Sextuple knockouts of a highly conserved and coexpressed AUXIN/INDOLE‐3‐ACETIC ACID gene set confer shade avoidance‐like responses in Arabidopsis

Abstract

AUXIN/INDOLE‐3‐ACETIC ACIDs are transcriptional repressors for auxin signalling. Aux/IAAs of Arabidopsis thaliana display some functional redundancy. The IAA3/SHY2 clade (IAA1, IAA2, IAA3 and IAA4) show strong sequence similarity, but no higher‐order mutants have been reported. Here, through CRISPR/Cas9 genome editing, we generated loss‐of‐function iaa1/2/3/4 mutants. The quadruple mutants only exhibited a weak phenotype. Thus, we additionally knocked out IAA7/AXR2 and IAA16, which are coexpressed with IAA1/2/3/4. Remarkably, under white light control conditions, the iaa1/2/3/4/7/16 mutants exhibited a shade avoidance‐like phenotype with over‐elongated hypocotyls and petioles and hyponastic leaves. The sextuple mutants were highly sensitive to low light intensity, and the hypocotyl cells of the mutants were excessively elongated. Transcriptome profiling and qRT‐PCR analyses revealed that the sextuple mutation upregulated IAA19/MSG2 and IAA29, two shared shade/auxin signalling targets. Besides, genes encoding cell wall‐remodelling proteins and shade‐responsive transcription regulators were upregulated. Using dual‐luciferase reporter assays, we verified that IAA2/IAA7 targeted the promoters of cell wall‐remodelling genes to inhibit their transcription. Our work indicates that the IAA1/2/3/4/7/16 gene set is required for the optimal integration of auxin and shade signalling. The mutants generated here should be valuable for exploring the complex interactions among signal sensors, transcription activators and transcription repressors during hormone/environmental responses.