# Autopolyploidization‐Induced Chromatin Remodeling Regulates Leaf Size Variation in Brassica rapa

## TL;DR

This study shows how genome duplication in Brassica rapa changes chromatin structure and gene activity, leading to differences in leaf size and plant traits.

## Contribution

The study reveals nonlinear chromatin and transcriptional reprogramming during autopolyploidization and identifies key transcription factors regulating leaf traits.

## Key findings

- Ploidy changes reprogram chromatin accessibility and histone modifications, altering gene expression.
- Transcription factors BrGRF13 and BrARF11 are crucial for leaf size and polarity during head development.
- Autopolyploidization drives phenotypic diversity and provides insights for polyploid crop improvement.

## Abstract

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.

This study demonstrates that monoploid, diploid, and autotetraploid Brassica rapa lines derived from the same genome exhibit distinct leaf morphology. Ploidy changes remodel chromatin accessibility and histone modifications to regulate gene expression, while key transcription factors BrGRF13 and BrARF11 control leaf size and polarity, driving phenotypic diversity and highlighting the role of autopolyploidization in trait variation and crop improvement.