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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Research » Research » Publications at this Location » Publication #361429

Research Project: Integrated Disease Management of Exotic and Emerging Plant Diseases of Horticultural Crops

Location: Horticultural Crops Research

Title: Tools for rapid characterization of Phytophthora infestans and Phytophthora ramorum using real-time PCR and microsatellites from genomic resources

Author
item Bilodeau, G - Canadian Food Inspection Agency
item Gagnon, M - Canadian Food Inspection Agency
item Levesque, C - Agriculture And Agri-Food Canada
item Kawchuk, L - Agriculture And Agri-Food Canada
item Wijekoon, C - Agriculture And Agri-Food Canada
item Feau, N - University Of British Columbia
item Bergeron, M - Natural Resources Canada
item Grunwald, Niklaus - Nik
item Brasier, C - Forestry Commission
item Webber, J - Forestry Commission
item Hamelin, R - University Of British Columbia

Submitted to: Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 11/5/2014
Publication Date: 1/1/2015
Citation: Bilodeau, G.J., Gagnon, M., Levesque, C.A., Kawchuk, L., Wijekoon, C.P., Feau, N., Bergeron, M., Grunwald, N.J., Brasier, C.M., Webber, J.F., Hamelin, R.C. 2015. Tools for rapid characterization of Phytophthora infestans and Phytophthora ramorum using real-time PCR and microsatellites from genomic resources. In: Proceedings of the 7th meeting of the International Union of Forest Research Organization (IUFRO) Working Party S07.02.09: Phytophthoras in forests and natural ecosystems; 11/9/14-11/14/14; Esquel, Argentina. Available: http://forestphytophthoras.org/sites/default/files/proceedings/IUFRO_Proceedings_2014.pdf. 33 p.

Interpretive Summary:

Technical Abstract: Oomycete pathogens such as Phytophthora infestans (Mont.) de Bary and Phytophthora ramorum Werres De Cock & Man in't Veld cause a devastating impacts worldwide. More DNA-based tools are needed to identify and characterize these species, where some genotypes/lineages may be more problematic than others. For example, some P. infestans strains are more resistant to fungicides and have preferred hosts. Mining the full genome sequences of these two organisms allowed development of markers for intraspecific genotyping. Our first objective was the development of Allele Specific Oligonucleotide-PCR (ASO-PCR) assays using real-time PCR to differentiate Canadian strains of P. infestans and the four lineages of P. ramorum (NA1, NA2, EU1 and EU2). The P. infestans genome revealed several regions containing SNPs within genes and in flanking sequences of microsatellite loci. Nine ASO-PCR assays were developed from these SNPs, allowing the unambiguous identification of the five dominant P. infestans Canadian genotypes from the most recent outbreaks. Two new ASO-PCR assays were developed in a gene coding for cellulose binding elicitor lectin (CBEL). Combined with two existing assays within the same gene region, it is now possible to identify all four lineages of P. ramorum, including the recently discovered EU2 lineage. Our second objective was to develop microsatellite markers to evaluate P. ramorum genetic diversity mostly within the NA2 lineage, where fewer markers are currently available. Analysis of the genome of the NA2 P. ramorum lineage revealed microsatellite loci that reveal polymorphism within this lineage. Previous markers were biased toward NA1 and did not reveal the level of polymorphism discovered using these new microsatellites. These DNA-based tools will contribute to the available genomic toolbox to assess the genetic