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

Cis-regulatory mutations underlie important crop domestication and improvement traits(1,2). 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 genes(3,4) 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 proliferation(5,6), 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.

Automated summary

The study found that targeted mutations in conserved promoter sequences of the repressor of stem cell proliferation, SlCLV3, have a weak impact on fruit locule number, but pairwise combinations of these mutations mildly enhance this trait, revealing additive and synergistic relationships. Conversely, the positive regulator of stem cell proliferation, SlWUS, is more tolerant to promoter perturbations. The results suggest that complex interactions among cis-regulatory variants can shape quantitative variation in crop traits.