VCF file of SNP data of 556 isolates of the wheat leaf rust fungus, Puccinia triticina from 11 world-wide regions

  • James Kolmer (Creator)
  • Adam C Herman (Creator)
  • Maria Ordonez (Creator)
  • Silvia E. Germán (Creator)
  • Alexy Morgounov (Creator)
  • Zack Pretorius (Creator)



This dataset includes SNPs of 556 isolates of the wheat leaf rust fungus, Puccina triticina from 11 worldwide regions that were mapped to the reference genome. This data was used to examine the population structure of Puccinia triticina on a worldwide basis, and to examine the evolutionary relationship between collections from a wheat progenitor, collections from durum wheat, and collections from common wheat. Groups of isolates that were highly related were found in distant continental regions, indicating past and current migration of this important wheat pathogen. Data is being released now in conjunction with publication of a primary research paper that describes this research.

We provide variant calls in VCF and fasta format. Fasta formatted data were used with the deposited python script to calculate the average number of pairwise differences between sequences. GBS SNP calls in Variant Call Format (bgzipped) GBS Haplotype sequence in fasta format (tarballed directory) Python script for calculating average number of pairwise differences using the fasta haplotypes as input. Names dependency file for python script. The excel file gives the virulence/virulence of the same isolates to 20 lines of Thatcher wheat that differ for single leaf rust resistance genes.
Date made available2019
PublisherData Repository for the University of Minnesota

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