Prime editing of an RR26-responsive cis-element enhances DAHPS2 expression and submergence tolerance in rice through the shikimate pathway

Early postgermination growth is critical for uniform seedling emergence in direct-seeded rice; however, the underlying regulatory mechanisms remain unclear. Here, we identified DS1, which encodes the shikimate pathway entry enzyme DAHPS2, from a dwarf and sterile mutant (ds1) in 'Huazhan' (HZ). Loss of DS1 disrupted the shikimate pathway, reduced indole-3-acetic acid (IAA) levels through the downstream tryptophan-dependent IAA biosynthesis pathway, and induced excessive jasmonic acid (JA) accumulation, resulting in severely impaired postgermination growth. Exogenous application of the auxin analog 1-naphthaleneacetic acid or the JA biosynthesis inhibitor diethyldithiocarbamic acid partially rescued the mutant phenotype. Conversely, DS1 overexpression elevated IAA levels, reduced JA accumulation, and promoted postgermination growth, facilitating rapid seedling emergence under submergence conditions. This effect was further validated in the 'Zhongjia 3' cultivar. We demonstrate that DS1 is transcriptionally activated by RR26, a type-B cytokinin (CK) response regulator, through direct binding to the DS1-7 cis element. Using prime editing, we precisely modified DS1-7 in HZ to generate transgene-free germplasm with improved DS1 expression and enhanced submergence tolerance. Collectively, our findings establish an RR26-DS1 module that regulates IAA-JA homeostasis through the shikimate pathway, providing mechanistic insights into postgermination growth and valuable genetic resources for breeding direct-seeded rice cultivars.