Single-feature polymorphism discovery in the barley transcriptome
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
Genome Biology 2005, 6:R54 doi:10.1186/gb-2005-6-6-r54Published: 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.