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BrCHR39, a novel chromatin remodeling ATPase, positively regulates apical dominance in Brassica rapa

ABSTRACT: Purpose: The transcriptomic profiling was performed to explain the release of apical dominance due to cell division among stem and bud in BrCHR39-silenced lines . Methods: The stems and axillary buds of the wild-type and BrCHR39-silenced brassica rapa grown for 8 weeks were collected, then immediately dipped in liquid nitrogen for RNA extraction using the TRIzol reagent (Invitrogen, Waltham, MA, USA) and pooled for sequencing. All samples were collected in three biological replicates. After DNaseI treatment, poly (A) mRNA was isolated with oligo (dT) magnetic beads and fragmented to short fragments. Then the first and second strand cDNA were synthesized. And library construction was completed after adding base A and sequencing adapters, end repair, and recovery of the target fragments. Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA) was used to detect the insert size of the library. The qualified cDNA libraries were sequenced by synthesis (SBS) technology using Illumina HiSeq 2500 high-throughput Sequencing platform. Results: In this study, auxin-related genes in the stems of transgenic plants showed a trend of decreasing expression from the beginning of biosynthesis to signal transduction. However, genes about auxin and cytokinin in the buds of transgenic plants were up-regulated totally. Thus we speculated that apical dominance is attributable to differential expression of multiple hormones. Conclusions: Our study provides a detailed analysis of biological replication of transgenic and wild-type transcriptome produced by RNA-seq technology. And specific pathways and associated genes were identified. Our results showed that RNA-seq based transcriptome characterization can provide ideas and basis for subsequent studies to analyze the causes of phenotypic variation. In this study, the reason why the silencing of BrCHR39 gene leads to the weakening of apical dominance was that the auxin signaling pathway was inhibited.

ORGANISM(S): Brassica rapa

PROVIDER: GSE197974 | GEO | 2025/03/02

REPOSITORIES: GEO

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Project description:Background Internodal characteristics are critical for cultivating knot-free Cunninghamia lanceolata, but limited knowledge of internode growing mechanisms has hindered breeding efforts for longer-internode types of C. lanceolata. In this study, we selected two clones with distinct internodal traits (C1 clone exhibited a 25.03% longer internodal length than C11) as materials. Enzyme-linked immunosorbent assay (ELISA) method and RNA-seq were used to investigate the changes in endogenous hormones and their associated transcriptional regulation during internodal growth and lateral bud formation. Result Our findings suggest that the differences in the dynamic rhythm of Indole-3-Acetic Acid (IAA) in apical buds are a key factor in C1's longer internodal growth. Specifically, IAA levels in C1 showed a significant decline at the S4 stage, which occurred later than in C11. Higher levels of IAA and cytokinins in the apical buds of C1 clone likely supported sustained internodal growth. The greater number of upregulated IAA-related genes in the upper phloem, including PIN1 and SAURs, which involved in polar transport and signal response, indicates a stronger capacity to establish apical dominance. The higher strigolactones (SLs) content, combined with IAA-driven apical dominance, delayed lateral bud emergence. Meanwhile, the lower brassinosteroids content and the high expression of brassinosteroid-activity-regulating genes such as UGT85A1 and BAS1 suggest that brassinosteroids (BRs) may serve as significant secondary hormonal signals promoting internodal growth. Weighted Gene Co-expression Network Analysis (WGCNA) further indicated that hormones transport may regulated by very-long-chain fatty acids (VLCFAs), coordinating both lateral bud emergence and internodal growth. Conclusion This study offers a preliminary understanding of the mechanisms behind internodal growth in C. lanceolata, providing insights for genetic control and germplasm selection in breeding, and serves as a guide for using exogenous hormone interventions to regulater internodal growth for cultivate of knot-free timber.

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BrCHR39, a novel chromatin remodeling ATPase, positively regulates apical dominance in Brassica rapa

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