A gene regulatory network critical for axillary bud dormancy directly controlled by Arabidopsis BRANCHED1

Sam W. van Es, Aitor Muñoz-Gasca, Francisco J. Romero-Campero, Eduardo González-Grandío, Pedro de los Reyes, Carlos Tarancón, Aalt D.J. van Dijk, Wilma van Esse, Alberto Pascual-García, Gerco C. Angenent, Richard G.H. Immink*, Pilar Cubas*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

1 Citation (Scopus)


The Arabidopsis thaliana transcription factor BRANCHED1 (BRC1) plays a pivotal role in the control of shoot branching as it integrates environmental and endogenous signals that influence axillary bud growth. Despite its remarkable activity as a growth inhibitor, the mechanisms by which BRC1 promotes bud dormancy are largely unknown. We determined the genome-wide BRC1 binding sites in vivo and combined these with transcriptomic data and gene co-expression analyses to identify bona fide BRC1 direct targets. Next, we integrated multi-omics data to infer the BRC1 gene regulatory network (GRN) and used graph theory techniques to find network motifs that control the GRN dynamics. We generated an open online tool to interrogate this network. A group of BRC1 target genes encoding transcription factors (BTFs) orchestrate this intricate transcriptional network enriched in abscisic acid-related components. Promoter::β-GLUCURONIDASE transgenic lines confirmed that BTFs are expressed in axillary buds. Transient co-expression assays and studies in planta using mutant lines validated the role of BTFs in modulating the GRN and promoting bud dormancy. This knowledge provides access to the developmental mechanisms that regulate shoot branching and helps identify candidate genes to use as tools to adapt plant architecture and crop production to ever-changing environmental conditions.

Original languageEnglish
Pages (from-to)1193-1209
Number of pages17
JournalNew Phytologist
Issue number3
Early online date27 Nov 2023
Publication statusPublished - Feb 2024


  • Arabidopsis
  • axillary bud dormancy
  • gene regulatory network
  • shoot branching
  • systems biology
  • TCP
  • transcription factors


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