Apical meristem transcriptome analysis identifies a role for the blue light receptor gene GhFKF1 in cotton architecture development

Cotton architecture is determined by the differentiation fate transition of axillary meristem (AM), and influences cotton yield and the efficiency of mechanized harvesting. We observed that the initiation of flowering primordium was earlier in early-maturing than that in late-maturing cultivars during the differentiation and development of AM. The RNA-Seq and expression level analyses showed that genes FLAVIN BINDING, KELCH REPEAT, F-BOX1 (GhFKF1), and GIGANTEA (GhGI) were in response to circadian rhythms, and involved in the regulation of cotton flowering. The gene structure, predicted protein structure, and motif content analyses showed that in Arabidopsis, cotton, rapseed, and soybean, proteins GhFKF1 and GhGI were functionally conserved and share evolutionary origins. Compared to the wild type, in GhFKF1 mutants that were created by the CRISPR/Cas9 system, the initiation of branch primordium was inhibited. Conversely, the knocking out of GhGI increased the number of AM differentiating into flower primordium, and there were much more lateral branch differentiation and development. Besides, we investigated that proteins GhFKF1 and GhGI can interact with each other. These results suggest that GhFKF1 and GhGI are key regulators of cotton architecture development, and may collaborate to regulate the differentiation fate transition of AM, ultimately influencing plant architecture. We describe a strategy for using the CRISPR/Cas9 system to increase cotton adaptation and productivity by optimizing plant architecture.