GhFPF1 positively regulates shade avoidance responses via interacting with GhNF-YA3 in cotton

Dense planting can create a shade environment which will stimulate plants to produce a series of shade avoidance responses (SAS). Thus far, slow progress has been made in research into the molecular mechanism of SAS in cotton. In this study, GhFPF1 was identified as a positive regulator of SAS in cotton. The expression of GhFPF1 was significantly upregulated in cotton stems and leaves in the low R:FR conditions. After mutating GhFPF1 using CRISPR technology, the elongation response of the mutant was weakened under high-density cultivating conditions. The constitutive expression of GhFPF1 in cotton resulted in typical SAS, such as a higher plant height, slow branching development and a reduced leaf inclination angle. Further assays showed that GhFPF1 interacted with GhNF-YA3, which is a transcription factor of nuclear factor Y (NF-Y) family. GhNF-YA3 was downregulated in low R:FR environment. The silencing of GhNF-YA3 led to significant internode elongation, which was similar to the phenotype caused by overexpressing GhFPF1 . Comprehensive studies suggested that the interaction between GhFPF1 and GhNF-YA3 competitively weakened the transcriptional regulation of three light-harvesting chlorophyll a/b-binding protein ( Lhc ) genes by GhNF-YA3. In addition, GhFPF1 was proved to be the target gene of HD-Zip II transcription factors GhHB2 and GhHB4 which were considered as positive regulators of SAS in other plants. This study uncovered the molecular mechanism by which GhFPF1 regulates SAS in cotton and enriched the regulatory network of SAS in plants. • GhFPF1 positively regulates shade avoidance responses (SAS) in cotton. • GhFPF1 interacts with GhNF-YA3 in vitro and in vivo . • Silencing of GhNF-YA3 led to SAS in cotton. • GhFPF1-GhNF-YA3 modulates light-harvesting chlorophyll-binding protein ( Lhc ) genes. • GhFPF1 may be the target gene of GhHB2 and GhHB4.