Population Structure of Late Blight (<i>Phytophthora infestans</i>) in Colombia and Ecuador and Downy Mildew (<i>Peronospora farinosa</i> f. sp. <i>spinaciae</i>) on Spinach in Arizona and California

In this study, Phytophthora infestans and Peronospora farinosa f. sp. spinaciae populations were analyzed using single nucleotide polymorphisms (SNPs). In Ecuador and Colombia, Phytophthora infestans causes significant damage to potato and tomato and the epidemiology is known to be highly clonal. Our objective was to measure population structure within the context of this clonal epidemiology using both synonymous and nonsynonymous markers. Candidate SNP sites were selected by comparing the draft genomes of the Ecuadorian isolates EC1-3527 and EC1-3626. Genotypes were assessed directly from infected tissue using a targeted sequencing approach. A total of 54 polymorphic sites were assessed in 93 infected plant samples revealing 28 unique multi-locus genotypes. Our results were consistent with previous studies indicating two clonal lineages are dispersed across both countries and the epidemiology is driven by clonal reproduction. Interestingly, the SNP markers revealed potentially functionally important, asexually-derived, genetic variation in nonsynonymous loci – including asexual variation in genes encoding RXLR effector proteins. This highlights the potential for rapid evolution within the context of clonal populations. The second pathogen, Peronospora farinosa f. sp. spinaciae 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 population structure of known historical races and isolates collected in 2014 from production fields in Yuma, Arizona and Salinas Valley, California were assessed using candidate synonymous SNPs identified by comparing sequence data from reference isolates of known races of the pathogen collected in 2009 and 2010. Genotypes were evaluated using targeted sequencing on genomic DNA extracted directly from infected plant tissue. Genotyping 26 historical and 167 modern samples at 46 SNP loci revealed 82 unique multi-locus genotypes. The unique genotypes clustered into six groups. The majority of isolates collected in 2014 were genetically similar, regardless of source location. The historical samples representing several of races showed greater genetic differentiation. Overall, the SNP data suggests within field genotypic variation was primarily a product of asexual development in production fields, whereas genetic diversity in the historical collection may be influenced by sexual recombination.