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Summary: Branch length is an important plant architecture trait in cotton (Gossypium) breeding. Development of cultivars with short branch has been proposed as a main object to enhance cotton yield potential, because they are suitable for high planting density. Here, we report the molecular cloning and characterization of a semi‐dominant quantitative trait locus, Short Branch Internode 1(GhSBI1), which encodes a NAC transcription factor homologous to CUP‐SHAPED COTYLEDON 2 (CUC2) and is regulated by microRNA ghr‐miR164. We demonstrate that a point mutation found in sbi1 mutants perturbs ghr‐miR164‐directed regulation of GhSBI1, resulting in an increased expression level of GhSBI1. The sbi1 mutant was sensitive to exogenous gibberellic acid (GA) treatments. Overexpression of GhSBI1 inhibited branch internode elongation and led to the decreased levels of bioactive GAs. In addition, gene knockout analysis showed that GhSBI1 is required for the maintenance of the boundaries of multiple tissues in cotton. Transcriptome analysis revealed that overexpression of GhSBI1 affects the expression of plant hormone signalling‐, axillary meristems initiation‐, and abiotic stress response‐related genes. GhSBI1 interacted with GAIs, the DELLA repressors of GA signalling. GhSBI1 represses expression of GA signalling‐ and cell elongation‐related genes by directly targeting their promoters. Our work thus provides new insights into the molecular mechanisms for branch length and paves the way for the development of elite cultivars with suitable plant architecture in cotton. [ABSTRACT FROM AUTHOR]

Cotton fiber is an indispensable raw material in the textile industry. Fiber length is an important fiber quality index, and the research on fiber length is also quite abundant. However, on the same ovule, there are only a few studies on the difference in fiber length development between the micropylar end and the chalazal end of the ovule. We elucidate the mechanism of fiber length differences at both ends of the ovule through the phenomics, transcriptome, and metabolome. The results show that 20, 25, and 30 days post anthesis (DPA) are the pivotal stages to causing the difference in fiber length at two ends of the ovules. Through the KEGG annotation of differentially expressed genes (DEGs), it was found that flavonoid biosynthesis, plant hormone signal transduction, and phenylpropanoid biosynthesis are enriched in DEGs, and similar conclusions were drawn in the analysis of differential abundant metabolites (DAMs). The results of in vitro culture of ovules showed that chlorogenic acid in the flavonoid pathway and scopolin downstream of the phenylpropanoid pathway have significant effects on fiber growth. Our research provide insights into the mechanism of cotton fiber elongation. [ABSTRACT FROM AUTHOR]