A complex tissue‐specific interplay between the Arabidopsis transcription factors AtMYB68, AtHB23, and AtPHL1 modulates primary and lateral root development and adaptation to salinity

SUMMARY Adaptation to different soil conditions is a well‐regulated process vital for plant life. AtHB23 is a homeodomain‐leucine zipper I transcription factor (TF) that was previously revealed as crucial for plant survival under salinity conditions. We wondered whether this TF has partners to perform this essential function. Therefore, TF cDNA library screening, yeast two‐hybrid, bimolecular fluorescence complementation, and coimmunoprecipitation assays were complemented with expression analyses and phenotypic characterization of silenced, mutant, overexpression, and crossed plants in normal and salinity conditions. We revealed that AtHB23, AtPHL1, and AtMYB68 interact with each other, modulating root development and the salinity response. The encoding genes are coexpressed in specific root tissues and at specific developmental stages. In normal conditions, amiR68 silenced plants have fewer initiated roots, the opposite phenotype to that shown by amiR23 plants. AtMYB68 and AtPHL1 play opposite roles in lateral root elongation. Under salinity conditions, AtHB23 plays a crucial positive role in cooperating with AtMYB68, whereas AtPHL1 acts oppositely by obstructing the function of the former, impacting the plant's survival ability. Such interplay supports the complex interaction between these TF in primary and lateral roots. The root adaptation capability is associated with the amyloplast state. We identified new molecular players that through a complex relationship determine Arabidopsis root architecture and survival in salinity conditions. Significance Statement Root plasticity, which is crucial to soil adaptation, is fine‐tuned by multiple biomolecules, including transcription factors and phytohormones. We revealed that the regulatory proteins AtHB23, AtMYB68, and AtPHL1 interact which each other in primary and lateral roots, playing essential roles in development and the stress response. Their cooperative and opposite functions vary depending on the root tissue and developmental stage.