ArticleMolecular biology and evolution2022
Deleterious Mutations and the Rare Allele Burden on Rice Gene Expression.
Article in Molecular biology and evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- PlantCAD2: A DNA foundation model for interpreting genomes across flowering plants.Cell genomics · 2026Article
- Downregulation is the dominant effect of new regulatory mutations in a fungal pathogen.Microbial genomics · 2026Article
- PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms.bioRxiv : the preprint server for biology · 2025Article
- Cross-species modeling of plant genomes at single-nucleotide resolution using a pretrained DNA language model.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Graphical pangenomics-enabled characterization of structural variant impact on gene expression in Brassica napus.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Low nucleotide diversity of the Plasmodium falciparum AP2-EXP2 gene among clinical samples from Ghana.Parasites & vectors · 2024Article
- Cross-species modeling of plant genomes at single nucleotide resolution using a pre-trained DNA language model.bioRxiv : the preprint server for biology · 2024Article
- Structural Variants and Speciation: Multiple Processes at Play.Cold Spring Harbor perspectives in biology · 2024Review
- Transposons are important contributors to gene expression variability under selection in rice populations.eLife · 2023Article
- A graph-based genome and pan-genome variation of the model plant Setaria.Nature genetics · 2023Article
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Abstract
Deleterious genetic variation is maintained in populations at low frequencies. Under a model of stabilizing selection, rare (and presumably deleterious) genetic variants are associated with increase or decrease in gene expression from some intermediate optimum. We investigate this phenomenon in a population of largely Oryza sativa ssp. indica rice landraces under normal unstressed wet and stressful drought field conditions. We include single nucleotide polymorphisms, insertion/deletion mutations, and structural variants in our analysis and find a stronger association between rare variants and gene expression outliers under the stress condition. We also show an association of the strength of this rare variant effect with linkage, gene expression levels, network connectivity, local recombination rate, and fitness consequence scores, consistent with the stabilizing selection model of gene expression.
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