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

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 polymor

SUBMITTER: Luo ZW 

PROVIDER: S-EPMC1894608 | biostudies-literature | 2007 Jun

REPOSITORIES: biostudies-literature