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

Aguirre, Lyndsey, Hendelman, Anat, Hutton, Samuel F, McCandlish, David M, Lippman, Zachary B (October 2023) Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size. Science, 382 (6668). pp. 315-320. ISSN 0036-8075

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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.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > quantitative biology organism description > plant bioinformatics > quantitative biology > quantitative genetics > quantitative epistasis bioinformatics > quantitative biology > quantitative genetics organism description > plant > tomato
CSHL Authors:	Aguirre, Lyndsey Hendelman, Anat McCandlish, David Lippman, Zachary B.
Communities:	CSHL labs > Lippman lab CSHL labs > McCandlish lab School of Biological Sciences > Publications
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	20 October 2023
Date Deposited:	31 Oct 2023 19:59
Last Modified:	29 Feb 2024 18:22
PMCID:	PMC10602613
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/41286

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