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The interaction between legumes and arbuscular mycorrhizal (AM) fungi is vital to the development of sustainable plant production systems. Here, we focus on a putative MYB-like (LjMAMI) transcription factor (TF) previously reported to be highly upregulated in Lotus japonicus mycorrhizal roots. Phylogenetic analyses revealed that the protein is related to a group of TFs involved in phosphate (Pi) starvation responses, the expression of which is independent of the Pi level, such as PHR1. GUS transformed plants and quantitative reverse transcription PCR revealed strong gene induction in arbusculated cells, as well as the presence of LjMAMI transcripts in lateral root primordia and root meristems, even in the absence of the fungus, and independently of Pi concentration. In agreement with its putative identification as a TF, an eGFP-LjMAMI chimera was localized to the nuclei of plant protoplasts, whereas in transgenic Lotus roots expressing the eGFP-LjMAMI fusion protein under the control of the native promoter, the protein was located in the nuclei of the arbusculated cells. Further expression analyses revealed a correlation between LjMAMI and LjPT4, a marker gene for mycorrhizal function. To elucidate the role of the LjMAMI gene in the mycorrhizal process, RNAi and overexpressing root lines were generated. All the lines retained their symbiotic capacity; however, RNAi root lines and composite plants showed an important reduction in root elongation and branching in the absence of the symbiont. The results support the involvement of the AM-responsive LjMAMI in non-symbiotic functions: i.e. root growth.

SUMMARY Plants adjust their architecture by modulating organ growth. This ability is largely dependent on phytohormones. While responses to phytohormones have been studied extensively, it remains unclear to which extent and how these responses are modulated in non‐reference strains. Here, we assess variation of root traits upon treatment with auxin, cytokinin and abscisic acid (ABA) in 192 Arabidopsis accessions. We identify common response patterns, uncover the extent of their modulation by specific genotypes, and find that the Col‐0 reference accession is not a good representative of the species in this regard. We conduct genome‐wide association studies and identify 114 significant associations, most of them relating to ABA treatment. The numerous ABA candidate genes are not enriched for known ABA‐associated genes, indicating that we largely uncovered unknown players. Overall, our study provides a comprehensive view of the diversity of hormone responses in the Arabidopsis thaliana species, and shows that variation of genes that are yet mostly not associated with such a role to determine natural variation of the response to phytohormones., Significance Statement Plant hormones are crucial for regulating root growth, but most studies were based on a single reference strain of Arabidopsis. Here, we study natural variation of root growth upon treatment with auxin, cytokinin and abscisic acid, and find that most strains respond very differently to hormones than the reference strain, and that this extensive natural variation is largely associated with genes that have not yet been implicated in playing a role in hormonal pathways.