Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/18/2007
Publication Date: 6/15/2007
Citation: Luo, Z.W., Potokina, E., Druka, A., Wise, R.P., Waugh, R., Kearsey, M.J. 2007. SFP genotyping from Affymetrix arrays is robust but largely detects cis-acting expression regulators. Genetics. 176:789-800. Interpretive Summary: Several recent studies have explored the possibility of using transcript abundance data from cRNA hybridizations to Affymetrix microarrays (Affymetrix, Santa Clara, CA) to reveal genetic polymorphisms that can be used as markers to genotype individuals in mapping populations. This article reports two new statistical methods for identifying single feature polymorphisms (SFPs) by modeling expression data from replicated Affymetrix microarrays on the Steptoe and Morex barley varieties and for mapping these SFPs in a doubled-haploid population from a cross of these two parental lines. The expression analysis was performed on Affymetrix Barley1 GeneChips using RNA taken from two tissues, seedling leaves and embryo-derived tissue from the germinating grain. The major aim was to define and validate a robust procedure for fast and reliable SFP genotyping in mapping populations that is appropriate to model organisms as well as agriculturally important but less tractable species. The availability of such an approach has wide value in genetical analysis of crop plants and farm animals and also in complementing information available in sequenced model organisms for researchers working in the field of genomics.
Technical Abstract: The recent development of Affymetrix chips designed from assembled EST sequences has spawned considerable interest in identifying single-feature polymorphisms (SFPs) from transcriptome data. SFPs are valuable genetic markers that 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 unsequenced genomes. To establish the sensitivity and specificity of prediction, we explored four methods for identifying SFPs from experiments involving two tissues in two commercial barleys and their doubled-haploid progeny. The methods were compared in terms of numbers of 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 that accurately predicted the SNP genotype of >98% of the doubled-haploid (DH) lines. They were highly enriched for features containing sequence polymorphisms, but all methods uniformly identified a majority of SFPs (approximately 64%) in features for which there was no sequence polymorphism while 5% mapped to different locations, indicating that "SFPs" mainly represent polymorphism in cis-acting regulators. All methods are efficient and robust at predicting markers for gene mapping.