ArticleMolecular systems biology2009
Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance.
Article in Molecular systems biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 21 citations in OpenAlex.
- Complex Relationships between Chromatin Accessibility, Sequence Divergence, and Gene Expression in Arabidopsis thaliana.Molecular biology and evolution · 2018Article
- Genetic Regulation of Transcriptional Variation in Natural Arabidopsis thaliana Accessions.G3 (Bethesda, Md.) · 2016Article
- Different Alleles of a Gene Encoding Leucoanthocyanidin Reductase (PaLAR3) Influence Resistance against the Fungus Heterobasidion parviporum in Picea abies.Plant physiology · 2016Article
- Systems genetics in "-omics" era: current and future development.Theory in biosciences = Theorie in den Biowissenschaften · 2013Review
- Bimodal expression level polymorphisms in Arabidopsis thaliana.Plant signaling & behavior · 2012Article
- Natural variation in Arabidopsis: from molecular genetics to ecological genomics.Plant physiology · 2012Review
- Article
- Reference-guided assembly of four diverse Arabidopsis thaliana genomes.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversity.Frontiers in plant science · 2011Article
- The case for resequencing studies of Arabidopsis thaliana accessions: mining the dark matter of natural genetic variation.F1000 biology reports · 2010Article
- A hyperactive quantitative trait locus allele of Arabidopsis BRX contributes to natural variation in root growth vigor.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays.Genome biology · 2010Article
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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