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

ABSTRACT: 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.

ORGANISM(S): Brassica rapa

PROVIDER: GSE308545 | GEO | 2026/02/18

REPOSITORIES: GEO

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Project description:Purpose: Mechanism of gene expression changes in autotetraploid drought resistance variation Methods: Leaves under control and drought treatment of 6h, 12h and 48h were sampled from diploid and the autotetraploid for RNA-seq. Total RNA was extracted from 100mg sample with RNeasy plant mini kit (Omega Biotech, China) and purified with RNase-Free DNase set. Following, cDNA library was constructed and the library concentration and insert size was respectively assessed on the Qubit2.0 (Invitrogen, USA) and Agilent Bioanalyzer 2100 system, and then the effective concentration of the library was accurately quantified through Q-PCR. Prepared high quality libraries were sequenced on Illumina HiSeq X-ten platform to generate paired-end raw reads. qRT–PCR validation was performed using SYBR Green assays. Results: The study findings showed that the autotetraploid sour jujube exhibited a superior drought tolerance and enhanced regrowth potential after dehydration in comparison with the diploid counterpart. The physiological responses gradually triggered important functions in the autotetraploid sour jujube under extreme drought conditions. Furthermore, a comparative transcriptome analysis showed that more differentially expressed genes (DEGs) were detected in autotetraploid after drought stress. Through GO enrichment analysis, many DEGs between the diploid and autotetraploid sour jujube after drought-stress exposure were respectively annotated to the oxidation–reduction process, photosystem, DNA binding transcription factor activity, oxidoreductase activity. Consistently, six reactive oxygen species scavenging-related genes were specifically differentially expressed, positive changes of the genes involved in glutathione metabolism pathways were greater and the lower O2− level and malonaldehyde (MDA) content and higher antioxidant enzymes activity were detected in the autotetraploid under drought-stress conditions. The higher chlorophyll content and differentially enriched genes during photosynthesis suggest that the photosynthetic system in the autotetraploid, having variations in stomatal and cellular characteristics, was enhanced during drought stress. In addition, DEGs in the autotetraploid after stress exposure were significantly enriched in DNA-replication and plant hormone, including auxin, abscisic acid and gibberellin signal-transduction pathways. Under osmotic stress conditions, genes associated with the synthesis and transport of osmotic regulatory substances including anthocyanin biosynthesis were differentially expressed, and the soluble sugar, soluble protein and proline contents were significantly higher in the autotetraploid. Moreover, several genes encoding transcription factors (TFs) including GRAS, Bhlh, MYB, WRKY and NAC were induced specifically or to higher levels in the autotetraploid under drought-stress conditions, and hub genes, LOC107403632, LOC107422279, LOC107434947, LOC107412673 and LOC107432609, related to up-regulated transcription factors in the autotetraploid compared with the diploid were identified. Conclusions: Owing to the whole-genome doubling, many functional genes in the autotetraploid plants were differentially expressed compared with in the diploid during drought stress, resulting in resistance difference.

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

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