Method

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

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

author email corresponding author email

Genome Biology 2005, 6:R54doi:10.1186/gb-2005-6-6-r54

Published:	11 May 2005

Subject areas: Methods, Genome studies

Abstract

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.