ArticleGenome research2011
Genetic architecture of regulatory variation in Arabidopsis thaliana.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- A Balanced Inversion Polymorphism Exhibits a Dominance Reversal at the Gene Expression Level that Depends on Developmental Context.Molecular biology and evolution · 2025Article
- Trans-regulatory loci shape natural variation of gene expression plasticity in Arabidopsis.Genetics · 2025Article
- Regulatory networks of coresident subgenomes during rapid fiber cell elongation in upland cotton.Plant communications · 2024Article
- Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast.Nature genetics · 2024Article
- Diallel panel reveals a significant impact of low-frequency genetic variants on gene expression variation in yeast.Molecular systems biology · 2024Article
- AtSNP_TATAdb: Candidate Molecular Markers of Plant Advantages Related to Single Nucleotide Polymorphisms within Proximal Promoters ofInternational journal of molecular sciences · 2024Article
- Dominance is common in mammals and is associated with trans-acting gene expression and alternative splicing.Genome biology · 2023Article
- Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster.G3 (Bethesda, Md.) · 2023Article
- Diallel panel reveals a significant impact of low-frequency genetic variants on gene expression variation in yeast.bioRxiv : the preprint server for biology · 2023Article
- Discovery of DNA polymorphisms via genome-resequencing and development of molecular markers between two barley cultivars.Plant cell reports · 2022Article
- Cis-regulatory sequences in plants: Their importance, discovery, and future challenges.The Plant cell · 2022Review
- Both Binding Strength and Evolutionary Accessibility Affect the Population Frequency of Transcription Factor Binding Sequences in Arabidopsis thaliana.Genome biology and evolution · 2021Article
- Parallel and population-specific gene regulatory evolution in cold-adapted fly populations.Genetics · 2021Article
- Association of CPT1A gene polymorphism with the risk of gestational diabetes mellitus: a case-control study.Journal of assisted reproduction and genetics · 2021Article
- From GWAS to Gene: Transcriptome-Wide Association Studies and Other Methods to Functionally Understand GWAS Discoveries.Frontiers in genetics · 2021Review
- Article
- The Role of Transcriptional Regulation in Hybrid Vigor.Frontiers in plant science · 2020Review
- Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes ofFrontiers in plant science · 2019Article
- GWAS with Heterogeneous Data: Estimating the Fraction of Phenotypic Variation Mediated by Gene Expression Data.G3 (Bethesda, Md.) · 2018Article
- Genetics ofeLife · 2018Article
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3 authors.
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Abstract
Studying the genetic regulation of expression variation is a key method to dissect complex phenotypic traits. To examine the genetic architecture of regulatory variation in Arabidopsis thaliana, we performed genome-wide association (GWA) mapping of gene expression in an F(1) hybrid diversity panel. At a genome-wide false discovery rate (FDR) of 0.2, an associated single nucleotide polymorphism (SNP) explains >38% of trait variation. In comparison with SNPs that are distant from the genes to which they were associated, locally associated SNPs are preferentially found in regions with extended linkage disequilibrium (LD) and have distinct population frequencies of the derived alleles (where Arabidopsis lyrata has the ancestral allele), suggesting that different selective forces are acting. Locally associated SNPs tend to have additive inheritance, whereas distantly associated SNPs are primarily dominant. In contrast to results from mapping of expression quantitative trait loci (eQTL) in linkage studies, we observe extensive allelic heterogeneity for local regulatory loci in our diversity panel. By association mapping of allele-specific expression (ASE), we detect a significant enrichment for cis-acting variation in local regulatory variation. In addition to gene expression variation, association mapping of splicing variation reveals both local and distant genetic regulation for intron and exon level traits. Finally, we identify candidate genes for 59 diverse phenotypic traits that were mapped to eQTL.
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