ArticleG3 (Bethesda, Md.)2016
Genetic Regulation of Transcriptional Variation in Natural Arabidopsis thaliana Accessions.
Article in G3 (Bethesda, Md.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Natural variation in regulatory code revealed through Bayesian analysis of plant pan-genomes and pan-transcriptomes.bioRxiv : the preprint server for biology · 2025Article
- Trans-regulatory loci shape natural variation of gene expression plasticity in Arabidopsis.Genetics · 2025Article
- Genome-wide expression QTL mapping reveals the highly dynamic regulatory landscape of a major wheat pathogen.BMC biology · 2023Article
- Beyond the reference: gene expression variation and transcriptional response to RNA interference in Caenorhabditis elegans.G3 (Bethesda, Md.) · 2023Article
- Interplay Between Polymorphic Short Tandem Repeats and Gene Expression Variation in Caenorhabditis elegans.Molecular biology and evolution · 2023Article
- Beyond the reference: gene expression variation and transcriptional response to RNAi inbioRxiv : the preprint server for biology · 2023Article
- The impact of species-wide gene expression variation on Caenorhabditis elegans complex traits.Nature communications · 2022Article
- Xylem systems genetics analysis reveals a key regulator of lignin biosynthesis inGenome research · 2020Article
- Genome-wide analysis of expression quantitative trait loci (eQTLs) reveals the regulatory architecture of gene expression variation in the storage roots of sweet potato.Horticulture research · 2020Article
- Evolution and Plasticity of the Transcriptome Under Temperature Fluctuations in the Fungal Plant PathogenFrontiers in microbiology · 2020Article
- Transcriptome-Based Prediction of Complex Traits in Maize.The Plant cell · 2020Article
- Secondary Wall Regulating NACs Differentially Bind at the Promoter at aFrontiers in plant science · 2018Article
- Gene co-expression network connectivity is an important determinant of selective constraint.PLoS genetics · 2017Article
- Bivariate genomic analysis identifies a hidden locus associated with bacteria hypersensitive response in Arabidopsis thaliana.Scientific reports · 2017Article
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Authors and funding
4 authors.
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Abstract
An increased knowledge of the genetic regulation of expression in Arabidopsis thaliana is likely to provide important insights about the basis of the plant's extensive phenotypic variation. Here, we reanalyzed two publicly available datasets with genome-wide data on genetic and transcript variation in large collections of natural A. thaliana accessions. Transcripts from more than half of all genes were detected in the leaves of all accessions, and from nearly all annotated genes in at least one accession. Thousands of genes had high transcript levels in some accessions, but no transcripts at all in others, and this pattern was correlated with the genome-wide genotype. In total, 2669 eQTL were mapped in the largest population, and 717 of them were replicated in the other population. A total of 646 cis-eQTL-regulated genes that lacked detectable transcripts in some accessions was found, and for 159 of these we identified one, or several, common structural variants in the populations that were shown to be likely contributors to the lack of detectable RNA transcripts for these genes. This study thus provides new insights into the overall genetic regulation of global gene expression diversity in the leaf of natural A. thaliana accessions. Further, it also shows that strong cis-acting polymorphisms, many of which are likely to be structural variations, make important contributions to the transcriptional variation in the worldwide A. thaliana population.
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