1
|
van Es SW, Muñoz-Gasca A, Romero-Campero FJ, González-Grandío E, de Los Reyes P, Tarancón C, van Dijk ADJ, van Esse W, Pascual-García A, Angenent GC, Immink RGH, Cubas P. A gene regulatory network critical for axillary bud dormancy directly controlled by Arabidopsis BRANCHED1. New Phytol 2024; 241:1193-1209. [PMID: 38009929 DOI: 10.1111/nph.19420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 10/21/2023] [Indexed: 11/29/2023]
Abstract
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.
Collapse
Affiliation(s)
- Sam W van Es
- Bioscience, Wageningen Plant Research, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
| | - Aitor Muñoz-Gasca
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Francisco J Romero-Campero
- Institute for Plant Biochemistry and Photosynthesis, Universidad de Sevilla - Consejo Superior de Investigaciones Científicas, Ave. Américo Vespucio 49, 41092, Seville, Spain
- Department of Computer Science and Artificial Intelligence, Universidad de Sevilla, Ave. Reina Mercedes s/n, 41012, Seville, Spain
| | - Eduardo González-Grandío
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Pedro de Los Reyes
- Institute for Plant Biochemistry and Photosynthesis, Universidad de Sevilla - Consejo Superior de Investigaciones Científicas, Ave. Américo Vespucio 49, 41092, Seville, Spain
| | - Carlos Tarancón
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Aalt D J van Dijk
- Bioinformatics, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
| | - Wilma van Esse
- Bioscience, Wageningen Plant Research, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
| | - Alberto Pascual-García
- Department of Systems Biology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Gerco C Angenent
- Bioscience, Wageningen Plant Research, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
| | - Richard G H Immink
- Bioscience, Wageningen Plant Research, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
| | - Pilar Cubas
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| |
Collapse
|