title: A new method for studying population genetics of cyst nematodes based on Pool-Seq and genomewide allele frequency analysis.
abstract: Cyst nematodes are important agricultural pests responsible for billions of dollars of losses each year. Plant resistance is the most effective management tool, but it requires a close monitoring of population genetics. Current technologies for pathotyping and genotyping cyst nematodes are time-consuming, expensive and imprecise. In this study, we capitalized on the reproduction mode of cyst nematodes to develop a simple population genetic analysis pipeline based on genotyping-by-sequencing and Pool-Seq. This method yielded thousands of SNPs and allowed us to study the relationships between populations of different origins or pathotypes. Validation of the method on well-characterized populations also demonstrated that it was a powerful and accurate tool for population genetics. The genomewide allele frequencies of 23 populations of golden nematode, from nine countries and representing the five known pathotypes, were compared. A clear separation of the pathotypes and fine genetic relationships between and among global populations were obtained using this method. In addition to being powerful, this tool has proven to be very time- and cost-efficient and could be applied to other cyst nematode species.
authors.affiliation: Agriculture and Agri-Food Canada, Horticulture Research and Development Centre, 430 boul. Gouin, St-Jean-sur-Richelieu, Québec, Canada, J3B 3E6.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Mimee
authors.affiliation: Agriculture and Agri-Food Canada, Horticulture Research and Development Centre, 430 boul. Gouin, St-Jean-sur-Richelieu, Québec, Canada, J3B 3E6.
authors.forename: Marc-Olivier
authors.initials: MO
authors.lastname: Duceppe
authors.affiliation: Agriculture and Agri-Food Canada, Horticulture Research and Development Centre, 430 boul. Gouin, St-Jean-sur-Richelieu, Québec, Canada, J3B 3E6.
authors.forename: Pierre-Yves
authors.initials: PY
authors.lastname: Véronneau
authors.affiliation: Agriculture and Agri-Food Canada, Horticulture Research and Development Centre, 430 boul. Gouin, St-Jean-sur-Richelieu, Québec, Canada, J3B 3E6.
authors.forename: Joël
authors.initials: J
authors.lastname: Lafond-Lapalme
authors.affiliation: Département de Phytologie, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, 2425 rue de l'Agriculture, Québec, Canada, G1V 0A6.
authors.forename: Martine
authors.initials: M
authors.lastname: Jean
authors.affiliation: Département de Phytologie, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, 2425 rue de l'Agriculture, Québec, Canada, G1V 0A6.
authors.forename: François
authors.initials: F
authors.lastname: Belzile
authors.affiliation: Agriculture and Agri-Food Canada, Horticulture Research and Development Centre, 430 boul. Gouin, St-Jean-sur-Richelieu, Québec, Canada, J3B 3E6.
authors.forename: Guy
authors.initials: G
authors.lastname: Bélair
mesh_terms: D000818:Animals; D018556:Crops, Agricultural / Q000469:parasitology; D005787:Gene Frequency; D005828:Genetics, Population / Q000379:methods*; D060005:Genotyping Techniques / Q000379:methods*; D009348:Nematoda / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D020641:Polymorphism, Single Nucleotide
keywords: Globodera rostochiensis; Pool-Seq; cyst nematode; genotyping-by-sequencing; population genetics