Dissecting cis-regulatory control of quantitative trait variation in a plant stem cell circuit
- 12 April 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Plants
- Vol. 7 (4), 419-427
- https://doi.org/10.1038/s41477-021-00898-x
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.Keywords
Funding Information
- Howard Hughes Medical Institute
- National Science Foundation (IOS-1546837, IOS-1732253)
- United States-Israel Binational Agricultural Research and Development Fund
- the Vaadia-BARD Postdoctoral Fellowship
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