HAR1 receptor kinase links nodule autoregulation with repression of auxin signaling and lateral root development

Nitrogen-fixing root nodules develop as lateral organs on legume roots and their formation is restricted by autoregulation of nodulation (AON), a systemic mechanism with unclear evolutionary origins. We identify Lotus japonicus NUCLEAR FACTOR Y subunit A4 (NF-YA4) gene as a central target of the leucine-rich repeat receptor kinase HAR1, which controls both AON and root system architecture. Under nonsymbiotic conditions, HAR1 suppresses expression of NF-YA4 and its close paralog NF-YA1, at least in part through a miR169-dependent mechanism, mirroring the Arabidopsis CLAVATA1/2-miR169-NF-YA module. Loss of HAR1 leads to NF-YA4 overexpression, broad transcriptional reprogramming, and induction of LATERAL ORGAN BOUNDARIES DOMAIN, STYLISH, and YUCCA auxin biosynthesis genes, enhancing auxin signaling and lateral root development. Grafting experiments show that HAR1 constrains NF-YA4-mediated branching both locally in roots and systemically from shoots. Because NF-YA4 functions partly redundantly with NF-YA1 to mediate nodule emergence, our results suggest a model in which duplication and neofunctionalization of an ancestral NF-YA-dependent pathway controlling lateral root development facilitated its recruitment to the nodulation program. They also raise the possibility that AON could have evolved, at least in part, through the co-option of a LRR-RK/miR169/NF-YA regulatory module that limited lateral root development.