This codebook.txt file was generated on 2022-03-10 by wilsonkm

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GENERAL INFORMATION
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1. Title of Dataset 
 SNP data of 56 Kazakhstani and 23 reference isolates of the wheat stem rust fungus, Puccinia graminis f. sp. tritici 

2. Author Information

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

  Associate or Co-investigator Contact Information
        Name: Les J. Szabo
           Institution:

  Associate or Co-investigator Contact Information
           Name: Alma Kokhmetova
           Institution:


  Associate or Co-investigator Contact Information
        Name: Alexey Morgunov
           Institution:

  Associate or Co-investigator Contact Information
           Name: Douglas Luster
           Institution:

  Associate or Co-investigator Contact Information
        Name: Yue Jin
           Institution:

3. Date of data collection: 2016-02-01 to 2020-02-01

4. Information about funding sources that supported the collection of the data: Sponsorship: Bill and Melinda Gates Foundation and the United Kingdom Department for International Development, Grant numbers: DRRW-OPPGD1389 and DGGW-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., Khokmetova, A., Szabo, L.J., Morgunov, A., Luster, D.G., and Jin, Y. 2022. Novel and unique virulences from a sexual population of Puccinia graminis f. sp. tritici in Kazakhstan. Phytopathology. (Under revision).


3. Links to other publicly accessible locations of the data:


4. Links/relationships to ancillary data sets:


5. Was data derived from another source?
           If yes, list source(s):


6. Recommended citation for the data:
 Olivera Firpo, Pablo; Szabo, Les J; Kokhmetova, Alma; Morgunov, Alexey; Luster, Douglas; Jin, Yue. (2022). SNP data of 56 Kazakhstani and 23 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/hgp6-t930. 

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DATA & FILE OVERVIEW
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1. File List
	A. Filename: SNP_Dataset_Kazakhstan_2310_loci.csv
	Short description:  SNP dataset (2310 loci)


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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>
Genotyping of 56 Kazakhstan isolates was performed using a custom Illumina Infinium single-nucleotide polymorphism (SNP) array (PgtSNP 3.0k chip) as described (Olivera et al., 2019). SNP calling was performed using GenomeStudio based on the following criteria: GenTran score >0.6 and >90% call rate (Olivera et al. 2019) which resulted in a data set of 2,310 loci.  


3. Instrument- or software-specific information needed to interpret the data:


4. Standards and calibration information, if appropriate:


5. Environmental/experimental conditions:


6. Describe any quality-assurance procedures performed on the data:


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