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Open Access Method

Restriction Site Tiling Analysis: accurate discovery and quantitative genotyping of genome-wide polymorphisms using nucleotide arrays

Melissa H Pespeni1*, Thomas A Oliver1, Mollie K Manier12 and Stephen R Palumbi1

Author affiliations

1 Department of Biology, Stanford University, Hopkins Marine Station, Oceanview Blvd Pacific Grove, CA 93950, USA

2 Current address: Department of Biology, 107 Life Sciences Complex, Syracuse University, Syracuse, NY 13244, USA

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Citation and License

Genome Biology 2010, 11:R44  doi:10.1186/gb-2010-11-4-r44

Published: 19 April 2010

Abstract

High-throughput genotype data can be used to identify genes important for local adaptation in wild populations, phenotypes in lab stocks, or disease-related traits in human medicine. Here we advance microarray-based genotyping for population genomics with Restriction Site Tiling Analysis. The approach simultaneously discovers polymorphisms and provides quantitative genotype data at 10,000s of loci. It is highly accurate and free from ascertainment bias. We apply the approach to uncover genomic differentiation in the purple sea urchin.