Single-nucleus transcriptomics reveals transcriptional dynamics underlying maize ligule development

The maize ligule arises from the preligule band (PLB) at the leaf blade-sheath boundary and provides a tractable system for investigating how boundary-associated positional cues direct local cell-fate specification and tissue outgrowth. Although key genes involved in ligule development have been identified and cell-resolved profiles are available for stages after PLB formation, how PLB acquires ligule identity and initiates outgrowth remains unclear at the cellular level. Here, we have used single-nucleus RNA sequencing to profile maize ligular regions at the preligule band and ligule outgrowth stages. The atlas resolved major cell populations and identified a ligule population supported by established marker genes, published laser microdissection transcriptomes, and RNA in situ hybridization. Pseudotime trajectory and co-expression network analyses resolved two sequential transcriptional programs corresponding to ligule initiation and subsequent outgrowth. ZmIDD30 was identified as a promising candidate transcriptional regulator, and molecular assays showed that it bound to the promoters of ZmPIN1c and ZmVG1 and activated their transcription, suggesting potential links to auxin transport and lipid metabolism during ligule development. Overall, these findings define a cell-resolved transcriptional progression in which a localized epidermal domain at the blade-sheath boundary progressively acquires ligule identity and progresses toward outgrowth.