SFP genotyping from Affymetrix arrays is robust but largely detects cis-acting expression regulators

The recent development of Affymetrix chips designed from assembled EST sequences in a wide range of species has spawned considerable interest in identifying single feature polymorphisms (SFPs) from transcriptome data. SFPs are valuable genetic markers which potentially offer a physical link to the structural genes themselves. However, most current SFP prediction methodologies were developed for sequenced species although SFPs are particularly valuable for species with complex and un-sequenced genomes. There is thus an urgent need to establish the sensitivity and specificity of prediction methods. We explored four methods for identifying SFPs from experiments involving two tissues in two commercial varieties of barley and their doubled-haploid progeny. The methods were compared in terms of the SFPs predicted and their ability to identify known sequence polymorphisms in the features, to confirm existing SNP genotypes and to match existing maps and individual haplotypes. We identified >4000 separate SFPs which accurately predicted the SNP genotype of over 98% of the DH lines. These SFPs were highly enriched for features containing sequence polymorphisms but all methods uniformly identified a majority of SFPs (~64%) in features for which there was no sequence polymorphism while 5% mapped to different locations. These results indicate that 'SFPs' mainly represent polymorphism in cis-acting regulators. All four prediction methods are highly efficient and robust at predicting markers for the purpose of genotyping and gene mapping but the source of the polymorphisms, whether true SFPs or simply expression markers, should be treated with considerable caution.

Key Words: SNP, barley, expression analysis, single feature polymorphisms

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