This readme.txt file was generated on 20240807 by Fiona Todd
Recommended citation for the data: 
Akakpo, R; Lee, EJ; Pacheco, JB; Rios, EF; Boukar, O; Volz, KM; Akinmade, H; Boote, KJ; Close, TJ; Muñoz-Amatriaín, M; Morrell, PL. (2024). Identification of genetic variation associated with high-temperature tolerance in cowpea. Retrieved from the Data Repository for the University of Minnesota, DOI

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GENERAL INFORMATION
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1. Title of Dataset
"Identification of genetic variation associated with high-temperature tolerance in cowpea"

2. Author Information


  Principal Investigator Contact Information
        Name: Peter Morrell
           Institution: University of Minnesota 
           Address: Department of Agronomy and Plant Genetics, 411 Borlaug Hall, 1991 Upper Buford Circle, Saint Paul, MN 55108
           Email: pmorrell@umn.edu
	   ORCID: 0000-0001-6282-1582

  Associate or Co-investigator Contact Information
        Name: María Muñoz-Amatriaín
           Institution: Universidad de  León
           Address: Departamento de Biología Molecular, Universidad de  León, 24071 León, Spain
           Email: mmuna@unileon.es
	   ORCID: 0000-0002-4476-1691

  Associate or Co-investigator Contact Information
        Name: Esteban Rios
           Institution: University of Florida
           Address: Agronomy Department, University of Florida, Gainesville, FL 32611
           Email: estebanrios@ufl.edu
	   ORCID: 0000-0003-3389-7195


3. Date published or finalized for release: 

4. Date of data collection (single date, range, approximate date): N/A

5. Geographic location of data collection (where was data collected?):  Datapoints across African continent, specific locations in IITA_cowpea_core_PP_data_test.kml  

6. Information about funding sources that supported the collection of the data: 
Foundation For Food & Agriculture Research, Unravelling the genetics of cowpea adaptation to high temperatures for legume improvement

7. Overview of the data (abstract): 


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SHARING/ACCESS INFORMATION
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1. Licenses/restrictions placed on the data: Creative Commons BY

2. Links to publications that cite or use the data: N/A

3. Was data derived from another source?
           If yes, list source(s): International Institute of Tropical Agriculture (IITA) Genebank Core collection, WorldClim2.1

4. Terms of Use: Data Repository for the U of Minnesota (DRUM) By using these files, users agree to the Terms of Use. https://conservancy.umn.edu/pages/policies/#drum-terms-of-use




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DATA & FILE OVERVIEW
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1. File List
   A. Filename: IITA_cowpea_core_PP_data_test.kml     
      Short description: file showing localities of cowpea landrace and wild samples in Google Earth        

   B. Filename: cowpea_490_stats_AA_rename.vcf.gz       
      Short description: Blocked GNU Zip Format (BGZF; gzip compatible) VCF file containing cowpea iSelect \
genotypes for 44,111 SNPs in 490 landrace and wild accessions. Data shown is after quality \
control        
        
   C. Filename: Partner_Favorites.vcf.gz        
      Short description: Blocked GNU Zip Format (BGZF; gzip compatible) VCF file containing cowpea iSelect \
genotypes for 47,808 SNPs in 490 cultivated accessions. Data shown is after quality \
control

2. Relationship between files: N/A        



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METHODOLOGICAL INFORMATION
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1. Description of methods used for collection/generation of data: Data from IITA core collection was cleaned, ending up with 580 cowpea landrace and wild accessions

2. Methods for processing the data: STRUCTURE version 2.3.4, ΔK calculation method, Structure Harvester, R package SNPRelate, GWAS models from GAPIT version 3 R package, FarmCPU, BLINK, HeirFstat R package, Spatial ancestry analysis, est-sfs

3. Instrument- or software-specific information needed to interpret the data: R studio, R packes SNPRelate, tess3, GAPIT version 3, q-value version 2.30.0, and HierFstat


4. Standards and calibration information, if appropriate: N/A


5. Environmental/experimental conditions: N/A


6. Describe any quality-assurance procedures performed on the data: Data reviewed with ITALLIC to eliminate inconsistent data points that could not be rectified by IITA genebank curators


7. People involved with sample collection, processing, analysis and/or submission: N/A