Population Structure of Peronospora effusa in the Southwestern United States

PLoS One. 2016 Feb 1;11(2):e0148385. doi: 10.1371/journal.pone.0148385. eCollection 2016.


Peronospora effusa is an obligate pathogen that causes downy mildew on spinach and is considered the most economically important disease of spinach. The objective of the current research was to assess genetic diversity of known historical races and isolates collected in 2014 from production fields in Yuma, Arizona and Salinas Valley, California. Candidate neutral single nucleotide polymorphisms (SNPs) were identified by comparing sequence data from reference isolates of known races of the pathogen collected in 2009 and 2010. Genotypes were assessed using targeted sequencing on genomic DNA extracted directly from infected plant tissue. Genotyping 26 historical and 167 contemporary samples at 46 SNP loci revealed 82 unique multi-locus genotypes. The unique genotypes clustered into five groups and the majority of isolates collected in 2014 were genetically closely related, regardless of source location. The historical samples, representing several races, showed greater genetic differentiation. Overall, the SNP data indicate much of the genotypic variation found within fields was produced during asexual development, whereas overall genetic diversity may be influenced by sexual recombination on broader geographical and temporal scales.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Genotype
  • Peronospora / genetics
  • Peronospora / physiology*
  • Principal Component Analysis
  • Probability
  • Reproducibility of Results
  • Southwestern United States

Grant support

Work was completed using funds from a United States Department of Agriculture-Specialty Crop Research Initiative grant (http://nifa.usda.gov/funding-opportunity/specialty-crop-research-initiative-scri) to JC, BB, and KL. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.