title: Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance.
abstract: In Arabidopsis thaliana, gene expression level polymorphisms (ELPs) between natural accessions that exhibit simple, single locus inheritance are promising quantitative trait locus (QTL) candidates to explain phenotypic variability. It is assumed that such ELPs overwhelmingly represent regulatory element polymorphisms. However, comprehensive genome-wide analyses linking expression level, regulatory sequence and gene structure variation are missing, preventing definite verification of this assumption. Here, we analyzed ELPs observed between the Eil-0 and Lc-0 accessions. Compared with non-variable controls, 5' regulatory sequence variation in the corresponding genes is indeed increased. However, approximately 42% of all the ELP genes also carry major transcription unit deletions in one parent as revealed by genome tiling arrays, representing a >4-fold enrichment over controls. Within the subset of ELPs with simple inheritance, this proportion is even higher and deletions are generally more severe. Similar results were obtained from analyses of the Bay-0 and Sha accessions, using alternative technical approaches. Collectively, our results suggest that drastic structural changes are a major cause for ELPs with simple inheritance, corroborating experimentally observed indel preponderance in cloned Arabidopsis QTL.
authors.affiliation: Department of Plant Molecular Biology, University of Lausanne, Biophore Building, Lausanne, Switzerland.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Plantegenet
authors.forename: Johann
authors.initials: J
authors.lastname: Weber
authors.forename: Darlene R
authors.initials: DR
authors.lastname: Goldstein
authors.forename: Georg
authors.initials: G
authors.lastname: Zeller
authors.forename: Cindy
authors.initials: C
authors.lastname: Nussbaumer
authors.forename: Jérôme
authors.initials: J
authors.lastname: Thomas
authors.forename: Detlef
authors.initials: D
authors.lastname: Weigel
authors.forename: Keith
authors.initials: K
authors.lastname: Harshman
authors.forename: Christian S
authors.initials: CS
authors.lastname: Hardtke
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D011110:Polymorphism, Genetic; D040641:Quantitative Trait Loci; D012045:Regulatory Sequences, Nucleic Acid