Autopolyploidization-Induced Chromatin Remodeling Regulates Leaf Size Variation in Brassica rapa

Whole-genome duplication is a key evolutionary mechanism influencing gene regulation and trait development; however, how successive genome duplications reshape chromatin at the genome-wide scale and thereby drive phenotypic innovation remains unclear. To dissect the effects of genome doubling on chromatin dynamics, gene expression, and associated trait differences, monoploid, diploid, and autotetraploid Brassica rapa L. ssp. pekinensis lines are generated with an identical genomic background and performed integrative analyses using ATAC-seq, ChIP-seq (H3K4me3, H3K27ac, H3K27me3), and RNA-seq. By establishing this uniform ploidy series, nonlinear and stage-specific chromatin and transcriptional reprogramming during autopolyploidization are revealed. Increased ploidy reprogrammed chromatin accessibility, characterized by reduced proximal and expanded distal regions, with effects particularly pronounced during the monoploid-to-diploid transition. Corresponding changes in H3K4me3 modifications near transcription start sites alter global gene expression. Numerous transcription factor genes are identified, of which BrGRF13 and BrARF11 are crucial regulators of leaf size and polarity during head development. Overall, this study elucidates the molecular basis by which ploidy variation drives chromatin remodeling and phenotypic divergence, providing new insights into how genome duplication shapes plant traits and informs polyploid crop improvement.