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

M.C. Gagnon, L. Kawchuk, X. Li, T.A.J. van der Lee, P.J.M. Bonants, C.A. Levesque, G.J. Bilodeau

Research output: Contribution to journalMeeting AbstractAcademic

Abstract

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.
LanguageEnglish
Pages262-263
JournalCanadian Journal of Plant Pathology = Revue Canadienne de Phytopathologie
Volume36
Issue number2
Publication statusPublished - 2014

Fingerprint

warts
Synchytrium endobioticum
Phytophthora infestans
potatoes
single nucleotide polymorphism
loci
microsatellite repeats
sampling
pathogens
genotype
oligonucleotides
transcriptomics
plant pathogens
genotyping
Netherlands
Canada
alleles
genomics
DNA
assays

Cite this

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title = "Identification and molecular characterization of Canadian strains of potato late blight and potato wart",
abstract = "Phytophthora infestans (Mont.) de Bary (potato lateblight) and Synchytrium endobioticum (Schilb.) Percival(potato wart) are plant pathogens with devastating impacton potato crops worldwide. For example, P. infestans wasthe causal agent of the Irish potato famine in 1845, whileS. endobioticum is one of the most important quarantinepathogens infecting potato. Both pathogens are present inCanada, and more diagnostic tools are needed to detect,identify and characterize them. The objective of thisproject is to develop single nucleotide polymorphisms(SNPs), microsatellites and allele specific oligonucleotides(ASO) from genomic and transcriptomic data toidentify and characterize Canadian strains of P. infestansand S. endobioticum. Mining of P. infestans genomerevealed several regions containing SNPs, both in genesand in flanking sequences of microsatellites loci. NineASO-PCR assays were developed from these SNPs,allowing the unambiguous identification of the fiveCanadian genotypes of this pathogen. Markers for 20microsatellite loci were also developed from the draftgenome sequence of S. endobioticum, obtained by NGSof a Dutch isolate of race 1. Until now, six loci weretested on a panel of samples from the Netherlands andCanada. Genotyping revealed that four loci were variable,and that our samples comprised at least five multilocusgenotypes. The two Canadian DNA samples tested wereidentical, and similar to the most frequent genotype found in our samples. Additional markers are needed to improveresolution and to determine if all the S. endobioticumstrains found in Canada have the same multilocusgenotype.",
author = "M.C. Gagnon and L. Kawchuk and X. Li and {van der Lee}, T.A.J. and P.J.M. Bonants and C.A. Levesque and G.J. Bilodeau",
year = "2014",
language = "English",
volume = "36",
pages = "262--263",
journal = "Canadian Journal of Plant Pathology = Revue Canadienne de Phytopathologie",
issn = "0706-0661",
publisher = "Taylor & Francis",
number = "2",

}

Identification and molecular characterization of Canadian strains of potato late blight and potato wart. / Gagnon, M.C. ; Kawchuk, L.; Li, X.; van der Lee, T.A.J.; Bonants, P.J.M.; Levesque, C.A.; Bilodeau, G.J.

In: Canadian Journal of Plant Pathology = Revue Canadienne de Phytopathologie, Vol. 36, No. 2, 2014, p. 262-263.

Research output: Contribution to journalMeeting AbstractAcademic

TY - JOUR

T1 - Identification and molecular characterization of Canadian strains of potato late blight and potato wart

AU - Gagnon, M.C.

AU - Kawchuk, L.

AU - Li, X.

AU - van der Lee, T.A.J.

AU - Bonants, P.J.M.

AU - Levesque, C.A.

AU - Bilodeau, G.J.

PY - 2014

Y1 - 2014

N2 - Phytophthora infestans (Mont.) de Bary (potato lateblight) and Synchytrium endobioticum (Schilb.) Percival(potato wart) are plant pathogens with devastating impacton potato crops worldwide. For example, P. infestans wasthe causal agent of the Irish potato famine in 1845, whileS. endobioticum is one of the most important quarantinepathogens infecting potato. Both pathogens are present inCanada, and more diagnostic tools are needed to detect,identify and characterize them. The objective of thisproject is to develop single nucleotide polymorphisms(SNPs), microsatellites and allele specific oligonucleotides(ASO) from genomic and transcriptomic data toidentify and characterize Canadian strains of P. infestansand S. endobioticum. Mining of P. infestans genomerevealed several regions containing SNPs, both in genesand in flanking sequences of microsatellites loci. NineASO-PCR assays were developed from these SNPs,allowing the unambiguous identification of the fiveCanadian genotypes of this pathogen. Markers for 20microsatellite loci were also developed from the draftgenome sequence of S. endobioticum, obtained by NGSof a Dutch isolate of race 1. Until now, six loci weretested on a panel of samples from the Netherlands andCanada. Genotyping revealed that four loci were variable,and that our samples comprised at least five multilocusgenotypes. The two Canadian DNA samples tested wereidentical, and similar to the most frequent genotype found in our samples. Additional markers are needed to improveresolution and to determine if all the S. endobioticumstrains found in Canada have the same multilocusgenotype.

AB - Phytophthora infestans (Mont.) de Bary (potato lateblight) and Synchytrium endobioticum (Schilb.) Percival(potato wart) are plant pathogens with devastating impacton potato crops worldwide. For example, P. infestans wasthe causal agent of the Irish potato famine in 1845, whileS. endobioticum is one of the most important quarantinepathogens infecting potato. Both pathogens are present inCanada, and more diagnostic tools are needed to detect,identify and characterize them. The objective of thisproject is to develop single nucleotide polymorphisms(SNPs), microsatellites and allele specific oligonucleotides(ASO) from genomic and transcriptomic data toidentify and characterize Canadian strains of P. infestansand S. endobioticum. Mining of P. infestans genomerevealed several regions containing SNPs, both in genesand in flanking sequences of microsatellites loci. NineASO-PCR assays were developed from these SNPs,allowing the unambiguous identification of the fiveCanadian genotypes of this pathogen. Markers for 20microsatellite loci were also developed from the draftgenome sequence of S. endobioticum, obtained by NGSof a Dutch isolate of race 1. Until now, six loci weretested on a panel of samples from the Netherlands andCanada. Genotyping revealed that four loci were variable,and that our samples comprised at least five multilocusgenotypes. The two Canadian DNA samples tested wereidentical, and similar to the most frequent genotype found in our samples. Additional markers are needed to improveresolution and to determine if all the S. endobioticumstrains found in Canada have the same multilocusgenotype.

M3 - Meeting Abstract

VL - 36

SP - 262

EP - 263

JO - Canadian Journal of Plant Pathology = Revue Canadienne de Phytopathologie

T2 - Canadian Journal of Plant Pathology = Revue Canadienne de Phytopathologie

JF - Canadian Journal of Plant Pathology = Revue Canadienne de Phytopathologie

SN - 0706-0661

IS - 2

ER -