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

Z. W. Luo, E. Potokina, A. Druka, R Wise, R. Waugh, M. J. Kearsey

    Research output: Contribution to journalArticle

    58 Citations (Scopus)

    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 (∼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.

    Original languageEnglish
    Pages (from-to)789-800
    Number of pages12
    JournalGenetics
    Volume176
    Issue number2
    DOIs
    Publication statusPublished - 19 Jun 2007

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