Single-feature polymorphism discovery in the barley transcriptome

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.