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Title: Use of microsatellite markers derived from whole genome sequence data for identifying polymorphism in Phytophthora ramorum

Author: Ivors, Kelly; Garbelotto, Matteo; De Vries, Ineke; Bonants, Peter;

Date: 2006

Source: In: Frankel, Susan J.; Shea, Patrick J.; and Haverty, Michael I., tech. coords. Proceedings of the sudden oak death second science symposium: the state of our knowledge. Gen. Tech. Rep. PSW-GTR-196. Albany, CA: Pacific Southwest Research Station, Forest Service, U.S. Department of Agriculture: 145

Publication Series: General Technical Report (GTR)

   Note: This article is part of a larger document. View the larger document

Description: Investigating the population genetics of Phytophthora ramorum, the causal agent of sudden oak death (SOD), is critical to understanding the biology and epidemiology of this important phytopathogen. Raw sequence data (445,000 reads) of P. ramorum was provided by the Joint Genome Institute. Our objective was to develop and utilize Simple Sequence Repeat (SSR) techniques for fingerprinting large numbers of P. ramorum isolates originating from different host species within Europe and the United States. Using a computer program developed at Plant Research International, 1334 potential microsatellite loci were identified. Primers were selected from over 110 flanking regions of SSRs and tested in PCR reactions to amplify repeats. Thirty-one polymorphic loci were identified and 14 primer sets were optimized for isolate genotyping. Three loci showed variation among nursery isolates from Europe and the United States, although no variation was identified among isolates from forests in the United States. This information provided insight regarding genetic variation within populations, identified new genotypes, and separated isolates into two distinct lineages correlated with continental provenances.

Keywords: microsatellites, Phytophthora ramorum, polymorphism

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Ivors, Kelly; Garbelotto, Matteo; De Vries, Ineke; Bonants, Peter 2006. Use of microsatellite markers derived from whole genome sequence data for identifying polymorphism in Phytophthora ramorum. In: Frankel, Susan J.; Shea, Patrick J.; and Haverty, Michael I., tech. coords. Proceedings of the sudden oak death second science symposium: the state of our knowledge. Gen. Tech. Rep. PSW-GTR-196. Albany, CA: Pacific Southwest Research Station, Forest Service, U.S. Department of Agriculture: 145

 


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