Transcript profiling and expression level mapping.

E Potokina, A Druka, Michael Kearsey

Research output: Contribution to journalArticle

3 Citations (Scopus)


Transcript abundance data from cRNA hybridizations to Affymetrix microarrays can potentially be used to identify genetic markers to facilitate high-throughput genotyping. We have shown that it is easily possible to use the information from Affymetrix expression arrays to accurately identify over 4,000 robust polymorphic transcript-derived markers (TDMs). We developed the method to identity TDM polymorphisms from experiments involving two tissues in two commercial varieties of barley and their doubled-haploid progeny. These TDMs represent ~18% of the total barley genes on the chip and can be used to predict the genotypes in an F(1)-derived, doubled-haploid population. According to our estimates, 35% of the TDMs reveal nucleotide polymorphism of the particular gene (single feature polymorphisms, SFPs) while 65% mark polymorphism resulting in extreme variation of gene expression (genetic expression markers, GEMs). These latter are probably mainly cis-acting regulators while a small proportion, approximately 5%, are loosely or un-linked transregulators.
Original languageEnglish
Pages (from-to)81-92
Number of pages12
JournalMethods in molecular biology
Publication statusPublished - 1 Jan 2009


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