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Summary Branching determines cotton architecture and production, but the underlying regulatory mechanisms remain unclear. Here, we report that the miR164‐GhCUC2 (CUP‐SHAPED COTYLEDON2) module regulates lateral shoot development in cotton and Arabidopsis. We generated OE‐GhCUC2m (overexpression GhCUC2m) and STTM164 (short tandem target mimic RNA of miR164) lines in cotton and heterologous expression lines for gh‐miR164, GhCUC2 and GhCUC2m in Arabidopsis to study the mechanisms controlling lateral branching. GhCUC2m overexpression resulted in a short‐branch phenotype similar to STTM164. In addition, heterologous expression of GhCUC2m led to decreased number and length of branches compared with wild type, opposite to the effects of the OE‐gh‐pre164 line in Arabidopsis. GhCUC2 interacted with GhBRC1 and exhibited similar negative regulation of branching. Overexpression of GhBRC1 in the brc1‐2 mutant partially rescued the mutant phenotype and decreased branch number. GhBRC1 directly bound to the NCED1 promoter and activated its transcription, leading to local abscisic acid (ABA) accumulation and response. Mutation of the NCED1 promoter disrupted activation by GhBRC1. This finding demonstrates a direct relationship between BRC1 and ABA signalling and places ABA downstream of BRC1 in the control of branching development. The miR164‐GhCUC2‐GhBRC1‐GhNCED1 module provides a clear regulatory axis for ABA signalling to control plant architecture.

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