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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Research » Research » Publications at this Location » Publication #342762

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

Location: Horticultural Crops Research

Title: Development and validation of polymorphic microsatellite loci for the NA2 lineage of Phytophthora ramorum from whole genome sequence data

Author
item Gagnon, Marie-claude - Canadian Food Inspection Agency
item Feau, Nicolas - University Of British Columbia
item Dale, Angela - University Of British Columbia
item Dhillon, Braham - University Of British Columbia
item Hamelin, Richard - University Of British Columbia
item Brasier, Clive - Forestry Commission
item Grunwald, Niklaus - Nik
item Briere, Stephan - Canadian Food Inspection Agency
item Bilodeau, Guillaume - Canadian Food Inspection Agency

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/21/2016
Publication Date: 3/16/2017
Citation: Gagnon, M., Feau, N., Dale, A.L., Dhillon, B., Hamelin, R.C., Brasier, C.M., Grunwald, N.J., Briere, S.C., Bilodeau, G.J. 2017. Development and validation of polymorphic microsatellite loci for the NA2 lineage of Phytophthora ramorum from whole genome sequence data. Plant Disease. 101(5):666-673. doi: 10.1094/PDIS-11-16-1586-RE.

Interpretive Summary: Phytophthora ramorum is the causal agent of sudden oak death and sudden larch death, and is also responsible for causing ramorum blight on woody ornamental plants. Molecular markers are available to characterize the genetic diversity of this pathogen. However, these markers do not work for all known clones of the pathogen. We developed markers in this study can be used to assess genetic diversity within and across clones of P. ramorum. These new markers are important for monitoring SOD emergence around the world.

Technical Abstract: Phytophthora ramorum is the causal agent of sudden oak death and sudden larch death, and is also responsible for causing ramorum blight on woody ornamental plants. Many microsatellite markers are available to characterize the genetic diversity and population structure of P. ramorum. However, only two markers are polymorphic in the NA2 lineage, which is predominant in Canadian nurseries. Microsatellite motifs were mined from whole-genome sequence data of six P. ramorum NA2 isolates. Of the 43 microsatellite primer pairs selected, 13 loci displayed different allele sizes among the four P. ramorum lineages, 10 loci displayed intralineage variation in the EU1, EU2, and/or NA1 lineages, and 12 microsatellites displayed polymorphism in the NA2 lineage. Genotyping of 272 P. ramorum NA2 isolates collected in nurseries in British Columbia, Canada, from 2004 to 2013 revealed 12 multilocus genotypes (MLGs). One MLG was dominant when examined over time and across sampling locations, and only a few mutations separated the 12 MLGs. The NA2 population observed in Canadian nurseries also showed no signs of sexual recombination, similar to what has been observed in previous studies. The markers developed in this study can be used to assess P. ramorum inter- and intralineage genetic diversity and generate a better understanding of the population structure and migration patterns of this important plant pathogen, especially for the lesser-characterized NA2 lineage.