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Single-feature polymorphism discovery in the barley transcriptome

Nils Rostoks1, Justin O Borevitz2*, Peter E Hedley1, Joanne Russell1, Sharon Mudie1, Jenny Morris1, Linda Cardle1, David F Marshall1 and Robbie Waugh1*

Author Affiliations

1 Scottish Crop Research Institute, Genome Dynamics, Invergowrie, Dundee, DD2 5DA, Scotland, UK

2 University of Chicago, Department of Ecology and Evolution, Chicago, IL 60637, USA

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Genome Biology 2005, 6:R54  doi:10.1186/gb-2005-6-6-r54

Published: 11 May 2005


A probe-level model for analysis of GeneChip gene-expression data is presented which identified more than 10,000 single-feature polymorphisms (SFP) between two barley genotypes. The method has good sensitivity, as 67% of known single-nucleotide polymorphisms (SNP) were called as SFPs. This method is applicable to all oligonucleotide microarray data, accounts for SNP effects in gene-expression data and represents an efficient and versatile approach for highly parallel marker identification in large genomes.