Tool for monitoring population dynamics

Monitoring of pathogen populations and lineages provides critical information for disease management including their migration pathways and emergence of novel lineages or races.  Simple sequence repeats (SSRs), also known as microsatellites, are choice marker systems for many organisms. In diploid or polyploid species these markers are non-anonymous, co-dominant and almost always selectively neutral, making them more powerful than anonymous markers such as AFLP. The SSR marker-based search function has been developed to allow for the monitoring and visualization of population dynamics within species. Currently, we have SSR data only from P. ramorum, which was generated by Nik Grünwald at USDA-ARS. Read a PLoS Pathogens (2009, 5(9): e100583) paper from his lab to get more detailed information about the loci and primers used to generate this data set. In addition to the SSR genotype, any of the information associated with the characterized P. ramorum isolates can be used as a query to search the isolates.  A GIS tool is available to visualize the distribution of individual isolates/genotypes.

Please refer the user guide to learn about the functionality of this new tool. If you are interested to post your SSR data through the Phytophthora Database, please contact Seogchan Kang.