This codebook.txt file was generated on 20220208 by wilsonkm

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GENERAL INFORMATION
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1. Title of Dataset 
SNP data of 18SPA092-1 and 25 reference isolates of the wheat stem rust fungus, Puccinia graminis f. sp. tritici 


2. Author Information

  Principal Investigator Contact Information
        Name: Pablo D. Olivera Firpo
           Institution: University of Minnesota
           Email: oliv0132@mn.edu

  Associate or Co-investigator Contact Information
        Name: Dolors Villegas
           Institution: Institute of Agrifood research and Technology (IRTA), Spain 

  Associate or Co-investigator Contact Information
           Name: Carlos Cantero-Martinez
           Institution: University of Lleida, Spain

  Associate or Co-investigator Contact Information
	Name: Les J. Szabo
	Institution: USDA-ARS Cereal Disease Laboratory

  Associate or Co-investigator Contact Information
	Name: Matthew N. Rouse           
	Institution: USDA-ARS Cereal Disease Laboratory

  Associate or Co-investigator Contact Information
	Name: Douglas Luster
	Institution: USDA-ARS Foreign Disease-Weed Science Research Unit 

  Associate or Co-investigator Contact Information
	Name: Radhika Bartaula
	Institution: University of Minnesota


  Associate or Co-investigator Contact Information
	Name: Marta Lopes
	Institution: Institute of Agrifood research and Technology (IRTA), Spain

  Associate or Co-investigator Contact Information
	Name: Yue Jin
	Institution: USDA-ARS Cereal Disease Laboratory

3. Date of data collection: 2019-02-10 to 2021-12-01

4. Information about funding sources that supported the collection of the data:
Sponsorship: The Bill & Melinda Gates Foundation and UK Aid from the British People (OPP1133199)

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SHARING/ACCESS INFORMATION
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1. Licenses/restrictions placed on the data:
CC0 1.0 Universal

2. Links to publications that cite or use the data:
Olivera P.D., Villegas, D., Cantero-Martinez, C., Szabo, L.J., Roouse, M.N., Luster, D.G., Bartaula, R., Lopes, M.S., and Jin, Y. 2022. A unique race of the wheat stem rust pathogen with virulence on Sr31 identified in Spain and reaction of wheat and durum cultivars to this race. Plant Pathology. (In press).

3. Links to other publicly accessible locations of the data: No


4. Was data derived from another source? No


5. Recommended citation for the data:
 Olivera Firpo, Pablo D; Villegas, Dolors; Cantero-Martinez, Carlos; Szabo, Les J; Rouse, Matthew N; Luster, Douglas; Bartaula, Radhika; Lopes, Marta; Jin, Yue. (2022). SNP data of 18SPA092-1 and 25 reference isolates of the wheat stem rust fungus, Puccinia graminis f. sp. tritici. Retrieved from the Data Repository for the University of Minnesota, https://doi.org/10.13020/qm6t-h952. 

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DATA & FILE OVERVIEW
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1. File List
	A. Filename: SNP_dataset_1838_loci.xlsx
	Short description: In the excel file, we provide the data of the 1838 loci from a custom Illumina SNP array (PgtSNP 3.0 K chip) of 26 isolates of the wheat rust fungus Puccinia graminis f. sp. tritici.


2. Are there multiple versions of the dataset? No.

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METHODOLOGICAL INFORMATION
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1. Description of methods used for collection/generation of data: 
<Include links or references to publications or other documentation containing experimental design or protocols used in data collection>

SNP genotyping was performed using a custom Illumina single nucleotide polymorphism (SNP) array (PgtSNP 3.0k chip) (Olivera et al., 2019, Phytopathology 105:917-928).


2. Methods for processing the data: <describe how the submitted data were generated from the raw or collected data>

SNP data was filtered by removing loci with with monomorphic or missing data (Olivera et al., 2019, Phytopathology 105:917-928) and a final set of 1,838 SNP loci was used for phylogenetic analysis. 


3. Describe any quality-assurance procedures performed on the data:
SNP loci were filtered for monomorphic and missing data.


4. People involved with sample collection, processing, analysis and/or submission:
Les Szabo, Pablo Olivera Firpo, Yue Jin