ArticleScience (New York, N.Y.)2023
Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size.
Article in Science (New York, N.Y.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Molecular integration of seasonal temperature signals in flowering time control.Nature reviews. Genetics · 2026Review
- TADs, CGVs, and compartmentalization in genomes: Providing a new way for crop domestication and improvement.Journal of integrative plant biology · 2026Review
- Turbocharging crop breeding with integrated biotechnology for a climate-resilient future.Journal of integrative plant biology · 2026Review
- COMPOSITUM 2/ WHEAT FRIZZY PANICLE dosage dependently regulates inflorescence and root architecture in Triticeae cereals.The Plant journal : for cell and molecular biology · 2026Article
- Inference of fitness landscapes with heterogeneous patterns of epistasis across sites.bioRxiv : the preprint server for biology · 2026Article
- Review
- Mapping structural variants in Populus tomentosa reveals adaptive signatures and improves prediction of wood properties.Nature communications · 2026Article
- Virus-induced transgene- and tissue culture-free heritable genome editing in tomato.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Circadian oscillations in chromatin accessibility systematically orchestrate rhythmic gene transcription in soybean.The Plant cell · 2026Article
- System drift in the evolution of plant meristem development.PLoS genetics · 2026Article
- Protein-protein interactions are a major source of epistasis in genetic interaction networks.Nature communications · 2026Article
- Inference and Visualization of Complex Genotype-Phenotype Maps.Molecular biology and evolution · 2026Article
- Pan-Angiosperm Analysis of the CLE Signaling Peptide Gene Family Unveils Paths, Patterns, and Predictions of Paralog Diversification.Molecular biology and evolution · 2025Article
- Turbo-charging crop improvement: harnessing multiplex editing for polygenic trait engineering and beyond.The Plant journal : for cell and molecular biology · 2025Review
- Inference and visualization of complex genotype-phenotype maps withbioRxiv : the preprint server for biology · 2025Article
- Programmable genome engineering and gene modifications for plant biodesign.Plant communications · 2025Review
- Through the lens of bioenergy crops: advances, bottlenecks, and promises of plant engineering.The Plant journal : for cell and molecular biology · 2025Review
- Transcription factor binding divergence drives transcriptional and phenotypic variation in maize.Nature plants · 2025Article
- In defense of funding foundational plant science.The Plant cell · 2025Article
- Epistasis and cryptic QTL identified using modified bulk segregant analysis of copper resistance in budding yeast.Genetics · 2025Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Epistasis between genes is traditionally studied with mutations that eliminate protein activity, but most natural genetic variation is in cis-regulatory DNA and influences gene expression and function quantitatively. In this study, we used natural and engineered cis-regulatory alleles in a plant stem-cell circuit to systematically evaluate epistatic relationships controlling tomato fruit size. Combining a promoter allelic series with two other loci, we collected over 30,000 phenotypic data points from 46 genotypes to quantify how allele strength transforms epistasis. We revealed a saturating dose-dependent relationship but also allele-specific idiosyncratic interactions, including between alleles driving a step change in fruit size during domestication. Our approach and findings expose an underexplored dimension of epistasis, in which cis-regulatory allelic diversity within gene regulatory networks elicits nonlinear, unpredictable interactions that shape phenotypes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.