Journal Articles Nature Plants Year : 2021

Dissecting cis-regulatory control of quantitative trait variation in a plant stem cell circuit

Xingang Wang
Daniel Rodríguez-Leal
Anat Hendelman
Matthias Benoit
Zachary B Lippman

Abstract

Cis-regulatory mutations underlie important crop domestication and improvement traits1,2. However, limited allelic diversity has hindered functional dissection of the large number of cis-regulatory elements and their potential interactions, thereby precluding a deeper understanding of how cis-regulatory variation impacts traits quantitatively. Here, we engineered over 60 promoter alleles in two tomato fruit size genes3,4 to characterize cis-regulatory sequences and study their functional relationships. We found that targeted mutations in conserved promoter sequences of SlCLV3, a repressor of stem cell proliferation5,6, have a weak impact on fruit locule number. Pairwise combinations of these mutations mildly enhance this phenotype, revealing additive and synergistic relationships between conserved regions and further suggesting even higher-order cis-regulatory interactions within the SlCLV3 promoter. In contrast, SlWUS, a positive regulator of stem cell proliferation repressed by SlCLV3 (refs. 5,6), is more tolerant to promoter perturbations. Our results show that complex interplay among cis-regulatory variants can shape quantitative variation, and suggest that empirical dissections of this hidden complexity can guide promoter engineering to predictably modify crop traits.
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Dates and versions

hal-04171669 , version 1 (26-07-2023)

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Cite

Xingang Wang, Lyndsey Aguirre, Daniel Rodríguez-Leal, Anat Hendelman, Matthias Benoit, et al.. Dissecting cis-regulatory control of quantitative trait variation in a plant stem cell circuit. Nature Plants, 2021, 7 (4), pp.419 - 427. ⟨10.1038/s41477-021-00898-x⟩. ⟨hal-04171669⟩

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