Autopolyploidization-induced chromatin remodeling regulates leaf size variation in Brassica rapa

Whole-genome duplication (WGD) is an evolutionary event that impacts gene regulation and trait development, but its role in chromatin remodeling and heritable phenotypic changes remains unclear. In this study, employing ATAC-seq, ChIP-seq (H3K4me3, H3K27ac, H3K27me3), and RNA-seq, we examined the epigenomic and transcriptomic dynamics in monoploid, diploid, and autotetraploid B. rapa (Brassica rapa), which share a genome from the same source. Our findings demonstrate that autopolyploidization exerts ploidy-dependent effects on the epigenome and transcriptome, characterized by nonlinear patterns, particularly pronounced during the monoploid-to-diploid transition. Increased ploidy leads to reprogramming chromatin accessibility, characterized by reduced-proximal versus expanded-distal regions. H3K4me3 modifications near transcription start sites alter global gene expression. We identified numerous transcription factor genes, of which BrGRF13 and BrARF11 are crucial to regulate leaf size and polarity during head development. This study is the first to utilize a monoploid system to reveal the mechanisms by which autopolyploidization regulates epigenetic changes through chromatin remodeling, filling a critical knowledge gap and providing novel insights into how polyploidization drives phenotypic variation in plants. Overall design: Leaf samples were collected during the heading transition stage from monoploid, diploid, and autotetraploid B. rapa plants derived from the same genome. Each ploidy group included biological replicates: three for RNA-seq and two for ChIP-seq (H3K4me3, H3K27ac, H3K27me3) and ATAC-seq. Monoploid samples served as the reference to assess the effects of increasing ploidy on chromatin accessibility, histone modifications, and gene expression.