Designed Alleles of ZmRap2.7 Decouple the Trade‐Off Between Early Flowering and Yield Penalty

Flowering time genes often exhibit pleiotropic effects. In particular, early flowering is frequently associated with reduced grain yield due to a shorter growth period. This trade-off poses a major challenge for developing early-maturing and high-yielding varieties, a key breeding objective in modern maize production. Here, we demonstrate that ZmRap2.7, a well-known flowering repressor in maize, positively regulates ear and kernel development. Knocking out ZmRap2.7 promoted flowering but reduced ear size and kernel weight. Integrated genetic and molecular analyses revealed a multi-pathway regulatory network: ZmRap2.7 delays flowering by directly repressing the florigen ZCN8 in leaves and regulating several flowering time genes in the shoot apical meristem (SAM); it increases ear size by inhibiting ZmMADS4 to sustain inflorescence meristem activity; and it enhances kernel weight by activating ZmGRAS11 to promote cell expansion during kernel development. A comprehensive transcriptomic comparison across four tissues showed that SAM and ear exhibited a greater overlap in differentially expressed genes, providing a potential molecular basis for the flowering-yield trade-off. To mitigate this trade-off, we edited the promoter and upstream enhancer of ZmRap2.7 and obtained three edited lines with specific downregulation of ZmRap2.7 in the SAM. This tissue-specific alteration likely underpins the decoupling of flowering time from yield-related traits, enabling early flowering without compromising yield. Our findings highlight the utility of cis-regulatory editing as a promising strategy for decoupling pleiotropic trade-offs in crop improvement, particularly for genes with tissue-differential regulatory architecture.