Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Nat Plants. 2021 Apr;7(4):419-427. doi: 10.1038/s41477-021-00898-x. Epub 2021 Apr 12.
Cis-regulatory mutations underlie important crop domestication and improvement traits. 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 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, 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. ), 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.
顺式调控突变是作物重要的驯化和改良性状的基础。然而，有限的等位基因多样性阻碍了大量顺式调控元件及其潜在相互作用的功能解析，从而使我们无法更深入地了解顺式调控变异如何对数量性状产生影响。在这里，我们对两个番茄果实大小基因中的 60 多个启动子等位基因进行了工程改造，以研究顺式调控序列及其功能关系。我们发现，靶向 SlCLV3（一种干细胞增殖抑制剂）保守启动子序列的突变对果实腔数的影响较弱。这些突变的成对组合轻度增强了这一表型，揭示了保守区域之间的累加和协同关系，并进一步表明 SlCLV3 启动子内存在更高阶的顺式调控相互作用。相比之下，SlWUS（SlCLV3 抑制的干细胞增殖正调控因子）对启动子的干扰更为耐受。我们的结果表明，顺式调控变异之间的复杂相互作用可以塑造数量性状的变异，并表明对这种隐藏复杂性的经验性剖析可以指导启动子工程，从而可预测性地修饰作物性状。
