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.