title: Development of Polymorphic Microsatellite Loci for Potato Wart from Next-Generation Sequence Data.
abstract: Synchytrium endobioticum is the fungal agent causing potato wart disease. Because of its severity and persistence, quarantine measures are enforced worldwide to avoid the spread of this disease. Molecular markers exist for species-specific detection of this pathogen, yet markers to study the intraspecific genetic diversity of S. endobioticum were not available. Whole-genome sequence data from Dutch pathotype 1 isolate MB42 of S. endobioticum were mined for perfect microsatellite motifs. Of the 62 selected microsatellites, 21 could be amplified successfully and displayed moderate levels of polymorphism in 22 S. endobioticum isolates from different countries. Nineteen multilocus genotypes were observed, with only three isolates from Canada displaying identical profiles. The majority of isolates from Canada clustered genetically. In contrast, most isolates collected in Europe show no genetic clustering associated with their geographic origin. S. endobioticum isolates with the same pathotype displayed highly variable genotypes and none of the microsatellite markers correlated with a specific pathotype. The markers developed in this study can be used to assess intraspecific genetic diversity of S. endobioticum and allow track and trace of genotypes that will generate a better understanding of the migration and spread of this important fungal pathogen and support management of this disease.
authors.affiliation: First and seventh authors: Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada; second and third authors: Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; fourth and fifth authors: Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A 5T1, Canada; and sixth author: Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada.
authors.forename: Marie-Claude
authors.initials: MC
authors.lastname: Gagnon
authors.affiliation: First and seventh authors: Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada; second and third authors: Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; fourth and fifth authors: Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A 5T1, Canada; and sixth author: Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada.
authors.forename: Theo A J
authors.initials: TA
authors.lastname: van der Lee
authors.affiliation: First and seventh authors: Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada; second and third authors: Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; fourth and fifth authors: Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A 5T1, Canada; and sixth author: Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada.
authors.forename: Peter J M
authors.initials: PJ
authors.lastname: Bonants
authors.affiliation: First and seventh authors: Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada; second and third authors: Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; fourth and fifth authors: Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A 5T1, Canada; and sixth author: Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada.
authors.forename: Donna S
authors.initials: DS
authors.lastname: Smith
authors.affiliation: First and seventh authors: Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada; second and third authors: Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; fourth and fifth authors: Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A 5T1, Canada; and sixth author: Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada.
authors.forename: Xiang
authors.initials: X
authors.lastname: Li
authors.affiliation: First and seventh authors: Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada; second and third authors: Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; fourth and fifth authors: Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A 5T1, Canada; and sixth author: Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada.
authors.forename: C André
authors.initials: CA
authors.lastname: Lévesque
authors.affiliation: First and seventh authors: Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada; second and third authors: Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; fourth and fifth authors: Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A 5T1, Canada; and sixth author: Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada.
authors.forename: Guillaume J
authors.initials: GJ
authors.lastname: Bilodeau
mesh_terms: D008411:Chytridiomycota / Q000235:genetics*; D004271:DNA, Fungal; D016681:Genome, Fungal; D005838:Genotype; D018895:Microsatellite Repeats; D010802:Phylogeny; D010935:Plant Diseases / Q000382:microbiology*; D011110:Polymorphism, Genetic; D011198:Solanum tuberosum / Q000382:microbiology*
chemical_list: D004271:DNA, Fungal