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United States Department of Agriculture

Agricultural Research Service

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Research Project: Population Structure of the Sudden Oak Death Pathogen Phytophthora ramorum in North America

Location: Horticultural Crops Research

2013 Annual Report

1a. Objectives (from AD-416):
To monitor the migration andpopulation structure of Phytophthora ramorum in North America using microsatellites

1b. Approach (from AD-416):
Isolates will be obtained from federal and/or state agencies from Canada and the US as SOD is detected. Select isolates from Europe will be included as references isolates. Microsatellite genotypes will be determined using a range of microsatellite loci characterizing all extant clonal lineages.

3. Progress Report:
This research was conducted in support of NP303 objective 2C of the parent project. Objective 1: To monitor the migration and population structure of Phytophthora ramorum in North America using microsatellites. We examined the genetic diversity of P. ramorum in US nurseries by microsatellite genotyping collected from the USA between 2004 and 2012. Of the three known P. ramorum clonal lineages, the most common lineage in the sample remains the NA1 clone. The EU1 and NA2 clonal lineages had more limited distributions and lower genetic diversities. Migration pathways were revealed by a single genotype shared among the majority of states and in the clustering of NA1 isolates into only two groups, one containing isolates from Connecticut, Oregon, and Washington and the other isolates from California and the remaining states. At the same time, several states showed genetic diversities as high as the three West Coast states and two-thirds of multilocus genotypes were limited in their distribution to one state. Together, these data suggest that migration, rapid mutation, and genetic drift all play a role in structuring the genetic diversity of P. ramorum in US nurseries. The inferred connections between states were consistent with USDA APHIS trace-forward and trace-back analyses revealing two predominant migration routes from the West coast originating either in California or the Pacific Northwest. This work demonstrates that analysis of variable microsatellites can be used to recreate the evolutionary history and putative migration patterns of clonal pathogens thus showing promise for similar forensic applications in other clonal organisms. We also were able to obtain a significant culture collection from Canada (courtesy of CFIA). This collection reveals presence of all three clonal lineages NA1, NA2, and EU1. NA2 and EU1 are dominant lineages. Using the program MIGRATE, we used Bayesian inference to estimate migration rate from Europe to North America and from North America to Europe. These estimates indicated that there was higher migration from Europe to North America. We then directly tested unidirectional migration against bidirectional migration using ML. The highest likelihood model was unidirectional migration from Europe to North America. This model was a significantly better fit to the data by a likelihood ratio test and AIC, which accounts for the different numbers of parameters in the models under comparison. This research established that EU1 likely migrated from Europe to North America (either British Columbia or Washington). Our work conducted with US Forest Service funding thus established that there were at least 4 global migrations of P. ramorum. NA1 into US, EU1 into Europe, EU1 from Europe to NA, and NA2 into North Western NA. Although a new EU2 lineage has been described in Europe, this lineage has to date not ben found in the USA, indicating a need for continue monitoring and vigilance in the USA. We recently genotyped a new focus of infection in Cape Sebastian, Curry County, Oregon, and compared this genotype to nursery populations from California, Oregon, Washington, and forest populations from Curry County. At this point we cannot assess where the isolates came from but work is ongoing to establish a route of invasion. Objective 2: To maintain an open-access, web-based database and culture collection with genotypic information. We maintain a comprehensive database in BioNumerics containing genotype, phenotype and passport information. This database contains information on AFLP, microsatellite and sequences for some or all of the isolates. A selection of information is regularly migrated to our website ( onto a searchable, relational database using MySQL. This website is regularly updated (1 to 2× per month). Before we publish any novel genotype information on our webpage we contact all parties, state and regulatory agencies involved in a new find to provide them with time to respond to a new find. Information is only posted if all agencies and parties involved agree to the release of information.

4. Accomplishments

Last Modified: 06/27/2017
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