect SNP array loci in BED format.
Referenced by
https://doi.org/10.1101/2025.04.09.647789
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This study was funded by the Foundation for Food & Agriculture Research (Award# ICRC20-0000000032) to EFR, KJB, MA-M, OB, and PLM. The authors thank Tchamba Marimagne (IITA Genebank, Nigeria) for his valuable input during passport data curation, and Fiona Todd (University of Minnesota, USA) for the curation of materials associated with the manuscript. This research was carried out with software and hardware support provided by the Minnesota Supercomputing Institute (MSI) at the University of Minnesota. This research benefited from the advice and guidance of Timothy J. Close (U. of California Riverside, USA).
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Akakpo, Roland; Morrell, Peter; Lee, Elaine; Pacheco, Jacob; Rios, Esteban; Kantar, Michael; Boukar, Ousmane; Volz, Kevin; Akinmade, Habib; Alonso, Luis; Boote, Kenneth; Muñoz-Amatriaín, María. (2025). Identification of genetic variation associated with high-temperature tolerance in cowpea. Retrieved from the Data Repository for the University of Minnesota (DRUM), https://hdl.handle.net/11299/273763.
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all_hits_MAF 3.bed.numbers
(295.68 KB)
cowpea_490_stats_AA_rename.vcf.gz
(4.74 MB)
cowpea_490_stats_AA_rename.vcf.gz.csi
(145.62 KB)
Cowpea_enviormental_ancest_822
(1.82 MB)
iSelect_ancestral.bed
(1.66 MB)
Partner_Favorites.vcf.gz
(2.16 MB)
README_WIP_Roland_Cowpea.txt
(4.49 KB)
VIGNA_rate6_ANCEST_ESTSFS.bed
(2.03 MB)
VIGNA_rate6_ANCEST.bed
(2.03 MB)
IITA_cowpea_core_PP_data_test.kml
(228.06 KB)
readme.txt
(7.27 KB)
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