Progressive meristem and single-cell transcriptomes reveal the regulatory mechanisms underlying maize inflorescence development and sex differentiation

Maize develops separate ear and tassel inflorescences with initially similar morphology but finally different architecture and sexuality. The detailed regulatory mechanisms underlying these changes still remain largely clear. In this study, through analyzing the time-course meristem transcriptomes and floret single-cell transcriptomes of ear and tassel we revealed the regulatory dynamics and pathways underlying inflorescence development and sex differentiation. Our study provides a deep understanding of the regulatory mechanisms underlying inflorescence development and sex differentiation in maize, laying the foundation to identify new regulators and pathways for maize hybrid breeding and improvement. To comprehensively reveal the regulatory dynamics underlying maize inflorescence differentiation and sex determination, we generated the time-course inflorescence meristems transcriptome by bulk RNA-seq and florets single-cell transcriptome by scRNA-seq.The meristem types include IM, SPM, SM, FM-stage1 (FM-S1), FM-S2 and FM-S3 in ear and tassel. FM-S2 and FM-S3 from ear and tassel were used for scRNA-seq. Next, to construct regulatory network of sex determination, we also generated the bulk RNA-seq data of ts1 and sk1 mutant and their WT using tassel or ear at early floret stage.