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Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size.

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.

SUBMITTER: Aguirre L

PROVIDER: S-EPMC10602613 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature

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Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size.

Aguirre Lyndsey L Hendelman Anat A Hutton Samuel F SF McCandlish David M DM Lippman Zachary B ZB

Science (New York, N.Y.) 20231019 6668

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 point ...[more]

PMID: 37856609

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Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size.

Publications

Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size.

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