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Use of microsatellite markers derived from whole genome sequence data for identifying polymorphism in Phytophthora ramorumAuthor(s): Kelly Ivors; Matteo Garbelotto; Ineke De Vries; Peter Bonants
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)
Station: Pacific Southwest Research Station
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DescriptionInvestigating 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.
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CitationIvors, 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
Keywordsmicrosatellites, Phytophthora ramorum, polymorphism
- Phenotypic diversification is associated with host-induced transposon derepression in the sudden oak death pathogen Phytophthora ramorum
- Identification of new polymorphic microsatellite markers in the NA1 and NA2 lineages of Phytophthora ramorum
- Clonal expansion of the Belgian Phytophthora ramorum populations based on new microsatellite markers
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