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

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::ß-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.

Shoot Branching Phenotyping in Arabidopsis and Tomato.

Shoot branching is an important trait that depends on the activity of axillary meristems and buds and their outgrowth into branches. It is remarkably plastic, being influenced by a number of external cues, such as light, temperature, soil nutrients, and mechanical manipulation. These are transduced into an internal hormone signaling network where auxin, cytokinins, and strigolactones play leading regulatory roles. Recently, sugars have also emerged as important signals promoting bud activation. These signals are in part integrated by the bud-specific growth repressor BRANCHED1 (BRC1).To understand how shoot branching is affected by particular growth conditions or in specific plant lines, it is necessary to count the number of branches and/or quantify other branch-related parameters. Here we describe how to perform such quantifications in Arabidopsis and in tomato.