Page Banner

United States Department of Agriculture

Agricultural Research Service

Related Topics

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

Location: Horticultural Crops Research

2012 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 attempts to develop molecular markers and implement techniques to monitor migration and population structure of P. ramorum in North America. In addition, all data obtained will be maintained in an open-access, web-based database. Currently, crucial isolates belonging to new lineages and up-to-date genotype information are often not generally available. As is the case for human pathogens such as HIV or the avian flu, a database of genotypic information will assist regulatory agencies in managing P. ramorum and assessing threat of further evolution and migration. Progress is presented separately for each of the objectives outlined in the original proposal. Our first object is 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 279 isolates collected from 19 states between 2004 and 2007. Of the three known P. ramorum clonal lineages, the most common lineage in the sample was NA1. 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 ofmultilocus 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 U.S. 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. Our second objective is 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. This research was conducted in support of objective 2C of the parent project.

4. Accomplishments

Last Modified: 10/18/2017
Footer Content Back to Top of Page