Identification and molecular characterization of Canadian strains of potato late blight and potato wart

Phytophthora infestans (Mont.) de Bary (potato late
blight) and Synchytrium endobioticum (Schilb.) Percival
(potato wart) are plant pathogens with devastating impact
on potato crops worldwide. For example, P. infestans was
the causal agent of the Irish potato famine in 1845, while
S. endobioticum is one of the most important quarantine
pathogens infecting potato. Both pathogens are present in
Canada, and more diagnostic tools are needed to detect,
identify and characterize them. The objective of this
project is to develop single nucleotide polymorphisms
(SNPs), microsatellites and allele specific oligonucleotides
(ASO) from genomic and transcriptomic data to
identify and characterize Canadian strains of P. infestans
and S. endobioticum. Mining of P. infestans genome
revealed several regions containing SNPs, both in genes
and in flanking sequences of microsatellites loci. Nine
ASO-PCR assays were developed from these SNPs,
allowing the unambiguous identification of the five
Canadian genotypes of this pathogen. Markers for 20
microsatellite loci were also developed from the draft
genome sequence of S. endobioticum, obtained by NGS
of a Dutch isolate of race 1. Until now, six loci were
tested on a panel of samples from the Netherlands and
Canada. Genotyping revealed that four loci were variable,
and that our samples comprised at least five multilocus
genotypes. The two Canadian DNA samples tested were
identical, and similar to the most frequent genotype found in our samples. Additional markers are needed to improve
resolution and to determine if all the S. endobioticum
strains found in Canada have the same multilocus
genotype.