Dynamic chromatin accessibility reveals BrKAN2 as a key regulator of Chinese cabbage leaf heading

Chinese cabbage forms a leafy head as its main edible organ, a process involving extensive morphological and transcriptional changes. Here, we employed ATAC-seq to profile a time-series chromatin accessibility landscape across key developmental stages of leaf heading. This analysis revealed highly dynamic, stage-specific chromatin accessible regions accompanied by distinct transcription factors activities. Genes associated with adaxial-abaxial polarity and hormone signaling displayed dynamic accessibility patterns, suggesting their critical roles in head formation. BrKAN2 emerged as a key candidate regulator. Mutant analysis in Chinese cabbage and overexpression in Arabidopsis significantly altered leaf morphology and dorsoventral polarity. Population genetic analysis further indicated strong selection on BrKAN2 in heading Brassica rapa . Integration of DAP-seq and ATAC-seq identified BrKAN2.1 target genes enriched in organ development and hormone-related pathways, which were validated by VIGS and EMSA. Auxin responsiveness assays underscored the importance of auxin signaling in heading. Collectively, these findings uncover a dynamic chromatin landscape underlying leaf heading and establish BrKAN2 as a central regulatory factor, offering new insights for genetic improvement of Chinese cabbage.